May be this website is useful for implicit solvent calculations.
http://apbs.sourceforge.net/
mohan
On 17/04/06,
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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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 2
Date: Mon, 17 Apr 2006 10:42:14 +0200
From: David van der Spoel < [EMAIL PROTECTED]>
Subject: Re: [gmx-users] Problems installing gromacs in a different
directory
To: [EMAIL PROTECTED], Discussion list for GROMACS users
<gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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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> 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 [EMAIL PROTECTED] .
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 3
Date: Mon, 17 Apr 2006 10:49:09 +0200
From: "X.Periole" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] questions about implicit solvent simulation
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
To: Discussion list for GROMACS users < gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
On Mon, 17 Apr 2006 00:07:29 -0700
"Gaurav Chopra" <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>
Subject: [gmx-users] question on g_cluster
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED] >
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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] question on g_cluster
To: Osman Yogurtcu < [EMAIL PROTECTED]>, Discussion list for
GROMACS users <gmx-users@gromacs.org>
Message-ID: < [EMAIL PROTECTED]>
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@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 [EMAIL PROTECTED].
> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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