[gmx-users] PMF calculation_ Constraint

[Justin Lemkul]

On 9/23/15 9:36 AM, Sepideh Kavousi wrote:
> Dear Justin.
> Thanks for response. I used constraint method because I wanted to calculate
> MSD, How does using a bigger box helps me? because when  I make box bigger,

I don't see how the constraint method relates to MSD.

A bigger box with the same length of reaction coordinate would avoid jumps 
across PBC.

-Justin

> I need to run a little bit to equilibrate system, and again the tocopherol
> can move and come out of the box.
>
> On Tue, Sep 22, 2015 at 5:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/22/15 3:46 PM, Sepideh Kavousi wrote:
>>
>>> Dear Gromacs users
>>>
>>> I want to calculate the PMF of tocopherol in DMPC bilayer system. For this
>>> means, I used Constraint method. the pull code in my .mdp file is :
>>>
>>> pull = constraint
>>> pull-geometry = distance    ;distance, direction, or cylinder
>>> pull-dim = N N Y
>>> pull-constr-tol = 1e-6
>>> pull-start = yes                    ;add current COM distance to
>>> pull_init?
>>> pull-print-reference = no
>>> pull-nstxout = 10000
>>> pull-nstfout = 5
>>> pull-ngroups = 2
>>> pull-ncoords = 1
>>> pull-group1-name = DMPC
>>> pull-group2-name = VIT
>>> pull-coord1-groups = 1 2
>>> pull-coord1-init = 0.0
>>>
>>>
>>> In my output file which shows force over time, we have some sudden
>>> diverges
>>> of force to a very high number.
>>> I realized it is because of the boundary condition, one part of molecule
>>> comes out of the box and enters from the other side of the box and it
>>> needs
>>> a huge force to keep the molecule at the same position. Can you please
>>> help
>>> me how to solve this problem
>>>
>>>
>> Use a bigger box, use a shorter reaction coordinate, or use an umbrella
>> sampling method that supports PBC.  I suspect any output using the
>> constraint method will be very poorly converged.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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