[gmx-users] gmx insert-molecules

[Justin Lemkul]

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On 6/7/17 2:46 PM, Shi Li wrote:
>>
>> On 6/7/17 1:20 PM, Li, Shi wrote:
>>> Dear GMX users,
>>>
>>> I have a pure solvent system A with 100 molecules. Then I randomly removed
>>> 10 molecules out of the box, but keep the box size. Now I want to do a gmx
>>> insert-molecule to insert 10 molecule B into the system box. The problem is
>>> molecule B is slightly larger than molecule A. So in some cases, I couldn't
>>> insert the exact 10 molecules of B into the system. Is there a way to
>>> automatically adjust the size of the box according to the radius of
>>> molecule B, so that they can fit in? Or, is there a better solution to do
>>> this?
>>>
>>
>> Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated
>> box of molecule A.  Works every time.
>>
>> -Justin
> 
> Thank you Justin,
> 
> In this case, I will need to apply a full equilibrium process (em, nvt, npt) to the new system, is that right?
> 
> I am trying to avoid the long step of equilibrium as I have many systems corresponding to different concentrations. I was thinking if I replace a small number of molecule A with molecule B (the system A is very large and pre-equilibriumed) then I only need to apply a short time-step of NPT in order to let the system expand or shrink. Then I can use the new system to continue replacing A with B to generate a new concentration. Is this practical?
> 
> The problem is when B is slightly larger than A, I can’t insert the same number of B into the system. Is there way to avoid the overlapping or force the molecule in?
You can reduce the vdW radius of atoms to *try* to force the molecules to fit, 
but then all you've done is introduce bad clashes that have to be subjected to 
minimization and re-equilibration.  So at that point, all you've done is build 
your system in the most inefficient way possible.  By trying to avoid 
equilibration, you've necessitated it :)

Build the system the robust way - solute first, then solvent.  It's ultimately 
less work and less prone to failure.

-Justin

-- 
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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

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