On 18/04/2012 12:10 AM, lloyd riggs wrote:
Included below (although Im terrified youll invalidate massive parallel work
with a single comment) is the .mdp file I used for 10 of the runs, basically it
was the only way I could get it to run. The time step is small because of the
small molecule involved, however I painstakingly looked up all parameters ten
times. Basically its only violation was with links, which seems to think
S-O---H isnt supposed to roatate so much, but the molecules degrees of freedom
(1/2 can rotate 360 from the other along a central axis) etc...
PR p-coupling is poor for stability during equilibration (since gen_vel
= yes), and it's always poor to start your production run (i.e. your
pulling) without prior equilibration. Equilibrate with berendsen, then
switch to PR for a bit and only then worry about pulling.
Mark
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