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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