[gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:
> O.K thanks Justine I'll look at these files and see if there is any
> weirdness.
> Just to make sure that there are no cut-off artefacts. If I  set the
> cut-offs to zero as in the following mdp file; that does mean that I am
> considering all electrostatic and LJ interactions between the molecules?
> and not including them at all. I assume the former given that there are
> both electrostatic and LJ energy values in the log and energy files.
> 

Correct.

-Justin

> Gavin
> 
> title       = Pull test
> cpp         =
> include     =
> define      =
> integrator  = md
> nsteps      = 50000000
> dt          = 0.002
> nstxout     = 250000
> nstvout     = 250000
> nstlog      = 250000
> nstenergy   = 5000
> nstfout     = 250000
> pbc         = no
> nstlist     = 10
> ns_type     = simple
> vdwtype     = cut-off
> rlist       = 0
> rvdw_switch = 0
> rvdw        = 0
> coulombtype = cut-off
> rcoulomb    = 0
> tcoupl      = nose-hoover
> tc_grps     = system
> tau_t       = 0.1
> ref_t       = 600
> gen_vel     = no
> gen_temp    =
> constraints = none
> comm_mode   = angular
> pull        = umbrella
> pull_geometry = distance
> pull_dim = Y Y Y
> pull_start = no
> pull_ngroups = 1
> pull_group0 = cage_1
> pull_group1 = cage_2
> pull_init1 = 2.59
> pull_rate1 = 0.0
> pull_k1 = 1000
> pull_nstxout = 1000
> pull_nstfout = 1000
> 
> 
> Justin A. Lemkul wrote:
>>
>> Gavin Melaugh wrote:
>>> 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?
>>>
>> For diagnosing weird behavior, I would always start with the primary
>> data, not any post-processed interpretation of it.  Use the pullx.xvg
>> file.  Any weird changes in sign or sudden changes in magnitude would
>> indicate problems.  If you start manipulating the data, you may be
>> hiding the real reason for the problem.
>>
>> -Justin
>>
>>> 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
>>>
> 
> 

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

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

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