[gmx-users] pbc atom

[Gavin Melaugh]

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.

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
>>
>