VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 31 2011 - 15:56:52 CDT

> i repeat, that doesn't say anything. have you made
> _any_ statistical analysis on the "quality" of your data?
> yes , I check it, don't worry about it
> how do did you determine equilibration?
> from check energy, temperature, pressure and thermodynamic properties. I
> have a "equlibrated" system
> do you have any independent parameters,
> that can confirm that you are actually correctly
> reproducing the simulation in the reference?
> do you use the same kind of thermostat?
> hoover thermostat, use "NPT hoover 0.2 0.2"
> what about long-range electrostatics?
> I used ewald precision 1d-6
> you cannot just say. i ran this simulation,
> i use this script and it doesn't give the same
> number, so the script has to be wrong.
>
> I repeat again, DO NOT WORRY ABOUT Equlibration!!!

i don't worry about equilibration, but i've been
just pointing out the many reasons that i've
seen in the past why people have seen
different numbers for properties computed
from MD trajectories, and you still don't
provide any convincing information that it
is not your data set that is at fault.

at this point, i have to give up. apparently,
VMD is not worthy of analyzing your data.
i suggest you try some other software instead.

gromacs for example comes with a g_hbond tool.
perhaps that is giving you a "better" result
and less trouble.

have a nice day,
     axel.

>
> Best Reagrds
> axel.
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.