[gmx-users] Generate the water box

[Barnett, James W]

Use "gmx editconf" first to create the box then "gmx solvate" to fill it with water (omitting -box directive this time).

--
James "Wes" Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarnet4 at tulane.edu​
LinkedIn​​


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Vy Phan <phanvy120690 at gmail.com>
Sent: Thursday, May 21, 2015 8:36 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Generate the water box

Dear all,
I can generate the cubic box or the rectangular box  with gmx solvate -cs
water.gro -box
 but I would like to have the octahedron box.I try many way but I can not.
How I can do it?

Thank a lot
Tuong Vy

2015-05-21 1:49 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 5/20/15 11:55 AM, 姚懿 wrote:
>
>> genbox without adding a protein.
>>
>>
> More specifically (and for 5.0):
>
> gmx solvate -cs water.gro -box (whatever size is needed)
>
> -Justin
>
>  On Wed, May 20, 2015 at 9:56 AM, Vy Phan <phanvy120690 at gmail.com> wrote:
>>
>>  Dear Gromacs Users,
>>>
>>> Can I generate only water on the Gromacs? I need water box only.
>>>
>>> Thank you
>>> Tuong Vy
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>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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>
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