[gmx-users] equilibration error

[Dallas Warren]

What is actually different in the mdp file between each of these
steps?  What about the cluster run on, or mdrun command used for each
of the steps?

How have you determined that each step in the process is long enough
i.e. what are you looking at to see if things have stabilised
sufficiently?

There is a recent discussion about this on the emailing list, but no
real solution was suggested …

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-June/120979.html

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On Thu, 11 Oct 2018 at 16:16, Stephani Macalino
<stephanimacalino at gmail.com> wrote:
>
> Hello,
> I am planing to do MD of a membrane protein bound to a ligand.
> I already have my files and I am doing my 6 step equilibration with
> reducing force constants.
> However, in the 5th step, it gave an error saying that the previous system
> (4th step) was not well equilibrated:
>
> Fatal error:
> 5 particles communicated to PME rank 0 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>
> I'm a newbie to this and don't completely understand the error.
> Since it says the previous system is not well equilibrated, should I
> increase the steps for equilibration?
>
> I am wary to change the force constant values since I did 100ns MD for apo
> WT and mutant structures for the same protein that I am now doing with the
> ligand.
>
> Hope you can suggest some ways to solve this problem. Thanks in advance!
>
> Regards,
> Stephani
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