Dear Chris,
Thank you for your message. I uploaded everything to the redmine. I will
let you know how the simulation with generated velocities went.
I asked the authors about any exemplary input that worked with tip5p and
oplsaa, but I did not get anything...
Best,
Grzegorz
On 2013-10-04 17:20, Christopher Neale wrote:
Dear Grzegorz:
From a quick look at your .mdp, I also suggest that you go back to
your system including the peptide that you had managed to finish EM
with modified flexible tip5p but then crashed with the standard rigid
tip5p during MD and try the MD again using gen-vel = yes
if you're still seeing problems, why not upload your water-only system
and your with-small-peptide test system to redmine. It's meant as a
place to start a discussion, share files, and help us not to foget
about a problem that may exist, so I am not sure why you hesitate.
Also, you said that the authors of that other OPLS-Tip5p paper had no
problems. You might ask them for .gro .mdp and .top files so that you
can see exactly what they did and how it differs from what you are
doing.
Chris.
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