[gmx-users] Error while performing a REMD simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 10 03:44:11 CEST 2011

Luis Miguel Medina Solano wrote:
> Hello,
> I used a -maxwarn 5, but I only obtain 1 warning,  (about obsolete entries that the .mdp file has).
> I used a solute-box distance of 0.34 in order to reduce the simulation box. I used before a solute-box distance of 1 nm and the problem persist. 

Don't reduce your box for convenience.  You're certain to break the model 
physics of your system, given the settings below, rendering probably any 
simulation that might run invalid.


Maybe this is unrelated to the underlying problem, but hopefully it helps in the 
long run.  Nothing worse than a reviewer saying, "Nice project, but 100% of the 
data are junk."

> my .mdp file is the next:
> title =
> cpp = /lib/cpp
> include =
> define =
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.004

In the absence of virtual sites, a 4-fs timestep is not likely to be stable, 
even with LINCS, and certainly not at high temperature.


> fourierspacing = 0.24

This is double the "normal" value, meaning your PME calculations will be less 
accurate than they probably should be.



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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