[gmx-users] Re: umbrella potential

[Stefan Hoorman]

>
>
> Stefan Hoorman wrote:
> > I have performed a series of umbrella sampling simulations in order to
> > do a WHAM analysis. The profile.xvg file I obtain is a continuous
> > descending line along my distance axis. There is no increase in energy
> > after my two structures separate. Perhaps I am doing something wrong.
>
> Sounds like it, but there's no way anyone on this list will know that
> unless you
> describe your system in greater detail - how you generated the starting
> configurations, how many windows you used and what distances that
> corresponds
> to, the pull parameters you've specified in your .mdp file, and anything
> else
> that might be pertinent.
>
> -Justin
>
> Ok, I've done the following. I have simulated my system (protein + ligand
> in water SPC with GROMOS96 53a6 forcefield, with PME, Nose-Hoover thermostat
> (310 K), parrinello-rahman barostat (1 atm), with the pull code for 15 ns,
> the pull code content of the mdp file is the following:
>
 pull  =  umbrella
pull_geometry  =  direction
pull_dim  =  Y Y N
pull_nstxout  =  10
pull_nstfout  =  1
pull_ngroups  =  1
pull_group0  = protein
pull_group1 = SLC
pull_vec1  =  1 1 0
pull_init1  =  0
pull_rate1  =  0.001
pull_k1  =  35
pull_constr_tol  =  1e-06
pull_pbcatom0  =  0
pull_pbcatom1  =  0

Analysing the distance between the groups I get a very shy increase in the
initial distance for the first 5 nanoseconds and after that the distance
between the two groups increase 5nm in the next 10ns.
>From this trajectory I have removed 30 structures. The first 10 were
obtained with a 500 ps interval between them and the other 20 in 250 ps
interval for the next 5ns. The final 5ns of the simulation are not of
interest since my Lennard jones and coulomb interaction between the two
structures fall to 0 after the first 9 ns of simulation.
I then simulated each of these windows for 500 ps with the following
mdp_pull content:

; Pull Code
pull  =  umbrella
pull_geometry  =  distance
pull_dim  =  Y Y N
pull_nstxout  =  10
pull_nstfout  =  1
pull_ngroups  =  1
pull_group0  = protein
pull_group1 = SLC
pull_vec1  =  1 1 0
pull_init1  =  0
pull_rate1  =  0
pull_k1  =  35
pull_constr_tol  =  1e-06
pull_pbcatom0  =  0
pull_pbcatom1  =  0

I have set the "pull_geometry" to distance since g_wham does not accept
"direction".
The distances between the two structures in each of the windows are (in nm):
0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 = 1.52; 2500 =
1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000 = 1.7; 5250 =
1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 = 1.91; 6750 =
1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04; 8000 = 2.16 ;
8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ; 9250 = 2.5 ; 9500 =
2.62 ; 9750 = 2.65 ; 10000 = 2.66
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090920/3bfeebae/attachment.html>