[gmx-users] Scalar virial
Tandia, Adama
TandiaA at Corning.com
Fri Feb 3 20:02:18 CET 2006
Dear All,
I'm running a NVT MD where I quench a system from 3000K to 1000K. At the
end of the quench, I want to use the following relation:
P = Rho*k_B*T + (1/3V) * < Sum_{i<j}[F(r_ij).r_ij] >
where Rho is a number density, V the volume of the system, and k_B the
Boltzmann constant.
1- How can one extract the scalar virial (< Sum_{i<j}[F(r_ij).r_ij] >)
from the simulation?
2- I have considered taking the scalar virial as
(1/3)(virial_XX+virial_YY+virial_ZZ) from the virial tensor, and
recalculate the pressure but there seems to be a problem in the values.
The pressure that I have from this calculation is very different from
that one calculated from the trace of the pressure tensor. I saw on the
list there was a bug in the virial calculation. Has this been fixed in
the version 3.2.1?
Anyone has an idea what is going on?
I thank you all very much in advance for your prompt answer.
Warm regards,
Adama
Adama Tandia
Modeling & Simulation
Corning INC
SP TD 01-01
Corning NY 14831 USA
Tel: 607 248 1036
Fax: 607 974 3405
www.corning.com
-----Original Message-----
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Today's Topics:
1. Re: trjconv PDB format problems (3.2.1) (Berk Hess)
2. RE: spurious dihedral warnings (Berk Hess)
3. RE: spurious dihedral warnings (Moore, Jonathan (J))
4. RE: spurious dihedral warnings (Berk Hess)
5. RE: spurious dihedral warnings (Berk Hess)
6. RE: spurious dihedral warnings (Moore, Jonathan (J))
7. Re: Re: converting pdb to gmx successfully - how? (Ken Rotondi)
8. RE: spurious dihedral warnings (Moore, Jonathan (J))
9. pair-distance distribution function (Jon Ellis)
10. Re: Multiple chains, cofactors and ligands--ffgmx unreliable?
(YOLANDA SMALL)
----------------------------------------------------------------------
Message: 1
Date: Fri, 03 Feb 2006 14:30:46 +0100
From: "Berk Hess" <gmx3 at hotmail.com>
Subject: Re: [gmx-users] trjconv PDB format problems (3.2.1)
To: gmx-users at gromacs.org
Message-ID: <BAY110-F3CD70D329AAD31E432A7A8E0D0 at phx.gbl>
Content-Type: text/plain; format=flowed
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] trjconv PDB format problems (3.2.1)
>Date: Fri, 03 Feb 2006 14:22:39 +0100
>
>Tamas Horvath wrote:
>>But... it's no big deal to change HEADER to REMARK, is it?
>According to the pdb standard HEADER is obligatory, which doesn't
>really
>bother me in itself. However you can also do a one-liner
>
>grep -v HEADER orig.pdb > new.pdb
>
>to get rid of it...
The Gromacs HEADER line is not in accordance with the PDB file format.
molscript also complains about it.
I think we should change it to TITLE.
Note that Gromacs read the title from the HEADER line,
we might want to make it backwards compatible.
Berk.
------------------------------
Message: 2
Date: Fri, 03 Feb 2006 14:34:36 +0100
From: "Berk Hess" <gmx3 at hotmail.com>
Subject: RE: [gmx-users] spurious dihedral warnings
To: gmx-users at gromacs.org
Message-ID: <BAY110-F310F5974B694F9EC9D02688E0D0 at phx.gbl>
Content-Type: text/plain; format=flowed
>From: "Moore, Jonathan (J)" <JMoore2 at dow.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: 'Discussion list for GROMACS users' <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] spurious dihedral warnings
>Date: Fri, 3 Feb 2006 07:27:12 -0600
>
>
>Berk,
>
>I don't understand this:
>
> > Specifying nucleic_imp_10 twice has no effect,
> > as the the definition ends with a comment, so the
> > second definition will be hidden in the comment of the first.
>
>What do you mean by "...the definition ends with a comment, so the
>second definition will be hidden in the comment of the first"?
>
>Are you saying that something like (an example from my system) " 13
3
>4 7 1 gd_17 gd_17" is not an allowed format for specifying the
A-
>and B-state dihedrals?
With the Gromos force-field there are no problems.
The problem is with Amber (and maybe other force-fields)
which has lines like:
#define nucleic_imp_10 180.00 4.18400 2 ; missing NA
impropers due to defined propers
Moving the comment to the next line would solve the problem.
Berk.
------------------------------
Message: 3
Date: Fri, 3 Feb 2006 07:36:13 -0600
From: "Moore, Jonathan (J)" <JMoore2 at dow.com>
Subject: RE: [gmx-users] spurious dihedral warnings
To: 'Discussion list for GROMACS users' <gmx-users at gromacs.org>
Message-ID:
<ABC7EC2CC650B748BA4B21F316E445007F4D8F at USMDLMDOWX004.dow.com>
Content-Type: text/plain
What I meant to say is that I've used the format to define the A- and
B-state bonded interactions for all atoms that are perturbed in any way,
but not "all" as I wrote below. I didn't specify B-state bonded
parameters for atoms that were unperturbed.
> But I've used that type of format (ending the line with the A-state
parameter set name followed by the B-state parameter set name) to
specify the A- and > B-states for all of the bonded interactions.
Jonathan Moore
------------------------------
Message: 4
Date: Fri, 03 Feb 2006 14:44:14 +0100
From: "Berk Hess" <gmx3 at hotmail.com>
Subject: RE: [gmx-users] spurious dihedral warnings
To: gmx-users at gromacs.org
Message-ID: <BAY110-F369FFF6B9631EFC1878BA58E0D0 at phx.gbl>
Content-Type: text/plain; format=flowed
>From: "Moore, Jonathan (J)" <JMoore2 at dow.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: 'Discussion list for GROMACS users' <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] spurious dihedral warnings
>Date: Fri, 3 Feb 2006 07:36:13 -0600
>
>
>What I meant to say is that I've used the format to define the A- and
>B-state bonded interactions for all atoms that are perturbed in any
>way, but not "all" as I wrote below. I didn't specify B-state bonded
>parameters for atoms that were unperturbed.
I didn't say anything about that.
Doing that is fine.
I you specify both the A and the B-state paramaters grompp will use them
both.
Berk.
------------------------------
Message: 5
Date: Fri, 03 Feb 2006 14:46:15 +0100
From: "Berk Hess" <gmx3 at hotmail.com>
Subject: RE: [gmx-users] spurious dihedral warnings
To: gmx-users at gromacs.org
Message-ID: <BAY110-F22D9A0E6D71C5C9165EC638E0D0 at phx.gbl>
Content-Type: text/plain; format=flowed
>From: "Moore, Jonathan (J)" <JMoore2 at dow.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: 'Discussion list for GROMACS users' <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] spurious dihedral warnings
>Date: Fri, 3 Feb 2006 07:36:13 -0600
>
>
>What I meant to say is that I've used the format to define the A- and
>B-state bonded interactions for all atoms that are perturbed in any
>way, but not "all" as I wrote below. I didn't specify B-state bonded
>parameters for atoms that were unperturbed.
Sorry, I misread your mail.
If all properties of the atoms involved don't change from the A to the B
state
and you specify only the A-state dihedral parameters,
grompp will silently copy the A-state parameters to the B-state.
Berk.
------------------------------
Message: 6
Date: Fri, 3 Feb 2006 08:42:26 -0500
From: "Moore, Jonathan (J)" <JMoore2 at dow.com>
Subject: RE: [gmx-users] spurious dihedral warnings
To: 'Discussion list for GROMACS users' <gmx-users at gromacs.org>
Message-ID:
<ABC7EC2CC650B748BA4B21F316E445007F4D90 at USMDLMDOWX004.dow.com>
Content-Type: text/plain
Berk,
OK, that makes sense and also explains the error I was getting...there
is a comment at the end of the gd_17 definition in the ffG45a4bon.itp
file that I'm using. Thanks for the explanation.
> The problem is with Amber (and maybe other force-fields) which has
> lines like:
> #define nucleic_imp_10 180.00 4.18400 2 ; missing NA
> impropers due to defined propers
>
> Moving the comment to the next line would solve the problem.
Thanks,
Jonathan
____________________________
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
1702 Building, Office 4E
Midland, MI 48674 USA
Phone: (989) 636-9765
Fax: (989) 636-4019
E Mail: jmoore2 at dow.com
------------------------------
Message: 7
Date: Fri, 3 Feb 2006 09:00:13 -0500
From: Ken Rotondi <ksr at chemistry.umass.edu>
Subject: Re: [gmx-users] Re: converting pdb to gmx successfully -
how?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <28bd02ce960ec8ba394c2df2cc0a7239 at chemistry.umass.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
David,
Unfortunately computers are not crazy, just very inflexible when
executing commands.
It sounds like your hydrogen data base file (ffXXXX.hdb) is not
complete. Are the warnings (without -missing, I really wouldn't use
that unless you are sure that you want to use incomplete molecules) of
the type:
WARNING: atom H62 is missing in residue ADE XXX in the pdb file
If that is the case you need to modify your .hdb file to include the
DNA hydrogens.
Good luck,
Ken
If it doesn't specify
On Feb 2, 2006, at 5:36 PM, David Mathog wrote:
> More progress, sort of.
>
> By changing C7 -> C5M in the DTHY records I finally managed to get
> pdb2gmx -ignh -missing to run to completion.
>
> That said, it does not appear to have worked correctly.
>
> 1. None of the DNA is protonated.
> 2. The protein is protonated
>
> which is craziness, it should be one way or the other.
>
> 3. There were 3 long bond warnings right after "Making bonds...".
> However I cannot figure out why they are there since the corresponding
> atom positions in the gmx output file don't correspond to atoms that
> make bonds in the rtp file.
>
> What do the position numbers in the long bond message refer to?
>
> Thanks,
>
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
> _______________________________________________
> 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
------------------------------
Message: 8
Date: Fri, 3 Feb 2006 08:08:48 -0600
From: "Moore, Jonathan (J)" <JMoore2 at dow.com>
Subject: RE: [gmx-users] spurious dihedral warnings
To: 'Discussion list for GROMACS users' <gmx-users at gromacs.org>
Message-ID:
<ABC7EC2CC650B748BA4B21F316E445007F4D93 at USMDLMDOWX004.dow.com>
Content-Type: text/plain
Berk,
Yes, thanks...that's what I expected. I sent the clarification about
what I meant to say before seeing your reply that provided me with the
understanding I was looking for.
> If all properties of the atoms involved don't change from the A to the
> B
> state and you specify only the A-state dihedral parameters,
> grompp will silently copy the A-state parameters to the B-state.
Jonathan
____________________________
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
1702 Building, Office 4E
Midland, MI 48674 USA
Phone: (989) 636-9765
Fax: (989) 636-4019
E Mail: jmoore2 at dow.com
------------------------------
Message: 9
Date: Fri, 03 Feb 2006 10:24:11 -0500
From: Jon Ellis <jon.ellis at utoronto.ca>
Subject: [gmx-users] pair-distance distribution function
To: gmx-users at gromacs.org
Message-ID: <43E3759B.2050806 at utoronto.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Daniela, thank you for your help.
I tried using g_rdf to calculate the vector lengths of all atom-pair
distances in a protein. I dumped a single frame from my trajectory using
trjconv, then ran
g_rdf -f protein.gro -o rdf -n protein.ndx -bin 0.001
This gave me what appeared to be a pair distance distribution, except
that it seemed to truncate the list at r=4.085 nm, and the P(r) value at
this r was non-zero. I know from other analyses that the protein should
have longer distances than 4 nm. I tried different bin sizes, and
different endq and startq values, but the result remained the same.
Is there something I'm missing, or can I not do pair-distance
distribution functions using g_rdf?
Cheers
Jon
>hi jon,
>
>g_rdf counts the radial distribution function of an index group around
>another index group.
>
>daniela
>
>
>Jon wrote:
>>/ Hello
>/>/
>/>/ Is there a program in Gromacs, or a standalone program, to
calculate the
>/>/ pair-distance distribution function P(r), aka the vector length
>/>/ distribution, for a protein?
>/>/
>/>/ The algorithm is P(r)=Dn(r)/nDr, where Dn(r) is the number of atom
pairs
>/>/ whose separation is between r-Dr/2 and r+Dr/2, and n is the total
number
>/>/ of atoms in the system.
>/>/
>/>/ I would appreciate any help.
>/>/
>/>/ Cheers
>/>/ Jon
>/>/ /
>
------------------------------
Message: 10
Date: Fri, 3 Feb 2006 11:16:51 -0500 (EST)
From: "YOLANDA SMALL" <yas102 at psu.edu>
Subject: Re: [gmx-users] Multiple chains, cofactors and ligands--ffgmx
unreliable?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <200602031616.LAA12494 at webmail2.cac.psu.edu>
Content-Type: text/plain
Thanks to Daniela, Yang and Tsjerk for a reply...your advice was
helpful.
Tsjerk, you were exactly correct, I did have multiple listings of the
directive
in my ligand and ions .itp files. But now you raise a point that
concerns
me....why is ffgmx not reliable?
I always check the energies and structures for unusual behavior
throughout the
simulations. How does this unreliability manifest itself? Which is the
most
highly recommended forcefield option in the gmx package?
Many thanks,
YAS
On Fri, 03 Feb 2006 09:37:27 +0100, Tsjerk Wassenaar wrote:
> Hi Yolanda,
>
> And then for the solution to your problem... The error in grompp
indicates
> that you call the force field defaults directive (ffgmx.itp) several
times.
> Probably, the prodrg server has added a statement similar to #include
"
> ffgmx.itp" to the itp files for the ligand and the cofactor. You
should
> delete those statements, which will probably solve the error.
>
> By the way, the ffgmx force field isn't particularly reliable.
>
> Cheers,
>
> Tsjerk
>
> On 2/3/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
> >
> > Run GMXRC.xxx according to the shell you are using before running
gromacs
> > programs.
> >
> > Yang Ye
> >
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org]
> > On Behalf Of YOLANDA SMALL
> > Sent: Friday, February 03, 2006 1:12 AM
> > To: Discussion list for GROMACS users
> > Subject: [gmx-users] Multiple chains, cofactors and ligands
> >
> > Dear users,
> >
> > I am having a problem with grompp which gives me the following
message:
> > Fatal error: Invalid order for directive defaults, file
> > ""/gromacs-3.2.1/share/top/ffgmx.itp"", line 4
> >
> > My simulation details:
> > An enzyme with 2 chains, 2 cofactors and 2 ligands in a 115 Angstrom
box
> > of
> > SPC
> > waters. The total system size is 150872 atoms. Each chain has a
separate
> > .itp
> > file created with pdb2gmx. Each cofactor and ligand has an .itp file
> > created
> > with PRODRG. The files are joined in the following topology file:
> >
> > ; Include forcefield parameters
> > #include "ffgmx.itp"
> >
> > ; Include chain topologies
> > #include "chain_A.itp"
> > #include "chain_B.itp"
> > #include "cofactor_A.itp"
> > #include "cofactor_B.itp"
> > #include "ligand_A.itp"
> > #include "ligand_B.itp"
> > #include "Na.itp"
> >
> > ; Include water topology
> > #include "spc.itp"
> >
> > ; Include generic topology for ions
> > #include "ions.itp"
> >
> > [ system ]
> > ; Name
> > 2 COMPLEXED WITH (Ligand)
> >
> > [ molecules ]
> > ; Compound #mols
> > Protein_A 1
> > Protein_B 1
> > SOL 346
> > COF_A 1
> > COF_B 1
> > LIG_A 1
> > LIG_B 1
> > NA 1
> > SOL 47872
> >
> > The problem:
> > I only get this message when the topology of the cofactor and ligand
are
> > included. When I run the simulation on the protein chains only
without
> > the
> > ligand and cofactor, it runs just fine. I double-checked the
topology of
> > the
> > ligand and cofactor and I don't see any errors. Do I need to change
the
> > defaults in the following ffgmx.itp file to get this to work????
(The
> > error
> > message points to line 4 of this file) If so, what should I change
the
> > defaults to?
> >
> > #define _FF_GROMACS
> > #define _FF_GROMACS1
> >
> > [ defaults ]
> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> > 1 1 no 1.0 1.0
> >
> > #include "ffgmxnb.itp"
> > #include "ffgmxbon.itp"
> >
> > Thanks in advance for your help,
> > YAS
> > _______________________________________________
> > 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
> >
> >
> > _______________________________________________
> > 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
> >
>
>
>
> --
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
> Hi Yolanda,
>
> And then for the solution to your problem... The error in grompp
> indicates that you call the force field defaults directive (ffgmx.itp)
> several times. Probably, the prodrg server has added a statement
> similar to #include "ffgmx.itp" to the itp files for the ligand and
the
> cofactor. You should delete those statements, which will probably
solve
> the error.
>
> By the way, the ffgmx force field isn't particularly reliable.
>
> Cheers,
>
> TsjerkOn 2/3/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
> Run GMXRC.xxx according to the shell you are using before running
gromacsprograms.Yang Ye-----Original Message-----From:
gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org]On Behalf Of YOLANDA SMALLSent:
Friday,
February 03, 2006 1:12 AMTo: Discussion list for GROMACS usersSubject:
[gmx-users] Multiple chains, cofactors and ligands
> Dear users,I am having a problem with grompp which gives me the
following
message:Fatal error: Invalid order for directive defaults,
file""/gromacs-3.2.1/share/top/ffgmx.itp"", line 4
> My simulation details:An enzyme with 2 chains, 2 cofactors and 2
ligands in a
115 Angstrom box ofSPCwaters. The total system size is 150872 atoms.
Each
chain has a separate.itpfile created with pdb2gmx. Each cofactor and
ligand has
an .itp file created
> with PRODRG. The files are joined in the following topology file:;
Include
forcefield parameters#include "ffgmx.itp"; Include chain
topologies#include
"chain_A.itp"#include "chain_B.itp"
> #include "cofactor_A.itp"#include "cofactor_B.itp"#include
"ligand_A.itp"#include "ligand_B.itp"#include "Na.itp"; Include water
topology#include "
> spc.itp"; Include generic topology for ions#include "ions.itp"[ system
];
Name2 COMPLEXED WITH (Ligand)[ molecules ]; Compound
#molsProtein_A
1
> Protein_B 1SOL 346COF_A 1COF_B
1LIG_A 1LIG_B 1NA 1SOL
47872The problem:I only get this message when the topology of the
cofactor
and ligand are
> included. When I run the simulation on the protein chains only
without
theligand and cofactor, it runs just fine. I double-checked the
topology
oftheligand and cofactor and I don't see any errors. Do I need to change
the
> defaults in the following ffgmx.itp file to get this to work???? (The
errormessage points to line 4 of this file) If so, what should I change
thedefaults to?#define _FF_GROMACS#define _FF_GROMACS1
> [ defaults ];
> nbfunc comb-rule
> gen-pairs fudgeLJ fudgeQQ 1
> 1
> no 1.0
> 1.0#include "ffgmxnb.itp"#include "ffgmxbon.itp"Thanks in advance for
your
help,YAS_______________________________________________gmx-users mailing
list
>
gmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPl
ease
don't post (un)subscribe requests to the list. Use thewww 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.orghttp://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use thewww
interface or
send it to gmx-users-request at gromacs.org.Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar,
M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute
(GBB)Dept. of
Biophysical Chemistry
> University of GroningenNijenborgh 49747AG Groningen, The
Netherlands+31 50 363
4336
> _______________________________________________
> 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.
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