[gmx-users] genbox command in gromacs-5.0.1
kalyan.chem.in at gmail.com
Wed Apr 8 16:14:54 CEST 2015
Thank you very much Justin. I need the solvated box. I have used "gmx
solvate -cp *.pdb -cs tip4p.gro -p topol.top -o *.pdb" . It has
successfully generated the solvent box.
On Wed, Apr 8, 2015 at 6:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 4/8/15 8:38 AM, Kalyanashis Jana wrote:
>> Dear all,
>> I have installed gromacs-5.0.1 version successfully but when I have run
>> genbox command, it has shown that "This tool has been removed from Gromacs
>> 5.0. Please see
>> for ideas how to perform the same tasks with the new tools."
>> In gromacs site, it is written that
>> This tool has been split to gmx solvate and gmx insert-molecules.
>> Can anyone please help me?
> With what task? genbox has been split based on two core functions:
> solvation and insertion of molecules. Start with "gmx help solvate" and
> "gmx help insert-molecules" to see how to use each.
> 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
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