[gmx-users] Simulation Crash...Reg

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 3 14:56:02 CEST 2011

Kishore wrote:
> Dear All,
> I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in 
> simple spc water in a dodecahedron box. I could easily walk through till 
> the NVT equilibration step after which every thing seems so right(after 
> 50000 steps with time step of 2fs using V-rescale thermostat the system 
> equilibrates to T=300K). But the NPT equilibration ( for 50000 steps 
> with time step of 2fs using Parrinello-rahman barostat) is crashing( 
> after 10000 steps) with too many LINCS warnings. Looking at the log file 
> I understand there are very high fluctuations in the temperatures after 
> a few steps from the start of the simulation. What can be the possible 
> reason for this kind of a behavior and what can be done to fix it?

Please post your .mdp file from the NPT equilibration.


> -- 


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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