[gmx-users] Crashes during protein-ligand simulation

James Starlight jmsstarlight at gmail.com
Sat Jul 7 17:08:06 CEST 2012


It seems that problem was in the big charge groups in the ligand.itp
file. In particularly I've devided largest group into several smaller
and there haven't any crashes been occured yet.

With my last system with the the default COM group I've obtained crash
on the 25ns with the error about ligand's big cngr exactly.

By the way could you tell me how I could analyse stability of the
protein-ligand system as well as contributions of the individual
non-covalent contacts with the .EDR file?

In my mdp file I've defined energygrps= Protein Ligand   as the
separate energy terms.

During analysis of the edr file I've observed some options like
LJ-SR:Protein-ADN     ( this value was slightly negative (-100) during my trr )
Coul-14:Protein-ADN ( this value was constantly zero )
Coul-SR:ADN-rest ( this value was equal to the LJ-SR:Protein-ADN  -100 )

What conclusions in general could I do based on that values ? How I
could measure stability of the ligand ( beside dirrect RMSD
measurement) from such energy terms?


2012/7/6, Justin A. Lemkul <jalemkul at vt.edu>:
> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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