[gmx-users] Umbrella sampling- force vs time plots

[Justin Lemkul]

On 7/9/13 12:56 PM, rookie417 wrote:
> Hello all,
>
> I am trying to understand the force vs time plots using Gromacs' umbrella
> sampling method. I am trying to pull a short polymer chain from the interior
> of a micelle and see what the PMF looks like. I use the following parameters
> to run the pulling simulation for 500ps to pull the polymer over a distance
> of 5nm:
>
> pull=umbrella
> pull_geometry=direction
> pull_vec1=1 0 0
> pull_start=yes
> pull_ngroups=1
> pull_group0=surf
> pull_group1=poly
> pull_rate1=0.01
> pull_k1=1000
>

Note that what you're doing is not umbrella sampling, but steered MD, which is a 
nonequilibrium process.  The "umbrella" pulling method is unfortunately named, 
as it is just a harmonic potential.  Umbrella sampling is a separate procedure, 
one that uses the "umbrella" method and zero pull rate.

> After the simulation, pullf.xvg plot I obtained is a linearly increasing
> plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
> sure if this is right. My question is, on what basis do we select the
> optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
> choice of parameters as long as the system does not deform? How does an

Basically, yes.  No one (to my knowledge) has done a systematic study of such 
parameters.  I suspect that is because they are largely dependent upon the 
system and the interactions you are trying to disrupt.

> ideal force-time plot look like and does the choice of pull_k1 affect the
> histogram?  It appears, the entire procedure depends on the choice of input
> of these two variables. I would greatly appreciate if someone can explain
> this concept.
>

There will be an initial increase in force until restoring forces are overcome, 
at which point forces decrease and level off.  I don't know about a comparison 
of force constants, but I suspect the result should be similar to varying the 
pull rate.  The progression will be steeper with faster pulling or a harder 
force constant, more shallow with slow pulling or a soft constant.  We addressed 
this topic in the supporting information for 
http://pubs.acs.org/doi/abs/10.1021/jp9110794.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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

==================================================