[gmx-users] pbc atom

[Gavin Melaugh]

O.K thanks anyway


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
>>
>>
>