[gmx-users] dihedral MM scan

Justin Lemkul jalemkul at vt.edu
Fri Jan 20 03:48:11 CET 2017

On 1/19/17 9:40 PM, Mohsen Ramezanpour wrote:
> Thanks Justin,
> I did the scan for the whole range from -180 to 180 in 10 intervals.
> I used emtol = 50, and restrain force of 100000 to have a better relaxation
> and restraining, respectively.
> Unfortunately, my MM profiles do not look similar to GAAMP QM or MM
> profiles, although I have used the suggested parameters.
> To check the method I am using and the parameters in the .mdp files, I did
> the MM scanning on a rotatable bond (CH2-CH2-CH2-CH3) similar to one can be
> found in a lipid tail.
> This dihedral was detected as a soft dihedral by GAAMP and there was a good
> agreement between QM and MM profiles.
> Here again, my MM profile from scanning does not seem reasonable.
> Most importantly, there is a very large barrier at angle 0 (ca. 300 times
> of energies in other angles). Besides, there are sudden increase or
> decrease in energy just by 10 degree of rotation.
> Any suggestion is appreciated in advance.

There's really nothing I can suggest without actually seeing the files (plots of 
the energy, the QM inputs and your topology).  Something is inconsistent but 
it's not clear what.



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


More information about the gromacs.org_gmx-users mailing list