[gmx-users] Error while performing a REMD simulation

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

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:
> 
> ; VARIOUS PREPROCESSING OPTIONS
> title =
> cpp = /lib/cpp
> include =
> define =
> 
> ; RUN CONTROL PARAMETERS
> 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.

<snip>

> fourierspacing = 0.24

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

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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