[gmx-users] pbc atom

[Gavin Melaugh]

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.

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
>>>>
>>
>>
>