On 1/11/14, 11:50 AM, Andres Ortega wrote:

Dear Gromacs Users

I was running de Umbrella Sampling Tutorial, and when i get the frames from
the trajectory, there are some frames like this:

489     5.3776196
490     5.3817739
491     5.3752654
492     5.3619911
493     5.3890083
494     5.3918220
495     5.4115819
496     5.4074620
497     5.4386061
498     5.4179682
499     5.3942749
500     5.3905423

is this ok? , they shouldn´t be always move away from the other molecule ?

This is perfectly fine. At this COM distance, there is no appreciable interaction between the reference and pulled groups, so the pulled group mostly just diffuses randomly at this point. Remember that the spring is pulled with constant velocity, but the pulled species only responds to both this applied force and the forces within the system, which at this point are just collisions with the solvent.



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

jalem...@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-requ...@gromacs.org.

Reply via email to