[gmx-users] MPIRUN error while running position restrained MD

Ragothaman Yennamalli ymr79in at yahoo.co.in
Fri Jan 26 13:09:49 CET 2007

Hi Tsjerk,
I completely agree with you. I am treating symptoms
rather than the problem. I read your previous comment
on the LINCS warning to Shangwa Han. I dont have any
unnatural amino acids in the protein and EM steps
converged to machine precision. I am attaching the
potential energy .xvg file after EM. I will look into
those atoms and see if I can resolve this problem.
--- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ragothaman,
> You would do good to try and find out what caused
> the error. You may
> be treating symptoms rather than problems now, and
> simply covering up
> some more severe wrong in your system. Maybe try to
> start a simulation
> after some while, using the same parameters as
> before. This might
> allow your system to relax sufficiently.
> Cheers,
> Tsjerk

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