[gmx-users] Estimated temperature by gmxchek

[Ester Chiessi]

Hi,

I'd like to perform MD of a polymeric network in SCP water, mantaining
chemical bonds across boundaries in PBC.
My conditions:
T=303 K (constant by Berendsen)
constant V (no pressure coupling)
timestep=0.5 fs

After about 40 ps of simulation, I met errors in applying settle to water and
shake to OH groups of the polymer.

I tried to make some controls and with:

gmxcheck -f recovery.tpr

I obtained:
....
Checking coordinate file recovery.tpr
Reading file recovery.tpr, VERSION 3.1.4 (double precision)
Reading file recovery.tpr, VERSION 3.1.4 (double precision)
7564 atoms in file
coordinates found
box         found
velocities  found

Kinetic energy: 19477.8 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 206.472 K or 309.708 K respectively.
.......
I found very strange the temperature! The number of degrees of freedom of my
system should be Natoms * 3 ( I only correct for the center of mass motion),
or not?
The 309.708 K value seems too far from 303 K, too.

Thanks for any possible suggestion!

Ester


--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328