[gmx-users] Re: questions about implicit solvent simulation
Mohan Boggara
mohanbabu.boggara at gmail.com
Mon Apr 17 15:20:35 CEST 2006
Hi Periole,
May be this website is useful for implicit solvent calculations.
http://apbs.sourceforge.net/
mohan
On 17/04/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
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> Today's Topics:
>
> 1. Re: LINCS Warning with MDRUN - Segmentation Fault
> (David van der Spoel)
> 2. Re: Problems installing gromacs in a different directory
> (David van der Spoel)
> 3. Re: questions about implicit solvent simulation (X.Periole)
> 4. Re: LINCS Warning with MDRUN - Segmentation Fault (X.Periole)
> 5. question on g_cluster (Osman Yogurtcu)
> 6. Re: question on g_cluster (David van der Spoel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 17 Apr 2006 10:43:46 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <44435542.3090002 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Gaurav Chopra wrote:
> > Hi
> >
> > I am getting the following error with mdrun. I have done a few things
> > but the system complains of 1-4 interactions and gives LINCS warning if
> > the constraints are not turned off in the mdp file. I also changed the
> > fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I
> > get 1-4 interaction table size error and then LINCS warning. The output
> > of mdrun for one of these peptides is as follows. I am working on normal
> > mode decoys of each peptide and many of the decoys have no problems with
> > mdrun but some gives this error and Segmentation Fault.
> >
> > Please advice.
> >
> >
> you need to minimize better, but if your structures are really bad it
> won't help either (e.g. when you have a sidechain sticking through a ring)
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 17 Apr 2006 10:42:14 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Problems installing gromacs in a different
> directory
> To: edumlopes at yahoo.com.br, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <444354E6.3080509 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Eduardo Martins Lopes wrote:
> > Greetins fellow Gromacs Users, I come to thee because when I tried to
> > install gromacs in a different directory without SU privileges I get the
> > following error (the last few log lines)
> > Do I need super-user privileges ?
> >
> > oppush.Tpo"; exit 1; fi
> > if cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
> > -DGMXLIBDIR=\"/home/debora/gromacs/share/top\"
> > -I/home/debora/fftw/include -O3 -fomit-frame-pointer -finline-functions
> > -Wall -Wno-unused -malign-double -funroll-all-loops -MT topcat.o -MD -MP
> > -MF ".deps/topcat.Tpo" -c -o topcat.o topcat.c; \
> > then mv -f ".deps/topcat.Tpo" ".deps/topcat.Po"; else rm -f
> > ".deps/topcat.Tpo"; exit 1; fi
> > if cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
> > -DGMXLIBDIR=\"/home/debora/gromacs/share/top\"
> > -I/home/debora/fftw/include -O3 -fomit-frame-pointer -finline-functions
> > -Wall -Wno-unused -malign-double -funroll-all-loops -MT topshake.o -MD
> > -MP -MF ".deps/topshake.Tpo" -c -o topshake.o topshake.c; \
> > then mv -f ".deps/topshake.Tpo" ".deps/topshake.Po"; else rm -f
> > ".deps/topshake.Tpo"; exit 1; fi
> > make[2]: *** [all-recursive] Error 1
> > make[2]: Leaving directory `/cluster/debora/gromacs-3.3.1/src'
> > make[1]: *** [all] Error 2
> > make[1]: Leaving directory `/cluster/debora/gromacs-3.3.1/src'
> > make: *** [all-recursive] Error 1
> >
> >
> > FFTW was installed perfectly. Am I wrong or those files inside the
> > /gromacs-3.3.1/src are installed in the /src directory ? I have tried
> > almost all combinations of fftw and gromacs and the same error is
> > displayed everytime...
> >
> > Thanks in advance
> >
> this works fine, I do it all the time.
> Typically you should do
> ./configure --prefix=/home/joe/gromacs
> or wherever you want it to go.
>
>
> > Eduardo Martins Lopes
> > Physics Student Universidade Federal de São Carlos - Brazil
> >
> > ------------------------------------------------------------------------
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> > <
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> >
> > - Instale agora e faça ligações de graça.
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 17 Apr 2006 10:49:09 +0200
> From: "X.Periole" <X.Periole at rug.nl>
> Subject: Re: [gmx-users] questions about implicit solvent simulation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <web-19040600 at mail3.rug.nl>
> Content-Type: text/plain; charset="gb2312"; format="flowed"
>
>
> Dear Linchen,
>
> As Mark already told you there is no implicit solvent
> implementation in GROMACS ! The reaction field and
> generalized reaction field options are corrections to the
> long range electrostatic interactions.
> If you want to use an different dielectric cosntant than
> one you have to specify it in the mdp file with the
> keywork epsilon. Check out the manual for this, it must
> be indicated.
>
> > I want to do a implicit solvent MD simulation. I
> >wonder whether gromacs can fullfill the goal, if so,
> >which option should I choose for electrostatics, reaction
> >field or generalized reaction field? And what rcoulomb
> >value is appropriate? if not, could I do a energy
> >minimization for my protein in an enviroment of
> >dielectric constant other than 1?
> > Thanks a lot for your attention:)
> >
>
> XAvier
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 17 Apr 2006 10:53:12 +0200
> From: "X.Periole" <X.Periole at rug.nl>
> Subject: Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <web-19040707 at mail3.rug.nl>
> Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
>
> On Mon, 17 Apr 2006 00:07:29 -0700
> "Gaurav Chopra" <gauravchopra at gmail.com> wrote:
> > Hi
> >
> > I am getting the following error with mdrun. I have done
> >a few things but
> > the system complains of 1-4 interactions and gives LINCS
> >warning if the
> > constraints are not turned off in the mdp file. I also
> >changed the fudgeQQ =
> > 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun
> >but I get 1-4
> > interaction table size error and then LINCS warning. The
> >output of mdrun for
> > one of these peptides is as follows. I am working on
> >normal mode decoys of
> > each peptide and many of the decoys have no problems
> >with mdrun but some
> > gives this error and Segmentation Fault.
> >
> > Please advice.
>
> The lincs warnning are on water molecules isn't it ???
>
> XAvier
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 17 Apr 2006 09:38:34 +0000 (GMT)
> From: Osman Yogurtcu <karmatech at yahoo.co.uk>
> Subject: [gmx-users] question on g_cluster
> To: gmx-users at gromacs.org
> Message-ID: <20060417093834.29692.qmail at web26302.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Is it possible to use g_cluster to cluster NAMD2 trajectories?
>
> I am trying to use g_cluster to cluster my NAMD2 deriven trajectories.
> First, I converted my .dcd trajectory into .pdb format. Then, tried this:
>
> >g_cluster -f mypdb.pdb -cl clusters.pdb
>
> and it did not work. Later, I converted my .pdb to .xtc and tried:
>
> >g_cluster -f myxtc.xtc -cl clusters.pdb
>
> does not work either. Should I include a Gromacs MD run specific .tpr
> topology file as well, though it is mentioned as "optional input"?
>
> I hope you can help me out,
>
> Best
>
> Osman N. Yogurtcu
>
> Center for Computational Biology and Bioinformatics
> Research Assistant
> Koc University
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> ------------------------------
>
> Message: 6
> Date: Mon, 17 Apr 2006 11:52:07 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] question on g_cluster
> To: Osman Yogurtcu <karmatech at yahoo.co.uk>, Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> Message-ID: <44436547.9070608 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Osman Yogurtcu wrote:
> > Hi,
> >
> > Is it possible to use g_cluster to cluster NAMD2 trajectories?
> >
> > I am trying to use g_cluster to cluster my NAMD2 deriven trajectories.
> > First, I converted my .dcd trajectory into .pdb format. Then, tried
> this:
> >
> > >g_cluster -f mypdb.pdb -cl clusters.pdb
> >
> > and it did not work. Later, I converted my .pdb to .xtc and tried:
> >
> > >g_cluster -f myxtc.xtc -cl clusters.pdb
> >
> > does not work either. Should I include a Gromacs MD run specific .tpr
> > topology file as well, though it is mentioned as "optional input"?
> >
> > I hope you can help me out,
> >
>
>
> try using -s reference.pdb
>
> > Best
> >
> > Osman N. Yogurtcu
> > Center for Computational Biology and Bioinformatics
> > Research Assistant
> > Koc University
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> _______________________________________________
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> gmx-users at gromacs.org
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>
> End of gmx-users Digest, Vol 24, Issue 55
> *****************************************
>
--
Mohan Boggara
Department of Chemical Engineering
University of Houston
S222 Engineering Bldg 1
Houston, Texas-77204, USA
Mobile: 1-713-259-2166
Office: 1-713-743-4314
http://polymer.chee.uh.edu/
All human actions have one or more of these seven causes: chance, nature,
compulsion, habit, reason, passion, and desire.-- Aristotle
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