[gmx-users] using ffgmx force field
Mohan Boggara
mohanbabu.boggara at gmail.com
Fri Apr 28 01:54:44 CEST 2006
Hi,
In the file FF.dat, it is mentioned that GROMACS force fields ffgmx and
ffgmx2 are DEPRECATED in the brackets. Does it mean I should not use it?
Can someone help me with this?
Mohan
On 27/04/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
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> Today's Topics:
>
> 1. Change default "nice" option for mdrun (was: Can not find
> file: topol.tpr) (Guillem Plasencia)
> 2. RE: Coul-LR in PME and in Reaction Field (pascal.baillod at epfl.ch)
> 3. aromatic hydrogens (Joanne Hanna)
> 4. Re: do_dssp error (Miguel Ortiz Lombardia)
> 5. RE: RE: Coul-LR in PME and in Reaction Field (Berk Hess)
> 6. topol.tpr made for 2 nodes while mdrun expected 8
> (Guillem Plasencia)
> 7. Re: do_dssp error (Guillem Plasencia)
> 8. problem in normal mode analysis (arunima singh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 27 Apr 2006 14:11:30 +0000
> From: "Guillem Plasencia" <guillem_pg at hotmail.com>
> Subject: [gmx-users] Change default "nice" option for mdrun (was: Can
> not find file: topol.tpr)
> To: gmx-users at gromacs.org
> Message-ID: <BAY108-F7C9112D022DD3B7A6B94BF4BD0 at phx.gbl>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
> Hello again gmxers,
>
> i've found the problem i had (Can not find file: topol.tpr). Silly problem
> with easy answer, i didn't had a local copy of this file in each node.
>
> I still have one more question. I'm using 2 boxes with 2 Intel P4 3Ghz
> processors (with hyperthreading on), but right now i'm just using only one
> of them because the other is busy (and it wouldn't be a reliable
> benchmark).
>
> I've done the test with lysozyme (cutoff) using only one of the CPUs in
> one
> of my machines, and got the low performance of 3,256 ps /day (it should
> be
> 1494). I'd like to know how it scalates, by running it using both
> physical
> CPUs inside this same machine, but when i do
>
> grompp <files> -np 2
> and
> mpirun n0 -np 2 mdrun <files> -np 2
>
> it complains that it was processed for two nodes, not just one. How do i
> run
> this job in parallel between the two CPUs in my box? I suppose that if i
> remove the second node in my LAM-MPI configuration it will still complain
> that it was prepared for two nodes, not just one. Also, i've read in the
> archives that threads aren't yet implemented, so using option -nt 2
> doesn't
> work neither.
>
> How do i do it?
>
> Thank you very much !
>
> Guillem Plasencia
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 27 Apr 2006 16:31:48 +0200 (MEST)
> From: pascal.baillod at epfl.ch
> Subject: [gmx-users] RE: Coul-LR in PME and in Reaction Field
> To: gmx-users at gromacs.org
> Message-ID: <1146148308.4450d5d482cd2 at imapwww.epfl.ch>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thank you very much, Berk!
>
> 1) That only leaves one unanswered point, that seems logical but of which
> I
> would like to be certain of.. Is there any accessible term in the reaction
> field
> implementation accounting for long-range electrostatic interaction due to
> the
> environnement dielectric? Or is this contribution simply added to Coul-SR?
>
> 2) Last, I have a situation that I cannot understand, comparing RF and PME
> for a
> 100 residue protein in a water cubic box of roughly 70*70*70A. Comparing
> contributions of energy groups (g_energy), I obtain:
>
> -Reaction field: |coul-SR prot-prot| > |coul-SR prot-other|
> -PME: |coul-SR prot-prot| < |coul-SR prot-other| (the opposite)
> (with "||" for absolute values)
>
> Would that be because of the long-range electrostatic contribution (with
> the
> environnement dielectric), added to coul-SR as I suggest in 1)?
>
> Thank you very much for your help!
>
> Pascal
>
>
>
>
> *******************************************************************************
> Pascal Baillod (PhD student)
>
> *******************************************************************************
> Swiss Federal Institute of Technology EPFL Tel:
> +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering , Fax:
> +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry
> pascal.baillod at epfl.ch
> Room BCH 4121, Avenue Forel,
> http://lcbcpc21.epfl.ch
> CH-1015 Lausanne
>
> *******************************************************************************
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 27 Apr 2006 15:29:34 +0100
> From: "Joanne Hanna" <J.F.Hanna at warwick.ac.uk>
> Subject: [gmx-users] aromatic hydrogens
> To: <gmx-users at gromacs.org>
> Message-ID: <s450e36e.046 at liberator.csv.warwick.ac.uk>
> Content-Type: text/plain; charset=US-ASCII
>
> Hi
>
> I have a question which has been puzzling me regarding the addition of
> hydrogens to atoms in aromatic rings. I am using force field ffG43a2 but do
> not have the GROMOS96 manual which is i assume the place to check how the
> force field was derived (please correct me if i am wrong) and I am confused
> as to why in a PHE residue all hydrogens (HC) are added to the carbons (C)
> in the aromatic group but in histidine, these carbon/hydrogen atoms are
> represented as atom typr CR1. This is mainly in connection to a topology
> that I have created of AMP, in which I have represented atoms 2C and 8C of
> the adenine ring as CR1 (on the guidance of Prodrg and the AMP topology in
> ffG43a2.rtp) and am now wondering whether these atoms should in fact be
> represented as explicitly as HC and C.
> Could any one give me any feedback on any of this and why would be most
> appropriate to do in line with the ffG43a2 force field.
>
> Many thanks
> Jo
>
>
>
>
>
>
>
>
>
>
>
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
>
> (02476) 574623
> J.F.Hanna at warwick.ac.uk
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 27 Apr 2006 16:40:28 +0200
> From: Miguel Ortiz Lombardia <molatwork at yahoo.es>
> Subject: Re: [gmx-users] do_dssp error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4450D7DC.8080302 at yahoo.es>
> Content-Type: text/plain; charset=ISO-8859-1
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Jahan,
>
> Sorry, I'm not a MSWindows user, so I can't help you here. I think you
> can set up a global environment variable somewhere in your control
> panel, but can't really tell you how.
>
> Good luck,
>
>
> Miguel
>
> jahanshah ashkani wrote:
> > Thanks for your reply.
> > I used from Gromacs on WindowsXP with command prompt. How can I change
> > DSSP path in this environment? Thank you very much.
> >
> > Sincerely yours,
> > Jahan
> >
> > */Miguel Ortiz Lombardia <molatwork at yahoo.es>/* wrote:
> >
> > Hi Jahan,
> >
> > First, you must make sure you have the dssp program; it doesn't come
> > with gromacs, but you can download it separately from:
> >
> > http://swift.cmbi.ru.nl/gv/dssp/
> >
> > Secondly, if 'setenv' is not working you are not on a csh/tcsh
> > shell. Try:
> >
> > export DSSP=/path_to_your_dssp_installation/dssp
> >
> > This should work if you are on a sh/bash shell.
> >
> >
> > HTH,
> >
> >
> > Miguel
> >
> >
> > jahanshah ashkani wrote:
> >> Hi,
> >> I have a problem with do_dssp command. When I ran it, I found this
> > fatal
> >> error ? DSSP executable does not exist. Then I
> >> used from setenv DSSP command, but I found this error ?setenv is not
> >> recognized as an internal or external command,..?
> >> I would be glad if you help me in this case.
> >> Thank you very much.
> >
> >> Sincerely yours,
> >> Jahan
> >
> >
> > ------------------------------------------------------------------------
> >> Yahoo! Messenger with Voice. Make PC-to-Phone Calls
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> >
> >
> >
> > ------------------------------------------------------------------------
> >
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
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> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > --
> > Miguel Ortiz Lombardía
> > Centro de Investigaciones Oncológicas
> > C/ Melchor Fernández Almagro, 3
> > 28029 Madrid, Spain
> > Tel. +34 912 246 900
> > Fax. +34 912 246 976
> > email: molatwork at yahoo.es
> > www: http://www.ysbl.york.ac.uk/~mol/
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Je suis de la mauvaise herbe,
> > Braves gens, braves gens,
> > Je pousse en liberté
> > Dans les jardins mal fréquentés!
> > Georges Brassens
> _______________________________________________
> 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
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> > ------------------------------------------------------------------------
> > New Yahoo! Messenger with Voice. Call regular phones from your PC
> > <
> http://us.rd.yahoo.com/mail_us/taglines/postman5/*http://us.rd.yahoo.com/evt=39666/*http://messenger.yahoo.com
> >
> > and save big.
>
>
> > ------------------------------------------------------------------------
>
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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>
> - --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900
> Fax. +34 912 246 976
> email: molatwork at yahoo.es
> www: http://www.ysbl.york.ac.uk/~mol/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Je suis de la mauvaise herbe,
> Braves gens, braves gens,
> Je pousse en liberté
> Dans les jardins mal fréquentés!
> Georges Brassens
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>
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>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 27 Apr 2006 16:49:35 +0200
> From: "Berk Hess" <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] RE: Coul-LR in PME and in Reaction Field
> To: gmx-users at gromacs.org
> Message-ID: <BAY110-F34FC809D2EB0A523397F818EBD0 at phx.gbl>
> Content-Type: text/plain; format=flowed
>
>
>
>
> >From: pascal.baillod at epfl.ch
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] RE: Coul-LR in PME and in Reaction Field
> >Date: Thu, 27 Apr 2006 16:31:48 +0200 (MEST)
> >
> >Thank you very much, Berk!
> >
> >1) That only leaves one unanswered point, that seems logical but of which
> I
> >would like to be certain of.. Is there any accessible term in the
> reaction
> >field
> >implementation accounting for long-range electrostatic interaction due to
> >the
> >environnement dielectric? Or is this contribution simply added to
> Coul-SR?
> >
> >2) Last, I have a situation that I cannot understand, comparing RF and
> PME
> >for a
> >100 residue protein in a water cubic box of roughly 70*70*70A. Comparing
> >contributions of energy groups (g_energy), I obtain:
> >
> >-Reaction field: |coul-SR prot-prot| > |coul-SR prot-other|
> >-PME: |coul-SR prot-prot| < |coul-SR prot-other| (the
> opposite)
> >(with "||" for absolute values)
> >
> >Would that be because of the long-range electrostatic contribution (with
> >the
> >environnement dielectric), added to coul-SR as I suggest in 1)?
>
> You can not simply compare this terms.
> Reaction-field is an approximation. It assumes a homogeneous dielectric
> medium beyond the cut-off which is clearly not true for your system.
> Your protein probably has charged residues which cause significant
> error with RF.
>
> Secondly the Coul-SR term does not contain 1/r.
> With RF it is 1/r plus the effect of the reaction field force.
> This might be what you call "long-range electrostatic contribution",
> but it is not really long-range.
> With PME is it erfc(beta*r)/r.
>
> Berk.
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 27 Apr 2006 15:06:30 +0000
> From: "Guillem Plasencia" <guillem_pg at hotmail.com>
> Subject: [gmx-users] topol.tpr made for 2 nodes while mdrun expected 8
> To: gmx-users at gromacs.org
> Message-ID: <BAY108-F29E7EDC3E10300177C2482F4BD0 at phx.gbl>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
> Hello gmxers,
>
> i've been struggling to make gromacs be able to use my 2 Dual CPU
> machines,
> without success.
> I'd like to know exactly how to configure lam and how to preprocess with
> grompp (and then execute with mpirun) in order to be able to run as many
> parallel processes in my 2 Dual CPU machines that sum 4 CPUs (8 with
> hyperthreading).
>
> My lam configuration file content is:
> lead7 cpu=4
> 192.168.1.9 cpu=4
>
> As a short brief, i've been able to run the same lisozyme cutoff benchmark
> in 4 parallel processes in only one node by commenting out the first line
> (the one which begins ..lead7) in my lam configuration file, and then
>
> preprocessing as:
> grompp -f cutoff.mdp -c conf.gro -p topol.top -np 4 -shuffle -sort
>
> and running with:
> mpirun C mdrun -s topol.tpr -nice 0 -np 4
>
> So far, everything worked fine.
>
> Problems arises when i try to include the other node (lead7).
>
> I preprocess benchmarck lisozyme with cutoff as follows:
> grompp -f cutoff.mdp -c conf.gro -p topol.top -np 8 -shuffle -sort
>
> I include -np 8 to split into 8 processes (is that ok?)
>
> but when i do
>
> mpirun C mdrun -s topol.tpr -nice 0 -np 8
>
> i get the error:
>
> Reading file topol.tpr, VERSION 3.3.1 (single precision)
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.1
> Source code file: init.c, line: 69
>
> Fatal error:
> run input file topol.tpr was made for 2 nodes,
> while mdrun expected it to be for 8 nodes.
> -------------------------------------------------------
>
> How can be that, if i used grompp with option -np 8 ?
>
> Any idea on how can i do it?
>
> Thank you very much for your help,
>
> Guillem Plasencia
> Spain
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 27 Apr 2006 15:13:52 +0000
> From: "Guillem Plasencia" <guillem_pg at hotmail.com>
> Subject: Re: [gmx-users] do_dssp error
> To: gmx-users at gromacs.org
> Message-ID: <BAY108-F3283C95128C72BB90D40EAF4BD0 at phx.gbl>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
> Hello Jahan,
>
> in WindowsXP, to set an environment variable, go to control panel (select
> classic view on the left pane), then select "System" icon.. Select
> "Advanced
> Options Tab", then select "Environment Variables" in the bottom.
>
> Hope this helps,
>
> Guillem Plasencia
> Spain.
>
>
> >jahanshah ashkani wrote:
> > > Thanks for your reply.
> > > I used from Gromacs on WindowsXP with command prompt. How can I change
> > > DSSP path in this environment? Thank you very much.
> > >
> > > Sincerely yours,
> > > Jahan
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: 27 Apr 2006 15:54:52 -0000
> From: "arunima singh" <arunima555 at rediffmail.com>
> Subject: [gmx-users] problem in normal mode analysis
> To: gmx-users at gromacs.org
> Message-ID: <20060427155452.13421.qmail at webmail45.rediffmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> hi,
> I m running normal mode on 8 processors for Lysozyme but it runs only 1293
> steps out of 22497 and ends with the message "MPI process rank 0 <n0,
> p17548> caught a SIGSEGV".
> Please tell me how to build the hessian gor NM.
> Arunima
>
>
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> *****************************************
>
--
Mohan Boggara
Graduate Research Assistant
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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