On Sun, 15 Jun 2008 19:07:48 +0300
Vitaly Chaban <[EMAIL PROTECTED]> wrote:
For methanol (200ps, dt=0.001):
frequency to write velocities = 5
frequency to write coordinates = 100
XP> Any rationale behind this difference? That might well result in
differences of C(t) at short times.
Yes, the difference is dictated by the pure logic.
That is a clear explanation! Thank you.
$ g_msd
2.3 (and it is true)
XP> How much of msd(t) did you use? The part of the curve you use to fit
XP> to Einstein equation will affect enormously the result!
200 ps of trajectory was used. It is quite enough.
It depends on many factors: the length of your simulation and the
convergence of your msd curve are two of them.
XP> Here you use 1001 points to integrate! Which result to 1001*0.005fs=5 ps!
I tried to determine the length of your velocity C(t) you used to extract
the correlation time.
It seems that you used 5 ps for the velocities and 200 ps for the msd!
That might be a reason fot differences, no?
XP> Again did you use the same length of the msd(t) to fit via Einstein
equation?
Sorry, there is no sense in what you say here.
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
