-1
hi all,
i am interested in doing full ab initio molecular dynamics using
gromacs, coupled to either GAMESS or Gaussian. i am not interested in
using any single or multilayer QM/MM scheme. it doesn't appear that
gromacs supports a full QM system. does anyone know the origin of this
limitation? or, perhaps any easy ways/tricks around it?
traditionally i would do this with other software, though i am
interested specifically in doing parallel tempering work at the ab
initio level, and gromacs is a good fit.
secondly, information on coupling gromacs to GAMESS or Gaussian is
sparse. any links to known documentation would be welcome!
thanks in advance,
anthony
--
Anthony B. Costa
Purdue University
Department of Chemistry
560 Oval Drive, #365
West Lafayette, IN 47907
------------------------------
Message: 2
Date: Sat, 13 Jun 2009 10:39:44 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Question about applying a restriction on the
movement of a molecule in z direction....
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a32f550.8070...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Alberto Sergio Garay wrote:
Hi all
I need to avoid that a solute molecule cross to the other side of my
lipid bilayer.and I have thought in several alternatives, which I'm
not
sure whether they are posible in gromacs so I decided to ask for
suggestions.
In a periodic system with one symmetric bilayer and one block of
solvent, there seems to be little value in such a restriction.
Could anyone give any possible alternative to restrict the movement
of
my molecule in the z direction only when it reaches a certain z
distance
from, for example the center of the bilayer ?
Pick a few key atoms in the bilayer, decide how far you want to let it
roam from the bilayer, do your Pythagoras and work out the maximum
displacement from a key atom that is consistent with your maximum
bilayer displacement, invoke a fudge factor, and use distance
restraints
on those key atoms.
Mark
------------------------------
Message: 3
Date: Sat, 13 Jun 2009 10:44:43 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] ab initio parallel tempering
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a32f67b.6070...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Anthony Costa wrote:
hi all,
i am interested in doing full ab initio molecular dynamics using
gromacs, coupled to either GAMESS or Gaussian. i am not interested in
using any single or multilayer QM/MM scheme. it doesn't appear that
gromacs supports a full QM system. does anyone know the origin of
this
limitation? or, perhaps any easy ways/tricks around it?
traditionally i would do this with other software, though i am
interested specifically in doing parallel tempering work at the ab
initio level, and gromacs is a good fit.
secondly, information on coupling gromacs to GAMESS or Gaussian is
sparse. any links to known documentation would be welcome!
I can only suggest starting here http://oldwiki.gromacs.org/index.php/QMMM
Mark
------------------------------
Message: 4
Date: Sat, 13 Jun 2009 12:00:11 +0530 (IST)
From: "Ms. Aswathy S" <aswat...@amritapuri.amrita.edu>
Subject: [gmx-users] Error in hdb file ffG43a1.hdb
To: gmx-users <gmx-users@gromacs.org>
Message-ID:
<29124151.2252521244874611261.javamail.r...@durga.amrita.ac.in>
Content-Type: text/plain; charset=utf-8
Hi,
I have upgraded my gromacs version to 3.3.3 from 3.2.1. When I tried
to run the pdb2gmx i got the follo: error. From the previous post I
guess that i should edit this ffG43a1.hdb. but my input is a protein
file so ..so is this necessary or any other way to rectify this
problem???
-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 3.3.3
Source code file: h_db.c, line: 95
Fatal error:
Error in hdb file ffG43a1.hdb:
Wrong number of control atoms (2 iso 3) on line:
1 1 N -C CA
Thanks in advance,
Aswathy
Dept. Biotechnology
Ext. 3108
------------------------------
Message: 5
Date: Sat, 13 Jun 2009 14:39:33 +0530 (IST)
From: "Ms. Aswathy S" <aswat...@amritapuri.amrita.edu>
Subject: Re: [gmx-users] Error in hdb file ffG43a1.hdb
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<9429901.2257241244884173226.javamail.r...@durga.amrita.ac.in>
Content-Type: text/plain; charset=utf-8
Please ignore this post. I rectified the problem by using the GMXLIB
export.
Thank you very much for all the support
Aswathy
Dept. Biotechnology
Ext. 3108
----- Original Message -----
From: "Ms. Aswathy S" <aswat...@amritapuri.amrita.edu>
To: "gmx-users" <gmx-users@gromacs.org>
Sent: Saturday, June 13, 2009 12:00:11 PM GMT +05:30 Chennai,
Kolkata, Mumbai, New Delhi
Subject: [gmx-users] Error in hdb file ffG43a1.hdb
Hi,
I have upgraded my gromacs version to 3.3.3 from 3.2.1. When I tried
to run the pdb2gmx i got the follo: error. From the previous post I
guess that i should edit this ffG43a1.hdb. but my input is a protein
file so ..so is this necessary or any other way to rectify this
problem???
-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 3.3.3
Source code file: h_db.c, line: 95
Fatal error:
Error in hdb file ffG43a1.hdb:
Wrong number of control atoms (2 iso 3) on line:
1 1 N -C CA
Thanks in advance,
Aswathy
Dept. Biotechnology
Ext. 3108
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