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).
cheers,
m.
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