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

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

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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