[gmx-users] Umbrella Sampling Tutorial

[Justin Lemkul]

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

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

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

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