[gmx-users] Thank Roland
mhviet at ifpan.edu.pl
mhviet at ifpan.edu.pl
Tue Mar 3 12:57:59 CET 2009
Thank Roland very much.
I have read it and I understood it a litle.
Wishing all good things come to you
Man Hoang Viet
>
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> Today's Topics:
>
> 1. regarding dimethylated lysine topology file (prasun kumar)
> 2. Re: How to define protein surface residues (Lee Soin)
> 3. about LINCS WARNING (mhviet at ifpan.edu.pl)
> 4. Re: about LINCS WARNING (Roland Schulz)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Mar 2009 03:06:17 -0800
> From: prasun kumar <prasun30 at gmail.com>
> Subject: [gmx-users] regarding dimethylated lysine topology file
> To: gmx-users at gromacs.org
> Message-ID:
> <a473abdb0903030306x1c8ef034gfad6f5b0dcb893cb at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Respected all
> I drew the structure using the drawing tool available in PRODRG server
> then I went for topology file generation,but the server is deleting
> almost
> all the hydrogen atoms while writing the topology file for gromacs
> can any one tell me why it is doing like this?
>
> another question I got that is
> how to change gromacs topology file to charmm topology file
> (I know for bond length and angle........but for dihedral(improper and
> proper))
> actually i want toi know which function gromacs is using for the
> calculation
> of dihedrals..........
> thanx in advance
>
> PRASUN (ASHOKA)
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> ------------------------------
>
> Message: 2
> Date: Tue, 3 Mar 2009 19:09:20 +0800
> From: Lee Soin <nomadoro at gmail.com>
> Subject: Re: [gmx-users] How to define protein surface residues
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <e2838e4e0903030309v5aa07d8y1732299774bbe57b at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks, but what I mean is to just find out the surface residues, not to
> calculate the surface area.
>
> 2009/3/3 David van der Spoel <spoel at xray.bmc.uu.se>
>
>> Lee Soin wrote:
>>
>>> Hello!
>>> I'm trying to find the surface residues of a protein. Maybe this should
>>> be
>>> calculated by myself and not using GROMACS. Can anybody tell me a
>>> feasible
>>> procedure for doing so? Thanks!
>>>
>> g_sas
>>
>> --
>>> Sun Li
>>> Department of Physics
>>> Nanjing University, China
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> Sun Li
> Department of Physics
> Nanjing University, China
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> ------------------------------
>
> Message: 3
> Date: Tue, 3 Mar 2009 12:19:45 +0100 (CET)
> From: mhviet at ifpan.edu.pl
> Subject: [gmx-users] about LINCS WARNING
> To: gmx-users at gromacs.org
> Message-ID:
> <a06ae90e88c90feef7e6c9a8948997ee.squirrel at webmail.ifpan.edu.pl>
> Content-Type: text/plain;charset=iso-8859-1
>
> Thank David very much
> I have tried and most of them work.
> And, When I run script_mini.mdp to minimize energy and it report LINCS
> warning (as below). So Can you tell me What LINCS WARNING mean?
>
> Step 16, time 0.032 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000000, max 0.000001 (between atoms 18 and 20)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 97 98 35.3 0.1000 0.1000 0.1000
>
>
>
>> Send gmx-users mailing list submissions to
>> gmx-users at gromacs.org
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>> or, via email, send a message with subject or body 'help' to
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>>
>>
>> Today's Topics:
>>
>> 1. Detail of Script.sh in Gromacs-4.0.3? (mhviet at ifpan.edu.pl)
>> 2. Re: How to define protein surface residues (David van der Spoel)
>> 3. Re: Detail of Script.sh in Gromacs-4.0.3? (David van der Spoel)
>> 4. SV: SV: [gmx-users] g_order version 4.0.x (Sarah Witzke)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 3 Mar 2009 10:37:05 +0100 (CET)
>> From: mhviet at ifpan.edu.pl
>> Subject: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
>> To: gmx-users at gromacs.org
>> Message-ID:
>> <24e6018b503b7a1516fccea3477b4d8d.squirrel at webmail.ifpan.edu.pl>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> Dear all
>>
>> I am newer in Gromacs. Now I am studying Gomacs for protein simulations.
>> I
>> am trying script files which used for gromacs-3. Can I do it? Does
>> Gromacs-4. have to use others script files? and If It have, Can you send
>> sript files to me for gromacs-4?
>> Thank you verry much!
>>
>> Yours truly,
>>
>> Man Hoang Viet
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 03 Mar 2009 10:52:07 +0100
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-users] How to define protein surface residues
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <49ACFDC7.6060402 at xray.bmc.uu.se>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Lee Soin wrote:
>>> Hello!
>>> I'm trying to find the surface residues of a protein. Maybe this should
>>> be calculated by myself and not using GROMACS. Can anybody tell me a
>>> feasible procedure for doing so? Thanks!
>>>
>> g_sas
>>
>>> --
>>> Sun Li
>>> Department of Physics
>>> Nanjing University, China
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 03 Mar 2009 10:54:42 +0100
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <49ACFE62.6030603 at xray.bmc.uu.se>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> mhviet at ifpan.edu.pl wrote:
>>> Dear all
>>>
>>> I am newer in Gromacs. Now I am studying Gomacs for protein
>>> simulations.
>>> I
>>> am trying script files which used for gromacs-3. Can I do it? Does
>>> Gromacs-4. have to use others script files? and If It have, Can you
>>> send
>>> sript files to me for gromacs-4?
>>> Thank you verry much!
>>
>> Have you tried?
>>
>> Most of them will work.
>>
>>>
>>> Yours truly,
>>>
>>> Man Hoang Viet
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Tue, 3 Mar 2009 11:37:56 +0100
>> From: "Sarah Witzke" <sawit02 at student.sdu.dk>
>> Subject: SV: SV: [gmx-users] g_order version 4.0.x
>> To: <jalemkul at vt.edu>, "Discussion list for GROMACS users"
>> <gmx-users at gromacs.org>
>> Message-ID:
>> <3BC166246158F845A8ABBACA9EEE1E2D09147BB0 at ADM-EXCH0C.adm.c.sdu.dk>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Good idea, I'll try that when I get home next week.
>>
>> -Sarah
>>
>> ________________________________
>>
>> Fra: gmx-users-bounces at gromacs.org på vegne af Justin A. Lemkul
>> Sendt: ma 02-03-2009 13:58
>> Til: Discussion list for GROMACS users
>> Emne: Re: SV: [gmx-users] g_order version 4.0.x
>>
>>
>>
>>
>>
>> Sarah Witzke wrote:
>>> Thank you David, I have filled a bugzilla.
>>>
>>
>> g_order works for me under version 4.0.4, perhaps try an upgrade?
>>
>> -Justin
>>
>> ________________________________
>>>
>>> Fra: gmx-users-bounces at gromacs.org på vegne af David van der Spoel
>>> Sendt: ma 02-03-2009 10:55
>>> Til: Discussion list for GROMACS users
>>> Emne: Re: [gmx-users] g_order version 4.0.x
>>>
>>>
>>>
>>> Sarah Witzke wrote:
>>>> Dear Gromacs users,
>>>>
>>>>
>>>>
>>>> I'm sorry to resend this email but I sent it yesterday (27 hours ago)
>>>> and I still haven't received it myself. I'm sorry for the
>>>> inconvenience
>>>> it might cause.
>>>>
>>>>
>>>>
>>>> Sarah
>>>>
>>>>
>>>> ________________________________
>>>>
>>>> Dear Gromacs Users,
>>>>
>>>>
>>>>
>>>> I have simulated a lipid bilayer (128 DMPC molecules) with some small
>>>> hydrophobic molecules. These small molecules go from the water into
>>>> the
>>>> bilayer and I now want to do some analysis to see, whether this has
>>>> changed e.g. membrane thickness or the order of the lipid tails. I'm
>>>> new to gromacs and this is my first try with analysis.
>>>>
>>>> For analysing the order of the lipid tales, I use g_order. The first
>>>> index file I created consisted of 28 groups - one for each of the 14
>>>> carbons (including the carbonyl-C) in the two chains. The atoms in
>>>> each
>>>> of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so
>>>> each of the 28 groups in the index file consist of 128 atoms (an entry
>>>> in make_ndx would look like this "a c15 & r DMPC").
>>>>
>>>> Then I tried g_order version 4.0.2:
>>>>
>>>>
>>>>
>>>> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b
>>>> 100000 -od dmpclim3_order_2.xvg
>>>>
>>>>
>>>>
>>>> I'm asked to "Select the group that contains the atoms you want to use
>>>> for the tetrahedrality order parameter calculation:" and then all the
>>>> 28 groups are listed. This was not what I had expected; I thought
>>>> g_order calculated the order parameter for all the tail carbons at
>>>> once. I tried just choosing group 0 to see what happened: Not much -
>>>> as
>>>> was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg.
>>>> This I found strange since I hadn't asked for them, but then I found
>>>> this bugzilla report:
>>>> http://www.gromacs.org/component/option,com_wrapper/Itemid,157/
>>>> <https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/>
>>>> (no. 264)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> After reading that I also tried to specify all carbons in one single
>>>> group and then run g_order again:
>>>>
>>>>
>>>>
>>>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>>>> 100000 -od dmpclim3_order_2.xvg
>>>>
>>>>
>>>>
>>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>>>>
>>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>>>>
>>>> Select the group that contains the atoms you want to use for the
>>>> tetrahedrality order parameter calculation:
>>>>
>>>> Group 0
>>>> (C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC)
>>>> has 3584 elements
>>>>
>>>> There is one group in the index
>>>>
>>>> Reading frame 0 time 100000.008
>>>>
>>>> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#
>>>>
>>>>
>>>>
>>>> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#
>>>>
>>>> Reading frame 11000 time 210000.016
>>>>
>>>>
>>>>
>>>> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted
>>>> deuterium order .xvg file.
>>>>
>>>>
>>>>
>>>> So, in the bugzilla report it also said that the problem had been
>>>> fixed
>>>> in the CVS. Unfortunately I don't know what this is, could anyone
>>>> explain me please?
>>>>
>>>>
>>>>
>>>> I tried g_order version 4.0.3 (again with the index file with only one
>>>> group):
>>>>
>>>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>>>> 100000 -od dmpclim3_order_3.xvg
>>>>
>>>>
>>>>
>>>> Taking z axis as normal to the membrane
>>>>
>>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>>>>
>>>> Using following groups:
>>>>
>>>> Groupname:
>>>> C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC
>>>> First atomname: C15 First atomnr 44
>>>>
>>>>
>>>>
>>>> Reading frame 0 time 100000.008 Number of elements in first
>>>> group: 3584
>>>>
>>>> Reading frame 11000 time 210000.016
>>>>
>>>>
>>>>
>>>> Read trajectory. Printing parameters to file
>>>>
>>>>
>>>>
>>>> Now two order files are generated: The wanted dmpclim3_order_3.xvg and
>>>> also order.xvg which I didn't request for. (No sg-ang.xvg and
>>>> sk-dist.xvg this time).
>>>>
>>>> Unfortunately neither of the obtained .xvg files contain any order
>>>> parameters:
>>>>
>>>>
>>>>
>>>> dmpclim3_order_3.xvg:
>>>>
>>>> # This file was created Sat Feb 28 20:02:09 2009
>>>>
>>>> # by the following command:
>>>>
>>>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>>>> 100000 -od dmpclim3_order_3.xvg
>>>>
>>>> #
>>>>
>>>> # g_order is part of G R O M A C S:
>>>>
>>>> #
>>>>
>>>> # Great Red Oystrich Makes All Chemists Sane
>>>>
>>>> #
>>>>
>>>> @ title "Deuterium order parameters"
>>>>
>>>> @ xaxis label "Atom"
>>>>
>>>> @ yaxis label "Scd"
>>>>
>>>> @TYPE xy
>>>>
>>>>
>>>>
>>>> order.xvg:
>>>>
>>>> # This file was created Sat Feb 28 20:02:09 2009
>>>>
>>>> # by the following command:
>>>>
>>>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>>>> 100000 -od dmpclim3_order_3.xvg
>>>>
>>>> #
>>>>
>>>> # g_order is part of G R O M A C S:
>>>>
>>>> #
>>>>
>>>> # Great Red Oystrich Makes All Chemists Sane
>>>>
>>>> #
>>>>
>>>> @ title "Order tensor diagonal elements"
>>>>
>>>> @ xaxis label "Atom"
>>>>
>>>> @ yaxis label "S"
>>>>
>>>> @TYPE xy
>>>>
>>>>
>>>>
>>>> I will be very thankful if anyone has any suggestions as to what I'm
>>>> doing wrong?
>>>>
>>>>
>>> Please submit a bugzilla.
>>> I fixed something before 4.0.3, but apparently not everything.
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>>> University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>> <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>>
>> End of gmx-users Digest, Vol 59, Issue 12
>> *****************************************
>>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 3 Mar 2009 06:36:02 -0500
> From: Roland Schulz <roland at utk.edu>
> Subject: Re: [gmx-users] about LINCS WARNING
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <c93c21390903030336l7133166dr4a662fb24547034 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Are you sure you are actually doing minimization and not MD? Check the
> integrator option in the mdp file. Also take a look at:
> http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
>
> Roland
>
> On Tue, Mar 3, 2009 at 6:19 AM, <mhviet at ifpan.edu.pl> wrote:
>
>> Thank David very much
>> I have tried and most of them work.
>> And, When I run script_mini.mdp to minimize energy and it report LINCS
>> warning (as below). So Can you tell me What LINCS WARNING mean?
>>
>> Step 16, time 0.032 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000000, max 0.000001 (between atoms 18 and 20)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 97 98 35.3 0.1000 0.1000 0.1000
>>
>>
>>
>> > Send gmx-users mailing list submissions to
>> > gmx-users at gromacs.org
>> >
>> > To subscribe or unsubscribe via the World Wide Web, visit
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > or, via email, send a message with subject or body 'help' to
>> > gmx-users-request at gromacs.org
>> >
>> > You can reach the person managing the list at
>> > gmx-users-owner at gromacs.org
>> >
>> > When replying, please edit your Subject line so it is more specific
>> > than "Re: Contents of gmx-users digest..."
>> >
>> >
>> > Today's Topics:
>> >
>> > 1. Detail of Script.sh in Gromacs-4.0.3? (mhviet at ifpan.edu.pl)
>> > 2. Re: How to define protein surface residues (David van der Spoel)
>> > 3. Re: Detail of Script.sh in Gromacs-4.0.3? (David van der Spoel)
>> > 4. SV: SV: [gmx-users] g_order version 4.0.x (Sarah Witzke)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Tue, 3 Mar 2009 10:37:05 +0100 (CET)
>> > From: mhviet at ifpan.edu.pl
>> > Subject: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
>> > To: gmx-users at gromacs.org
>> > Message-ID:
>> > <24e6018b503b7a1516fccea3477b4d8d.squirrel at webmail.ifpan.edu.pl>
>> > Content-Type: text/plain;charset=iso-8859-1
>> >
>> > Dear all
>> >
>> > I am newer in Gromacs. Now I am studying Gomacs for protein
>> simulations.
>> I
>> > am trying script files which used for gromacs-3. Can I do it? Does
>> > Gromacs-4. have to use others script files? and If It have, Can you
>> send
>> > sript files to me for gromacs-4?
>> > Thank you verry much!
>> >
>> > Yours truly,
>> >
>> > Man Hoang Viet
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Tue, 03 Mar 2009 10:52:07 +0100
>> > From: David van der Spoel <spoel at xray.bmc.uu.se>
>> > Subject: Re: [gmx-users] How to define protein surface residues
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > Message-ID: <49ACFDC7.6060402 at xray.bmc.uu.se>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> > Lee Soin wrote:
>> >> Hello!
>> >> I'm trying to find the surface residues of a protein. Maybe this
>> should
>> >> be calculated by myself and not using GROMACS. Can anybody tell me a
>> >> feasible procedure for doing so? Thanks!
>> >>
>> > g_sas
>> >
>> >> --
>> >> Sun Li
>> >> Department of Physics
>> >> Nanjing University, China
>> >>
>> >>
>> >> ------------------------------------------------------------------------
>> >>
>> >> _______________________________________________
>> >> gmx-users mailing list gmx-users at gromacs.org
>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://www.gromacs.org/search before
>> >> posting!
>> >> Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> >
>> > --
>> > David van der Spoel, Ph.D., Professor of Biology
>> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>> University.
>> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
>> +4618511755.
>> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 3
>> > Date: Tue, 03 Mar 2009 10:54:42 +0100
>> > From: David van der Spoel <spoel at xray.bmc.uu.se>
>> > Subject: Re: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > Message-ID: <49ACFE62.6030603 at xray.bmc.uu.se>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> > mhviet at ifpan.edu.pl wrote:
>> >> Dear all
>> >>
>> >> I am newer in Gromacs. Now I am studying Gomacs for protein
>> simulations.
>> >> I
>> >> am trying script files which used for gromacs-3. Can I do it? Does
>> >> Gromacs-4. have to use others script files? and If It have, Can you
>> send
>> >> sript files to me for gromacs-4?
>> >> Thank you verry much!
>> >
>> > Have you tried?
>> >
>> > Most of them will work.
>> >
>> >>
>> >> Yours truly,
>> >>
>> >> Man Hoang Viet
>> >>
>> >> _______________________________________________
>> >> gmx-users mailing list gmx-users at gromacs.org
>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://www.gromacs.org/search before
>> >> posting!
>> >> Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> >
>> > --
>> > David van der Spoel, Ph.D., Professor of Biology
>> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>> University.
>> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
>> +4618511755.
>> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 4
>> > Date: Tue, 3 Mar 2009 11:37:56 +0100
>> > From: "Sarah Witzke" <sawit02 at student.sdu.dk>
>> > Subject: SV: SV: [gmx-users] g_order version 4.0.x
>> > To: <jalemkul at vt.edu>, "Discussion list for GROMACS users"
>> > <gmx-users at gromacs.org>
>> > Message-ID:
>> > <3BC166246158F845A8ABBACA9EEE1E2D09147BB0 at ADM-EXCH0C.adm.c.sdu.dk>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > Good idea, I'll try that when I get home next week.
>> >
>> > -Sarah
>> >
>> > ________________________________
>> >
>> > Fra: gmx-users-bounces at gromacs.org på vegne af Justin A. Lemkul
>> > Sendt: ma 02-03-2009 13:58
>> > Til: Discussion list for GROMACS users
>> > Emne: Re: SV: [gmx-users] g_order version 4.0.x
>> >
>> >
>> >
>> >
>> >
>> > Sarah Witzke wrote:
>> >> Thank you David, I have filled a bugzilla.
>> >>
>> >
>> > g_order works for me under version 4.0.4, perhaps try an upgrade?
>> >
>> > -Justin
>> >
>> > ________________________________
>> >>
>> >> Fra: gmx-users-bounces at gromacs.org på vegne af David van der Spoel
>> >> Sendt: ma 02-03-2009 10:55
>> >> Til: Discussion list for GROMACS users
>> >> Emne: Re: [gmx-users] g_order version 4.0.x
>> >>
>> >>
>> >>
>> >> Sarah Witzke wrote:
>> >>> Dear Gromacs users,
>> >>>
>> >>>
>> >>>
>> >>> I'm sorry to resend this email but I sent it yesterday (27 hours
>> ago)
>> >>> and I still haven't received it myself. I'm sorry for the
>> inconvenience
>> >>> it might cause.
>> >>>
>> >>>
>> >>>
>> >>> Sarah
>> >>>
>> >>>
>> >>> ________________________________
>> >>>
>> >>> Dear Gromacs Users,
>> >>>
>> >>>
>> >>>
>> >>> I have simulated a lipid bilayer (128 DMPC molecules) with some
>> small
>> >>> hydrophobic molecules. These small molecules go from the water into
>> the
>> >>> bilayer and I now want to do some analysis to see, whether this has
>> >>> changed e.g. membrane thickness or the order of the lipid tails. I'm
>> >>> new to gromacs and this is my first try with analysis.
>> >>>
>> >>> For analysing the order of the lipid tales, I use g_order. The first
>> >>> index file I created consisted of 28 groups - one for each of the 14
>> >>> carbons (including the carbonyl-C) in the two chains. The atoms in
>> each
>> >>> of the 128 lipid molecules have the same atom name (e.g. c1, c2...)
>> so
>> >>> each of the 28 groups in the index file consist of 128 atoms (an
>> entry
>> >>> in make_ndx would look like this "a c15 & r DMPC").
>> >>>
>> >>> Then I tried g_order version 4.0.2:
>> >>>
>> >>>
>> >>>
>> >>> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b
>> >>> 100000 -od dmpclim3_order_2.xvg
>> >>>
>> >>>
>> >>>
>> >>> I'm asked to "Select the group that contains the atoms you want to
>> use
>> >>> for the tetrahedrality order parameter calculation:" and then all
>> the
>> >>> 28 groups are listed. This was not what I had expected; I thought
>> >>> g_order calculated the order parameter for all the tail carbons at
>> >>> once. I tried just choosing group 0 to see what happened: Not much -
>> as
>> >>> was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg.
>> >>> This I found strange since I hadn't asked for them, but then I found
>> >>> this bugzilla report:
>> >>> http://www.gromacs.org/component/option,com_wrapper/Itemid,157/
>> >>> <
>> https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/
>> >
>> >>> (no. 264)
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> After reading that I also tried to specify all carbons in one single
>> >>> group and then run g_order again:
>> >>>
>> >>>
>> >>>
>> >>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>> >>> 100000 -od dmpclim3_order_2.xvg
>> >>>
>> >>>
>> >>>
>> >>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>> >>>
>> >>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>> >>>
>> >>> Select the group that contains the atoms you want to use for the
>> >>> tetrahedrality order parameter calculation:
>> >>>
>> >>> Group 0
>> >>>
>> (C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC)
>> >>> has 3584 elements
>> >>>
>> >>> There is one group in the index
>> >>>
>> >>> Reading frame 0 time 100000.008
>> >>>
>> >>> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#
>> >>>
>> >>>
>> >>>
>> >>> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#
>> >>>
>> >>> Reading frame 11000 time 210000.016
>> >>>
>> >>>
>> >>>
>> >>> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted
>> >>> deuterium order .xvg file.
>> >>>
>> >>>
>> >>>
>> >>> So, in the bugzilla report it also said that the problem had been
>> fixed
>> >>> in the CVS. Unfortunately I don't know what this is, could anyone
>> >>> explain me please?
>> >>>
>> >>>
>> >>>
>> >>> I tried g_order version 4.0.3 (again with the index file with only
>> one
>> >>> group):
>> >>>
>> >>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>> >>> 100000 -od dmpclim3_order_3.xvg
>> >>>
>> >>>
>> >>>
>> >>> Taking z axis as normal to the membrane
>> >>>
>> >>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>> >>>
>> >>> Using following groups:
>> >>>
>> >>> Groupname:
>> >>>
>> C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC
>> >>> First atomname: C15 First atomnr 44
>> >>>
>> >>>
>> >>>
>> >>> Reading frame 0 time 100000.008 Number of elements in first
>> >>> group: 3584
>> >>>
>> >>> Reading frame 11000 time 210000.016
>> >>>
>> >>>
>> >>>
>> >>> Read trajectory. Printing parameters to file
>> >>>
>> >>>
>> >>>
>> >>> Now two order files are generated: The wanted dmpclim3_order_3.xvg
>> and
>> >>> also order.xvg which I didn't request for. (No sg-ang.xvg and
>> >>> sk-dist.xvg this time).
>> >>>
>> >>> Unfortunately neither of the obtained .xvg files contain any order
>> >>> parameters:
>> >>>
>> >>>
>> >>>
>> >>> dmpclim3_order_3.xvg:
>> >>>
>> >>> # This file was created Sat Feb 28 20:02:09 2009
>> >>>
>> >>> # by the following command:
>> >>>
>> >>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>> >>> 100000 -od dmpclim3_order_3.xvg
>> >>>
>> >>> #
>> >>>
>> >>> # g_order is part of G R O M A C S:
>> >>>
>> >>> #
>> >>>
>> >>> # Great Red Oystrich Makes All Chemists Sane
>> >>>
>> >>> #
>> >>>
>> >>> @ title "Deuterium order parameters"
>> >>>
>> >>> @ xaxis label "Atom"
>> >>>
>> >>> @ yaxis label "Scd"
>> >>>
>> >>> @TYPE xy
>> >>>
>> >>>
>> >>>
>> >>> order.xvg:
>> >>>
>> >>> # This file was created Sat Feb 28 20:02:09 2009
>> >>>
>> >>> # by the following command:
>> >>>
>> >>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b
>> >>> 100000 -od dmpclim3_order_3.xvg
>> >>>
>> >>> #
>> >>>
>> >>> # g_order is part of G R O M A C S:
>> >>>
>> >>> #
>> >>>
>> >>> # Great Red Oystrich Makes All Chemists Sane
>> >>>
>> >>> #
>> >>>
>> >>> @ title "Order tensor diagonal elements"
>> >>>
>> >>> @ xaxis label "Atom"
>> >>>
>> >>> @ yaxis label "S"
>> >>>
>> >>> @TYPE xy
>> >>>
>> >>>
>> >>>
>> >>> I will be very thankful if anyone has any suggestions as to what I'm
>> >>> doing wrong?
>> >>>
>> >>>
>> >> Please submit a bugzilla.
>> >> I fixed something before 4.0.3, but apparently not everything.
>> >>
>> >> --
>> >> David van der Spoel, Ph.D., Professor of Biology
>> >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>> University.
>> >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
>> +4618511755.
>> >> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> >> <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/>
>> >> _______________________________________________
>> >> gmx-users mailing list gmx-users at gromacs.org
>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://www.gromacs.org/search before
>> >> posting!
>> >> Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >>
>> >>
>> >> _______________________________________________
>> >> gmx-users mailing list gmx-users at gromacs.org
>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://www.gromacs.org/search before
>> >> posting!
>> >> Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >>
>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul
>> > Graduate Research Assistant
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > _______________________________________________
>> > gmx-users mailing list gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/search before
>> posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > gmx-users mailing list
>> > gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/search before
>> posting!
>> >
>> > End of gmx-users Digest, Vol 59, Issue 12
>> > *****************************************
>> >
>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
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