[gmx-users] problems with g_wham

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 8 15:43:47 CEST 2010

Gavin Melaugh wrote:
> Hi Justin
> I am not using periodic boundary conditions for the simulations. I may
> have sorted it out now. I was generating velocities in the umbrella.mdp
> file, I have since set gen_vel = no, and the histogram has the correct
> shape (should this make a difference?)

If you generate velocities without doing equilibration, then your system may not 
be at equilibrium and thus you are doing inaccurate sampling.  Thus, if your 
system gets kicked in the wrong direction, the umbrella potential may have to 
fight to pull the desired group back to where it thinks it should be, might be 
overcompensating, etc.


> Cheers
> Gavin
> Justin A. Lemkul wrote:
>> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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