[gmx-users] Umbrella Sampling Tutorial
Andres Ortega Guerrero
og_andres15 at hotmail.com
Sat Jan 18 04:45:43 CET 2014
Universidad del Valle
El 13/01/2014, a las 8:59, "Thomas Schlesier" <schlesi at uni-mainz.de> escribió:
> Since the spring has a finite force constant, it is quite naturally that one observes fluctuations in the distance (between reference and pulled group) and forces.
> Am 11.01.2014 22:45, schrieb gromacs.org_gmx-users-request at maillist.sys.kth.se:
>>> >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.
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