[gmx-users] Umbrella Sampling Tutorial

[Thomas Schlesier]

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