[gmx-users] Box of water

Dallas Warren Dallas.Warren at monash.edu
Tue May 1 04:23:24 CEST 2012

Easiest solution can think of, make box that is of sufficient size the when filled contains 846 waters, fill with waters, use editconf to scale the box size to that which you require, run EM to get the waters back to the dimensions they should be.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of cuong nguyen
Sent: Tuesday, 1 May 2012 12:21 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Box of water


I tried to add -maxsol 846 to the command and got the box with 846 water molecules. However, when I use VMD to visualize the box, these molecules concentrate on 1/3 the box space. I do need the molecules to spread out whole box.

2012/5/1 Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>>

On 4/30/12 10:02 PM, cuong nguyen wrote:
Dear Gromacs Users,

I used the command "genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10"
to create box of 3010 water molecules. However, now I need to create a same size
box with only 846 water molecules. Please help me to do this.

Use the -maxsol option when invoking genbox.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080<tel:%28540%29%20231-9080>


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Nguyen Van Cuong
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