[gmx-users] simulation using tabulated dihedral potentials.
iitdckc at gmail.com
Mon Dec 9 15:51:29 CET 2013
On Mon, Dec 9, 2013 at 6:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 12/9/13 8:09 AM, Chandan Choudhury wrote:
>> On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> Do your tabulated functions work on a toy system, like butane?
>>> No Mark. I didnot try with butane. The simulation stops when I
>> tabulated dihedral potential.
> Which is precisely why Mark is suggesting that you test something simple.
> If the simulation runs using a normal potential, but fails with your
> tabulated potential, that suggests quite strongly that your tabulated
> potential is not sound. So you need to go back to something very simple
> that should have a very obvious outcome and scrutinize its success or
> failure, then move on to something slightly more complex, etc until it
> fails and you identify where the problem lies.
Thanks for the reply.
Initially the system had 80 chains. Now I reduced it to single chain. The
single chains consisted of just 12 Coarse Grained beads.
The simulation proceeds very smoothly for 200000000 steps.
The tabulated bond, tab. angle and tab. dihedral potentials were on.
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> 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