[gmx-users] pbc atom

[Gavin Melaugh]

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> I have looked at the movies but it's very hard to tell what's going on
>> as I save teh trajectories every 250000 steps for every 50000000 step
>> simulation (100 ns). Ill look at them  again in more detail and post
>> back.
>>
>
> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
> any weird jumps or sudden changes in position might occur.  Mapping
> that information back onto the trajectory could help focus your
> attention.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
>>>> O.K thanks anyway
>>>>
>>> I saw the plots you posted during a conversation with Chris, but I'll
>>> ask the obvious anyway: have you watched the trajectories for any of
>>> the problematic windows?  It didn't seem like you had two metastable
>>> states, but maybe having a look at the movie would shed some light on
>>> what's going on.  I know that's the first thing I'd do.
>>>
>>> -Justin
>>>
>>>> Justin A. Lemkul wrote:
>>>>> Gavin Melaugh wrote:
>>>>>> Thanks Justin
>>>>>>
>>>>>> Have you any idea why when generating umbrella histograms for the
>>>>>> pmf I
>>>>>> would get two peaks in the histograms above a distance of 2 nm, but
>>>>>> below 2 nm I get well behaved histograms that lead to a very
>>>>>> good profile in the pmf. To the best of my knowledge the
>>>>>> configurations
>>>>>> are all very well equilibrated at their respective COM distances.
>>>>>> Umbrella sampling is performed on all windows using a force
>>>>>> constant of
>>>>>> 1000 kj/mol at 600 K.
>>>>>>
>>>>> Sorry, no clue.
>>>>>
>>>>> -Justin
>>>>>
>>>>>> Cheers
>>>>>>
>>>>>> Gavin
>>>>>>
>>>>>> Justin A. Lemkul wrote:
>>>>>>> Justin A. Lemkul wrote:
>>>>>>>> Gavin Melaugh wrote:
>>>>>>>>> Hi all
>>>>>>>>>
>>>>>>>>> I am generating a series of configurations using the pull code to
>>>>>>>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
>>>>>>>>> output
>>>>>>>>> from grommp gives me info on pbc atom.
>>>>>>>>>
>>>>>>>>> Pull group  natoms  pbc atom  distance at start     reference at
>>>>>>>>> t=0
>>>>>>>>>        0        72        36
>>>>>>>>>        1        72       360   4.290                 4.290
>>>>>>>>>
>>>>>>>>> why is this so?
>>>>>>>>>
>>>>>>>> grompp always assigns the numerical middle atom of a group as the
>>>>>>>> PBC 
>>>>>>> ...unless over-ridden by providing a different value for
>>>>>>> pbc_pullatom1.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>>> reference point.  In the case of pbc=no, it shouldn't matter.
>>>>>>>>
>>>>>>>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>>> Cheers
>>>>>>>>>
>>>>>>>>> Gavin
>>>>
>>
>>
>