[gmx-users] problem vwith ethanol-water solution

[Ehsan Sadeghi]

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?

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

Kind regards,
Ehsan



----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, October 31, 2013 1:18:07 PM
Subject: Re: [gmx-users] problem vwith ethanol-water solution



On 10/31/13 2:25 PM, Ehsan Sadeghi wrote:
> Hi gmx users,
>
> I want to solvate nafion molecules in a 3:1 ethanol water solution. I used
> genbox with -ci option to add ethanol to water when generating the box, but
> it did not work. Then, first I solvated the ethanol in water, and then added

What "did not work?"  In the absence of exact commands and description of the 
undesirable output, there's little to suggest from such statements.

> the nafion to the system, but these 3 molecules each sit a part from each
> other in the box in the pdb file. Any suggestion?
>

http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

-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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