[gmx-users] RE: Including quadrupole-charge interaction in GROMACS (WU Yanbin)
Ran Friedman
ran.friedman at lnu.se
Thu Jun 16 09:16:21 CEST 2011
Hi,
Not implemented in Gromacs AFAIK.
Note that (1) even the definition of a quadruple isn't straightforwards and depends on the orientation and (2) common FF parameters were not developed with higher ordered multiple taken into account.
@Article{Plattner2009,
author = "Plattner, N and Meuwly, M",
title = {Higher order multipole moments for molecular dynamics simulations},
journal = "J Mol Model",
year = "2009",
volume = "15",
pages = "687-694"
}
Ran
------------------------------------------------
Ran Friedman
Biträdande Lektor (Assistant Professor)
Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden
Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.friedman at lnu.se
http://lnu.se/ccbg
------------------------------------------------
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Today's Topics:
1. Re: CHARMM forcefield (Justin A. Lemkul)
2. Re: local pressure calcuation for Gromacs-4.5 (Justin A. Lemkul)
3. Including quadrupole-charge interaction in GROMACS (WU Yanbin)
4. g_density (chris.neale at utoronto.ca)
5. Position restraints (Tom Dupree)
6. Re: Position restraints (Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Wed, 15 Jun 2011 17:11:08 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] CHARMM forcefield
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DF91FEC.8080206 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
simon sham wrote:
> Hi,
> I have two questions about using the charmm force field.
> 1. Do we still need to use the two perl scripts, convert_charmm_
> to_gromacs.pl and fix_top_for_charmm.pl?
No.
> 2. I got the following note when I tried to do energy minim. with grompp:
>
> NOTE 1 [file topol.top]:
> The largest charge group contains 12 atoms.
> Since atoms only see each other when the centers of geometry of the charge
> groups they belong to are within the cut-off distance, too large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should consist of a few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>
> Is this a problem?
>
Yes. CHARMM topologies should not use charge groups. You should invoke pdb2gmx
with the -nochargegrp option to create a proper topology.
-Justin
> Thanks for your insight!
>
> Simon
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 2
Date: Wed, 15 Jun 2011 17:17:53 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] local pressure calcuation for Gromacs-4.5
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DF92181.2090805 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Amit Choubey wrote:
> Dear all,
>
> Could anyone direct me to the manual for local pressure calculation or a
> place where everything is mentioned about it ? I have been only able to
> collect bits and pieces from the mailing lists.
>
That's probably all there is to be found. There's no manual linked from the git
web interface or the ftp site.
-Justin
> Thank you
> Amit
>
> On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 15/06/2011 9:09 PM, Jianguo Li wrote:
>> Dear all,
>>
>> I have made a test calculation of local pressure using version 4.5
>> for my membrane simulation using CHARMM FF. When rerun the
>> simulation, mdrun gives the localpressure data. Howeve, instead of
>> giving an anveraged data of the local pressure, mdrun gives a
>> separate file for each frame, so I got many files:
>> localpressure.dat0, localpressure.dat1, localpressure.dat2,
>> localpressure.dat3 ......
>> Then I need to calculate the pressure tensor for each frame and
>> make average. but these localpressure.dat files are very big (each
>> file is about 30 Mb), occupying large space of the hard disk. Can
>> anyone give some suggestions on how to fix this? Thank you very much!
>
> I would expect that the output frequency is configurable, but can
> only suggest you consult what documentation exists for this version.
> Your main alternatives are
>
> * to compress the files with (say) bzip2 or (less effective) gzip
> and construct a script to uncompress them singly and analyse them
> "on the fly" (AMBER users do a bit of this kind of thing, Google around)
> * to discard ones that are too frequent. However, judging from the
> numbers below, every 100ps is probably OK.
>
> Mark
>
>
>> The command is:
>> mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o
>> box_md5_rerun.trr -g md5_rerun.log -localpgrid 0.1
>> And the output message is:
>> ........
>> Dumping local pressure based on 1 frames to localpressure.dat0...
>> Reading frame 2 time 119400.000
>>
>> Dumping local pressure based on 1 frames to localpressure.dat1...
>> Reading frame 3 time 119500.000
>>
>> Dumping local pressure based on 1 frames to localpressure.dat2...
>> Reading frame 4 time 119600.000
>>
>> Dumping local pressure based on 1 frames to localpressure.dat3...
>> Reading frame 5 time 119700.000
>>
>> Dumping local pressure based on 1 frames to localpressure.dat4...
>> Reading frame 6 time 119800.000
>> .......
>>
>> Cheers,
>> Jianguo
>>
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Justin A. Lemkul <jalemkul at vt.edu> <mailto:jalemkul at vt.edu>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org>
>> *Sent:* Friday, 10 June 2011 07:10:35
>> *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5
>>
>>
>>
>> Amit Choubey wrote:
>> > Thanks Justin, I tried to install the recent git version but the
>> configure file is missing. How should I install this version ?
>> >
>>
>> Run the bootstrap script. It generates the configure script.
>>
>> -Justin
>>
>> >
>> > On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>>> wrote:
>> >
>> >
>> >
>> > Amit Choubey wrote:
>> >
>> > Dear all,
>> >
>> > I saw an unanswered post at
>> >
>> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
>> >
>> > It is about calculating local pressure in v 4.5 when using
>> > CHARMM FF. Could someone give me some pointers about this?
>> >
>> >
>> > I don't know what the development status of version 4.5 is,
>> but you
>> > can access it at:
>> >
>> >
>> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>> >
>> > It hasn't been merged with release-4-5-patches in some time,
>> so many
>> > resolved bugs won't be fixed.
>> >
>> > -Justin
>> >
>> > -- ========================================
>> >
>> > Justin A. Lemkul
>> > Ph.D. Candidate
>> > ICTAS Doctoral Scholar
>> > MILES-IGERT Trainee
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>> 231-9080 <tel:%28540%29%20231-9080>
>> > <tel:%28540%29%20231-9080>
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting!
>> > Please don't post (un)subscribe requests to the list. Use the www
>> > interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>> > <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> >
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> <tel:%28540%29%20231-9080>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> Please don't post (un)subscribe requests to the list. Use the
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> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Wed, 15 Jun 2011 16:45:04 -0500
From: WU Yanbin <wuyb02 at gmail.com>
Subject: [gmx-users] Including quadrupole-charge interaction in
GROMACS
To: gmx-users at gromacs.org
Message-ID: <BANLkTin--B9Rr0dX+yRXokExRww0Cc8S6Q at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear GMXers,
Is there a way in GROMACS to include quadrupole-charge interaction?
Or is there a standard to way to mimic quadrupole moment using partial
charge?
Thank you.
Best,
Yanbin
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Message: 4
Date: Wed, 15 Jun 2011 22:43:28 -0400
From: chris.neale at utoronto.ca
Subject: [gmx-users] g_density
To: gmx-users at gromacs.org
Message-ID: <20110615224328.22l1pidrko40k0w8 at webmail.utoronto.ca>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Dear Matthias:
Did you run trjconv -center -pbc mol at some point before running
g_density? With pbc, there are multiple ways to put the center of a
system at the center of the box. This can lead to having the water
slab in the center of the unit cell and the bilayer on the top and
bottom z.
Without seeing the commands and the output, it is hard to say any more.
Chris.
-- original message --
Hi,
I have aligned a trajectory to a reference structure and have now run
g_density on both the original and the aligned trajectory in order to
find the bilayer headgroup position and the bilayer thickness.
g_density works fine with the original trajectory but there seems to
be a bug when running it to the aligned structure (Alignment done
using trjconv -fit progressive).
The density is calculated along the z direction (-d Z). The density
for positive z is calculated correctly, but the density for negative z
is shifted about 15nm to to the top end of the box size, as if the
density distribution along the z-axis were discontinuous.
Other then stitching the data together by hands, are there any obvious
better solutions?
Thanks,
Matthias
------------------------------
Message: 5
Date: Thu, 16 Jun 2011 11:54:50 +1000
From: Tom Dupree <t.dupree at unsw.edu.au>
Subject: [gmx-users] Position restraints
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<1FFC0F40B2B7CF44A5FBC162C2469DD03A81128979 at INFPWEC003.ad.unsw.edu.au>
Content-Type: text/plain; charset="us-ascii"
Greetings all,
I have run into a little bit of a problem.
I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr.
However when I get to the simulation step I can't get grompp to work.
I ran
genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr
As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range.
Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files? Furthermore can I actually do a constraint matrix over multiple molecules?
Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions)
All the best,
Tom
Fatal error:
[ file subset.itp, line 145 ]:
Atom index (5222) in constraints out of bounds (1-5149).
This probably means that you have inserted topology section "constraints"
in a part belonging to a different molecule than you intended to.
In that case move the "constraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
My topology file
;
; File 'topol.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Tue May 31 11:44:23 2011
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.3
;
; Command line was:
; pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif
#include "topol_Protein_chain_A2.itp"
#ifdef POSRES
#include "posre_Protein_chain_A2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B2.itp"
#ifdef POSRES
#include "posre_Protein_chain_B2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B3.itp"
#ifdef POSRES
#include "posre_Protein_chain_B3.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B4.itp"
#ifdef POSRES
#include "posre_Protein_chain_B4.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
___________________________________________________________________
------------------------------
Message: 6
Date: Thu, 16 Jun 2011 17:00:26 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Position restraints
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DF9AA0A.1030303 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 16/06/2011 11:54 AM, Tom Dupree wrote:
> Greetings all,
>
> I have run into a little bit of a problem.
>
> I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr.
> However when I get to the simulation step I can't get grompp to work.
As genrestr -h will warn you, its output is only useful for the first
molecule.
GROMACS position restraints will not give you any implementation-related
speed-up, only one from reducing the sampling volume. Freeze groups will
give you some speed-up (at the cost of making your results depend on
your frozen configuration), but you will usually not be able to use both
constraints and NPT as well.
> I ran
>
> genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr
Such a constraint or distance restraint matrix can only work
intra-[moleculetype], and so is futile for your case.
> As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range.
Yep
> Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files?
Sure, use editconf with some appropriate index groups (and maybe -resnr)
to create subset structures that will then produce output from genrestr
suitable for use with grompp.
> Furthermore can I actually do a constraint matrix over multiple molecules?
Not without uniting the [moleculetypes]. Do note that the various kinds
of restraints, constraints and freeze groups are all distinct
approaches, and attempting to mix them can be asking for trouble. Be
sure to use the right terminology when asking for help :-)
Mark
> Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions)
>
>
> All the best,
>
> Tom
>
>
> Fatal error:
> [ file subset.itp, line 145 ]:
> Atom index (5222) in constraints out of bounds (1-5149).
> This probably means that you have inserted topology section "constraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "constraints" section to the right molecule.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> My topology file
> ;
> ; File 'topol.top' was generated
> ; By user: onbekend (0)
> ; On host: onbekend
> ; At date: Tue May 31 11:44:23 2011
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.5.3
> ;
> ; Command line was:
> ; pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v
> ;
> ; Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_A.itp"
> #endif
> #include "topol_Protein_chain_A2.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_A2.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B2.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B2.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B3.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B3.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B4.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B4.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> ___________________________________________________________________
>
>
------------------------------
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