[gmx-users] restraint

[Justin Lemkul]

On 10/25/16 6:11 AM, Mouri Ahmed wrote:
> Dear Dr. Justin,
>
> Thank you very much for the help.
>
> In the gromacs tutorial, protein and ligand are being pulled away from each
> other.
>
> In the pull_md.mdp file, which option I need to change to make them close?
>

A negative pull rate pulls the two species closer together.  A zero pull rate 
keeps them at a specified distance.

-Justin

>
> Best Regards
> Mouri
>
> On Tue, Oct 25, 2016 at 8:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/25/16 5:24 AM, Mouri Ahmed wrote:
>>
>>> Hi
>>>
>>> I want to use distance restraint between protein and ligand in gromacs.
>>>
>>> I am confused with the problem.
>>>
>>> Anyone have any ideas?
>>>
>>>
>> Use the pull code.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

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