[gmx-users] Pull code, Velocity distribution

Samadashvili Nino 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.



More information about the gromacs.org_gmx-users mailing list