[gmx-users] gmx insert-molecules

[Shi Li]

>>> 
>>> Again, please don't reply to the entire digest.
>> 
>> Sorry about the inconvenience, I am not very familiar with the process. Hope this is right now.
>>> 
>>> Neither approach avoids having re-equilibrate the system.  Your approach of
>>> inserting B into an existing box of A perturbs the system and requires a new
>>> equilibration.  This is especially true if you play tricks like messing with vdW
>>> radii to force B into small voids in A.  You need to minimize and equilibrate,
>>> because these are new systems.
>>> 
>>> My approach is less prone to failure and ultimately I would expect it to take
>>> less time overall because you will not have instances in which the insertion of
>>> B into A fails and requires you to revisit those systems, change seeds, hack vdW
>>> radii, and potentially deal with problematic minimizations.
>>> 
>> 
>> I would like to solvate the box too, it is indeed less effort. In our approach, we want to have a box with a fixed number of A+B, that?s why we want to manually replace certain number of A with B, so that we still maintain the same total number of molecules but create different concentration. If I solvate the box with A, then the number of molecule A goes into the box will not be the number we want it to be. Is there ways to define the number of solvent when we do the gmx solvate?
>> 
> 
> Yes, that is exactly what -maxsol does.

Thank you!

But that’s the maximum number of solvent to add into the box, right? Can I solvate the box with a fixed number of solvent molecule? If the size of the box is a little small, will it automatically adjust the box size to insure the right number of solvent can go in?

Shi
> 
> -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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