[gmx-users] pbc atom

[Gavin Melaugh]

For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the displacement along a given vector component?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> 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
>>
>
> That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
> group, then displacement (dX,dY,dZ) of the pull group relative to the
> reference.  Not all terms may be present, depending on the axis along
> which you're pulling, i.e. if you only pull along Z, there will be two
> terms in pullx.xvg - Z and dZ.
>
> -Justin
>
>> 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
>>>>
>>
>>
>