From: lorix <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] on NVE and pressure
Date: Mon, 16 Apr 2007 12:25:15 +0200
Hi Berk and Jelger,
Thanks for your comments...
Yes I equilibrated the system with Berendsen thermostat and barostat for
100ps and 200 ps and then switched them off.
I thought that the coupling could have an influence in the final
trajectory, because of the atom velocities scaling (?).
Why does not make sense to run NVE after NPT?
You don't specify what your goals are, so I have to guess what you want.
MD is inherently chaotic and velocity correlations decay quickly,
so using NVE does, in general, not provide "better" velocities than NVT.
NVT is usually what you want when your system is in thermal equilibrium.
Only when you have energy dissipation after an event which takes your system
out of thermal equilibrium, i.e. pumps energy into the system,
it makes sense to use NVE.
However, when you equilibrate using NVT, this energy will already be
dissipated.
The two systems (15000 and 40000 atoms) I am simulating at NVE both show
increasing total energy:
The first system had -154442 kJ mol^-1 as average for the 7-207 psec NPT
equilibration and -168837 kJ mol^-1 as average value for 1500-2000 ps of
NVE.
The second system had -445679 kJ mol^-1 as average for the 14-114 psec NPT
equilibration and -465630 kJ mol^-1 as average for the 300-600 ps of NVE
equilibration.
For energy conservation you should not look at the average energy,
but the energy drift during your NVE simulation.
Berk.
_________________________________________________________________
The average US Credit Score is 675. The cost to see yours: $0 by Experian.
http://www.freecreditreport.com/pm/default.aspx?sc=660600&bcd=EMAILFOOTERAVERAGE
_______________________________________________
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
