[gmx-users] Re: Umbrella Sampling settings

[Thomas Schlesier]

But you need each of these lines for both cases (SMD and US). Probably 
one could skip two lines and use the default values, but it's better to 
set them manually. See below for comments (comments are under the 
related entry):


> Thanks for your reply. But when I don't understand why these extra lines
> are needed to set when are not advantageous practically! :-( Sincerely,
> Shima ----- Original Message ----- From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at gromacs.org> Cc: Sent: Friday, July 12, 2013
> 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13
> 4:21 PM, Shima Arasteh wrote:
>> >Hi,
>> >
>> >I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window.
>> >Some mdp file settings for running US, as I found in US tutorial are :
>> >; Pull code
>> >pull? ? ? ? ? ? = umbrella
how do you want to pull (umbrella / constant force / ...)
>> >pull_geometry?  = distance
second part for 'how to pull' ; see the manual
>> >pull_dim? ? ? ? = N N Y
in which direction do you want to pull
>> >pull_start? ? ? = yes
should the initial distance of 'pull_group0' and 'pull_group1' be added 
to 'pull_init1'
>> >pull_ngroups? ? = 1
number of pulled groups
>> >pull_group0? ?  = Chain_B
referene group
>> >pull_group1? ?  = Chain_A
pulled group
>> >pull_init1? ? ? = 0
place where origin of the potential is place
>> >pull_rate1? ? ? = 0.0
pulling veloity (default value could be 0, but if you want to pull with 
a zero-velocity it's safer to give this value manually
>> >pull_k1? ? ? ?  = 4000? ? ? ; kJ mol^-1  nm^-2
force constant for umbrella / force for constant force
>> >pull_nstxout? ? = 1000? ? ? ; every 2 ps
output coordinates
>> >pull_nstfout? ? = 1000? ? ? ; every 2 ps
output forces
>> >
>> >

So, you see each line is sensible, there are no 'extra' lines.

Greetings
Thomas


>> >But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling!
>> >
> All of them are related to umbrella sampling.? Pulling (steered MD) and umbrella
> sampling simply use common parts of the "pull code" in Gromacs because US
> requires a restraint potential.? Whether or not that restraint potential induces
> net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate,
> restrain to a given set of conditions) is the only difference.? Both processes
> require reference and "pull" groups, geometry information, etc.
>
> -Justin