[gmx-users] Pull code, Velocity distribution

Samadashvili Nino nino.samadashvili at aalto.fi
Sat Nov 17 14:29:24 CET 2012


 Sorry for bothering you with the same question but just want to make sure that I am getting my results correctly.
I run simulations where two blocks of ice are in a sliding contact for 5 ns (using pull code). As an output of the simulation I have pullf.xvg file which I use for 'g_analyze -f pullf.xvg' command and assume that the average force it prints is the average pulling force calculated with the  U = 1/2K(vt-(x-x0))^2 harmonic potential.

Sorry again for double checking!



From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Friday, November 02, 2012 5:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pull code, Velocity distribution

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?


> 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



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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