[gmx-users] pbc atom

[Justin A. Lemkul]

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
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================