[gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 11 12:49:09 CET 2011

Mark Abraham wrote:
> On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote:
>> Sorry, in previous mail i did not write md protocol in details what i
>> followed for simulation. after energy minimization steps i did PR for 200
>> ps and then run the production MD. Even i did vacuum energy minimization
>> before adding solvent for all systems. I used steep followed by cg for
>> prot-solvent energy minimization which reached up to minimum applied 
>> force
>> 100 KJ/mol/nm.
> Your results suggest you did not equilibrate well enough. See the link I 
> gave last time.

Either that, or incorrect ligand parameters or .mdp settings are being applied, 
breaking the force field model and causing the crash.  Without seeing the .mdp 
and relevant topology(ies), it's impossible to say.



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


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