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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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 ([EMAIL PROTECTED])
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" < [EMAIL PROTECTED]>
Subject: [gmx-users] Change default "nice" option for mdrun (was: Can
not find file: topol.tpr)
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
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: [EMAIL PROTECTED]
Subject: [gmx-users] RE: Coul-LR in PME and in Reaction Field
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED] >
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 [EMAIL PROTECTED]
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" <[EMAIL PROTECTED]>
Subject: [gmx-users] aromatic hydrogens
To: <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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
[EMAIL PROTECTED]
------------------------------
Message: 4
Date: Thu, 27 Apr 2006 16:40:28 +0200
From: Miguel Ortiz Lombardia <[EMAIL PROTECTED] >
Subject: Re: [gmx-users] do_dssp error
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: < [EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>/* 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
>
>
> ------------------------------------------------------------------------
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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: [EMAIL PROTECTED]
> 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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- --
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: [EMAIL PROTECTED]
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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------------------------------
Message: 5
Date: Thu, 27 Apr 2006 16:49:35 +0200
From: "Berk Hess" <[EMAIL PROTECTED]>
Subject: RE: [gmx-users] RE: Coul-LR in PME and in Reaction Field
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed
>From: [EMAIL PROTECTED]
>Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>To: gmx-users@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" <[EMAIL PROTECTED]>
Subject: [gmx-users] topol.tpr made for 2 nodes while mdrun expected 8
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
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" < [EMAIL PROTECTED]>
Subject: Re: [gmx-users] do_dssp error
To: gmx-users@gromacs.org
Message-ID: < [EMAIL PROTECTED]>
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" <[EMAIL PROTECTED]>
Subject: [gmx-users] problem in normal mode analysis
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
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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