[gmx-users] Required

ms devicerandom at gmail.com
Tue Aug 3 19:07:29 CEST 2010

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.

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


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