[gmx-users] Re: Questions WHAM

lloyd riggs lloyd.riggs at gmx.ch
Wed Apr 18 08:56:41 CEST 2012

-------- Original-Nachricht --------
> Datum: Wed, 18 Apr 2012 03:13:09 +1000
> Von: Mark Abraham <Mark.Abraham at anu.edu.au>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Re: Questions

> 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.

I had woundered as I always have to throw out the first 2 picosecounds about the init velocity.  I did equilibrate each first untill there was no change with bereendsen and nose-hoover, so from my mistake thats what I have had to do for the data.  Is there any other critiques, as I COULD USE THEM.

Aside, I have a wierd problem where WHAM reads 1 file then not the next.  Then, I use as mentioned a text editor and it reads 2 different files for input, but not the others that had worked.  I cant figure out why it reads one say with tabs spacing, and the next with 2 bar spaces, and the next with only bar space 1?  In the end I can find one or two differences in emacs or editors, but then the final .xvg files all have different spacing as above and then I cant read all of them in to get the proper weighted scores?



> Mark
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