[gmx-users] Crashes during protein-ligand simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 6 21:59:25 CEST 2012

On 7/6/12 3:56 PM, James Starlight wrote:
> Justin,
> I've experimented with 2 dirrerent COM groups
> comm-grps       = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups
> comm-grps       = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups
> but the crashes were in both cases after 12- 15ns of simulation
> this time I've changed to the
> comm-grps       = System
> and there have not been any crashes yet (to this time I've already
> calculated addition 20ns after privious crhased simulation using
> checkpoint file for the last simulation ). But it's posible that it
> was lucky coincidence :)
> Could you tell me how I could devide largest group in the above
> axample into several smaller sub-groups ? Should I do that separation
> randomly or there are most correct way for that ? (e.g within third
> cgnr separate all nitrogens and oxygens with corresponded hydrogens in
> the separate cgrp's from carbons)

Look at existing examples in the force field .rtp file.  In general, a charge 
group consists of a functional group (amine, carboxylate, etc) or small CHn 
units.  Generally there are 2-4 atoms per charge group.  There is some 
discussion on these topics in the manual.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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