[gmx-users] energy terms in following runs
ester.chiessi at uniroma2.it
Fri Feb 21 14:52:32 CET 2003
Anton Feenstra wrote:
> Ester Chiessi wrote:
> > In md0.log I read:bUncStart = FALSE
> Which should be 'TRUE'. But then, tpbconv will change that for you
> (option -unconstrained, default is yes).
I thought (from the manual) default was no.
> Is this the md0.log for
> your first or second run? If it is from the second, something
> strange happened with tpbconv. Are you using the right .tpr file?
md0.log is that for the second run and the .tpr file is right.
> > To prepare the second run, I used grompp giving in -c the last .gro
> > file of the first run.
> What are the differences in your .mdp and/or .top file for the first
> and second runs?
In the .mdp of the second run I saved coordinates and velocities every 500
steps, instead of 100 steps in the first run (the time step is the same in
> > Then, with tpbconv, I gave in -f the .trr file of the first run and
> > the tpbconv output told me that the last frame will be used.
> > Perhaps I shouldn't specify -c in grompp?
> Irrelevant, these coordinates will be replaced by tpbconv.
> grompp does require you to give a .gro file, though.
I performed other calculations as follow:
run a : 1000 steps with time step 0.0002 ps
run b : 1000 steps with time step 0.0006 ps (from the last frame of 'a')
(I'd like gradually to increase the time step)
Necessarily I repeated the grompp ( by inserting unconstrained_start=yes
in the .mdp file ).
In the md0.log of run 'b' I find: bUncStart =TRUE.
Energy terms of the last frame of 'a' are different from the corresponding
of the first frame of 'b'. In particular, T (around 300K) increases of
aboult 7 degrees and the bond term varies of about 3 percent.
Pheraps this happened because I changed the time step?
I'd like to be sure of the continuity of the dynamics towards the
equilibrium in a procedure that goes on by following steps.
Thanks for every contribution,
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
e-mail: ester.chiessi at uniroma2.it
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