[gmx-users] Re: Questions WHAM

[Justin A. Lemkul]

lloyd riggs wrote:
> -------- 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.
> 

I would say that if you are regenerating velocities, you need to get rid of a 
lot more than 2 ps, especially with Nose-Hoover.  Even Berendsen will likely not 
re-converge that quickly.

> 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?
> 

There may be some fixed-format requirement for reading the input.  The 
difference between space and tab is irrelevant, but the position of the columns 
may be significant.  Check the code to be sure.  It would be more useful to see 
concrete examples; right now I'm afraid I don't fully understand what the 
problem is as far as what you're doing.  If your creating Frankenstein files, 
there is always the possibility of some nefarious, subtle human error that you 
can't see ;)

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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