[gmx-users] pbc atom

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Aug 25 16:22:59 CEST 2010

Dear Chris and Justin

I ran a simulation for two water molecules (100 ns). It only took 5
minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel
=yes, and gen temp =600 (using Nose Hoover). This produced a histogram
with one main peak. I then took the final configuration from that
simulation and ran the simulation again for the exact same duration and
parameters etc, with the only exception that I set gen_vel = no. The
resulting histogram did indeed have two main peaks. I am now currently
running the simulation of my two cage molecules using berensden
thermostat to see if there is a difference.

Many Thanks


chris.neale at utoronto.ca wrote:
> Dear Gavin:
> What happens if you replace your reference group by a single water
> molecule and your pulled group by a single water molecule and run the
> 2.35 nm simulation again. Do you get the same two-peaked histogram?
> What about if you use a system with a single water for the reference
> and your regular pulled group?
> You should not need to run 100 ns to get an idea about the shape of
> that histogram so it should be a quick test. This is usually how I
> figure things out -- see how much I can reduce the complexity and
> maintain the problem.
> Chris.
> -- original message --
> Hi Chris
> I have generated a histogram from the my.data file and i get a histogram
> with the exact same profile as that generated from g_wham. Also on
> comparison of the dx, dy, dz values in the g_dist file with the vaules
> in the pullx.xvg file I notice that the magnitudes of the vectors are
> identical but their signs are opposite. e.g.
> g_dist file
> -2.2756047   -0.0369981    0.3126130
> pullx.xvg file
> 2.2756  0.036998        -0.312613
> Cheers
> Gavin
> Please note that there is a significantly more interaction between the
> molecules below 2 nm whereas above they interact very weakly (from
> viewing the trajectories)

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