[gmx-users] mdp

Mouri Ahmed mouriahmedmou at gmail.com
Tue Oct 18 01:27:09 CEST 2016


Hi

Thanks Justin and Parvez for your suggestions.

Can I use "constraints=none" for coarse-grain protein also?


Best Regards
Mouri




On Mon, Oct 17, 2016 at 8:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/16/16 2:16 PM, Parvez Mh wrote:
>
>> Hey;
>>
>> Go through the link <http://manual.gromacs.org/online/mdp_opt.html#bond>.
>> You will get everything about your purpose. By the way,  you could use
>> *constraints=none
>> .  *But you have to make sure you use proper *timestep* while using no
>> constraint.
>>
>>
> Constraints such as SETTLE for rigid water would also have to be turned
> off with "define = -DFLEXIBLE" but most water models are not designed to be
> used in flexible form, so this is not typically done during MD.
>
> -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.
>


More information about the gromacs.org_gmx-users mailing list