[gmx-users] energy terms in following runs

[Ester Chiessi]

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
both runs).

> > 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.
>
> --
> Groetjes,
>
> Anton

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,

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