[gmx-users] Packmol starting .pdb and proper equilibration

[Dr. Vitaly Chaban]

On Thu, Oct 30, 2014 at 12:30 PM, Ioanna Styliari
<paxids at nottingham.ac.uk> wrote:
> Thank you both for your prompt replies.
>
> Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or is it just by a trial-error approach?


If your number of cores gives an error, try another number of cores.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




> Justin: Although 1fs works, I was aiming for 2fs steps in the MD but it crashes. I was thinking to run the first 2ns with 1fs and then try to continue it with 2fs onwards to see what happens, but it crashed at 700ps of my MD. I am using GROMOS96 53a6.
> My equilibration "concern" regards the system: should it be equilibrated as a whole or should I equilibrate one part of it at a time, keeping the others fixed? (which was a suggestion I had but I am unsure how to do it)
>
> Again, thank you
>
> Ioanna
>
> _ _ _ _ _ _ _ _ _ _ _ _ _
> Miss Ioanna Danai Styliari
> PhD Candidate
> Centre for Doctoral Training in
> Targeted Therapeutics and Formulation Sciences
> School of Pharmacy
> University of Nottingham
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