[gmx-users] problem vwith ethanol-water solution

[Justin Lemkul]

On 10/31/13 7:03 PM, Ehsan Sadeghi wrote:
> Thanks Justin,
>
>
> Here is the steps that I followed:
>
> pdb2gmx -f eth.pdb -o eth.gro -p eth.top
>
>
> pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top
>
>
> editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5
>
>
> genbox -cp box.gro -cs spc216.gro -ci eth.gro -nmol 1000 -o solvated.gro
>
> I got the box with ionomer in ethanol and water solution. However, I only have 400 of eth and 423 water molecule. The box wasn't large enough?
>

Follow the advice at the link I posted before.  Trying to add ethanol while 
simultaneously solvating is a bad idea.  If genbox cannot add 1000 ethanol 
molecules without trying to do anything else, then yes, the box is simply too 
small.  At this point, we can't say because it could simply be that simultaneous 
solvation might have been competing for available box volume.

> What should I do with .top file? I have the .top file for ionomer and .top file for one eth molecule.
>

It is simple to covert between .top and .itp and #include them however you see 
fit.  Probably the conceptually easiest methhod is to consider ethanol just like 
any other solvent (i.e. water) and #include it within the .top for the ionomer, 
which is just like any other solute.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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