[gmx-users] Umbrella Sampling Tutorial

[Andres Ortega Guerrero]

Thanks ! 



Andrés Ortega 
Ing. Electrónica 
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.
> Greetings
> Thomas
> 
> 
> Am 11.01.2014 22:45, schrieb gromacs.org_gmx-users-request at maillist.sys.kth.se:
>>> 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
> 
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