[gmx-users] Pull code, Velocity distribution
nino.samadashvili at aalto.fi
Fri Nov 2 15:52:19 CET 2012
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?
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?
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?
Thank you for your attention to this matter.
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