[gmx-users] mdrun blowing up with PME node error in 1 window of umbrella sampling

[Agnivo Gosai]

Dear All

I did not run any further equilibration / minimization on the particular
windows. I tested two cases :

1. Used lesser number of nodes for mdrun - the problem got solved.
2. Used same number of nodes as before but put -npme = 0 , problem got
solved.

I do not know the reason , but my results seem to match published
literature. So I am happy.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

On Wed, Mar 4, 2015 at 2:38 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Dear Users
>
> I am using umbrella sampling to calculate free energy of binding between
> two biomolecules , in certain different environments.
> This is my standard work flow for all the cases.
>
> 1. Topology preparation, solvation etc.
> 2. Energy Minimization using steepest descent and 50,000 steps.
> 3. 1 ns position restrained NVT equilibration.
> 4. 1 ns position restrained NPT equilibration.
> 5. 500 ps SMD run of the equilibrated structure keeping one molecule fixed
> and pulling the other.
> 6. Extracting around 40 - 50 windows from the SMD trajectory.
> 7. 100 ps NPT equilibration and 10 ns umbrella sampling for each window.
> 8. Generate PMF.
>
> For 3 cases I did the above and had no issues. However , recently for
> "only one" window each in 2 cases my umbrella sampling runs crashed with
> the following message :
>
> 2 particles communicated to PME node 10 are more than 2/3 times the cut
> off of the domain decomposition cell of their charge groups in dimension x.
>
> So , I read previous forum mails and the manual and I guess I can do the
> following :-
>
> 1. Another energy minimization and a longer NPT equilibration of the
> particular window before doing the umbrella sampling run. But, is this
> advisable ?
>
> Kindly suggest.
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
>