[gmx-users] gmx insert-molecules

[Justin Lemkul]

On 6/8/17 9:15 AM, Shi Li wrote:
>>>>
>>>> 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?
> 

No, you have to make sure the box is large enough.  Box adjustment is a dynamics 
process, not anything that the preparation tools do.  So either gmx 
insert-moleucles for both A and B, or gmx solvate for A with -maxsol.  Either 
way, you need to know the per-molecule volume to create a reasonably sized box.

-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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