[gmx-users] Pull code, Velocity distribution

[Justin Lemkul]

On 11/2/12 10:52 AM, Samadashvili Nino wrote:
> Hello,
>
>         I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how  Gromacs is calculating the pulling force (pullf.xvg) during sliding.  Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential?

This should be correct.

> I am using following parameters:
>
> pull                           = umbrella
> pull_geometry            = direction_periodic
> pull_dim                    = Y Y Y
> pull_start                   = yes
> pull_ngroups              = 1
> pull_group0                = ICE_A
> pull_group1                = ICE_B
> pull_pbcatom0           = 0
> pull_pbcatom1           = 0
> pull_vec1                  = 1 0 0
> pull_rate1                  = 0.004
> pull_k1                      = 10000
>
> Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B?

Yes.

> Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the  distribution plot calculated from the coordinates and they dont match.
> The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs?

How what is calculated?  How are you creating your own distributions from the 
coordinates?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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