[gmx-users] about LINCS WARNING

mhviet at ifpan.edu.pl mhviet at ifpan.edu.pl
Tue Mar 3 12:19:45 CET 2009


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



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> Today's Topics:
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>    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
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
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>
> --
> 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!
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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
>
>
> --
> 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
>>
>>
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>
> --
> ========================================
>
> 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
>
> ========================================
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> *****************************************
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