[gmx-users] Required

[Jafar Azamat]

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Dear users GROMACS





I have a problem using GROMACS





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.





Where the problem comes from??


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.





Thanks alot

Jafar Azamat 

Molecular Simulations Lab.
Faculty of 
Basic Sciences
Azerbaijan University of Tarbiat Moallem.
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