[gmx-users] problems with g_wham

[Justin A. Lemkul]

Have you watched the trajectory?  That will show you what your pull group is 
doing.  Is this a periodicity effect?  It should be fairly obvious iff the sign 
of dX, etc flip-flops in the pullx.xvg file.

-Justin

Gavin Melaugh wrote:
> Thanks Chris and Justin
> 
> I do get the output I want from grompp(below). The distance of 5.507 nm
> is the distance that I want to start with and I assume it is therefore
> the equilibrium distance for the harmonic potential. The COM distances
> from the simulations fluctuate around this value which is what I want,
> although my histogram is the wrong shape.
> 
> Pull group  natoms  pbc atom  distance at start     reference at t=0
>        0               84        42
>        1               84       126                  
> 5.507                 5.507
> 
> Cheers
> 
> Gavin
> 
> chris.neale at utoronto.ca wrote:
>> I missed that pull_start = yes, sorry. So Gavin, your run should have
>> stayed around the starting position. Make the histogram directly and
>> you should get a better idea.
>>
>> Chris.
>>
>> -- original message --
>>
>>
>> To clarify, the tutorial sets "pull_init1 = 0" because it is used in
>> conjunction
>> with "pull_start = yes," in order to take the starting COM distance as
>> the
>> reference.  Check the grompp output to verify that you're getting what
>> you think
>> you should be.  Otherwise, you'd have to set "pull_start = no" and
>> modify your
>> .mdp file to reflect the proper value of pull_init1 for every window.
>>
>> -Justin
>>
>>
>>
>>
> 

-- 
========================================

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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