[gmx-users] Multiple mdp simulations; tinit

[Anton Feenstra]

Martina Bertsch, PhD wrote:
> I thought that the -t flag passed the structure and velocities from the 
> last frame of the trr file to the preprocessor. If so, why is grompp 
> looking for a gro file?

grompp expects a .gro file, although in this case it doesn't actually
need it.

> My third question concerns the tinit parameter (in ps) in the mdp file. 
> As described above, my simulation consists of the following phases:
> heating: 0-20 ps,
> equilibration: 20-220 ps,
> cooling: 220-230 ps,
> equilibration: 230-430 ps etc,
> all with a 1-fs step.
> If the tinit = 0 at the beginning of the first simulation phase 
> (heating), what value should be assigned to this variable in the 
> subsequent equilibration phase: should it simply be 20, because the 
> previous phase ended at 20 ps, or should it be set to 20.001 because the 
> next timestep number is 20001? Or is it the next whole number, 21?

It mainly depends whether you will ba analyzing the combined simulations
as one. If not, it is probably simplest to start tinit at 0 for each
separate part. Of so, you should set tinit to exactly the same value
as the last frame of the previous part; since you are starting from that
last frame, it will be identical to the first frame of the next part
and hence should have the same timestamp.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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