[gmx-users] problems with g_wham

[Gavin Melaugh]

Many thanks

Justin A. Lemkul wrote:
>
>
> 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.
>
> -Justin
>
>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>
>>
>