[gmx-users] Hbond occupancy

[Justin Lemkul]

On 7/8/16 9:01 AM, Amali Guruge wrote:
> Thank you very much Eric for the answer. Could you please give information
> regarding to the command use in this calculation? Thank you.
>

You can't get, e.g. % occupancy directly but the gmx hbond output (-hbn -hbm) 
can be post-processed with a simple script to extract the information.  I have a 
script that does this; contact me off-list if you can't figure it out (it's a 
good programming exercise :).

-Justin

> On Fri, Jul 8, 2016 at 5:31 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
> wrote:
>
>> gmx hbond
>>
>>> On 8 Jul 2016, at 12:24, Amali Guruge <amaligg2010 at gmail.com> wrote:
>>>
>>> Dear All,
>>>
>>> Can anyone know how to calculate H bond occupancy with Gromacs?
>>>
>>> Thank you
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-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================