[gmx-users] about LINCS WARNING
Roland Schulz
roland at utk.edu
Tue Mar 3 12:36:02 CET 2009
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
>
>
>
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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!
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> >> 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!
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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
> >
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > 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
> > *****************************************
> >
>
>
> _______________________________________________
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--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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