[gmx-users] Required

Mark Abraham mark.abraham at anu.edu.au
Wed Aug 4 04:01:11 CEST 2010

----- Original Message -----
From: ms <devicerandom at gmail.com>
Date: Wednesday, August 4, 2010 3:07
Subject: Re: [gmx-users] Required
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> On 03/08/10 17:32, Jafar Azamat wrote:
> >When the program runs by
> >"pdb2gmx" Option, the file X.top doesnot any information about force
> >constant X.pdb file and I enter informations handling in this file.
> Your question does not make any sense, can you try to rephrase it?
> >In addition,How can I make in Gromacsa regular cluster 
> structure of a
> >molecule ?
> >
> >
> >Whether by
> >g_cluster option? If this option could be to do this,
> >please help me to make a cluster structure from a adamantine 
> molecule in a
> >box
> >in sizes: x=10, y=10, z=10 an put 125 number from adamantane 
> mulecule( in
> >each
> >direction 5 molecule means 5*5*5and
> >distance every molecule of each other will be 1 nm) in this box.
> As far as I know, you can either try to use genbox with a 
> solvent different from water (i.e. your adamantane), or write a 
> script using editconf. You can find documentation online for both.

genconf is a better match for what the OP is trying to do.


> g_cluster does a completely different thing (it clusters 
> together similar structures from a trajectory).
> cheers,
> m.
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