[gmx-users] Re: Questions

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 17 19:13:09 CEST 2012

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.


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