[gmx-users] Multiple mdp simulations; tinit

[Martina Bertsch, PhD]

Greetings.

I would like to perform the following MD simulation:
1) Heating from 300 to 600 K in 20 ps;
2) Equilibration at 600 K for 200 ps;
3) Cooling from 600 to 500 K in 10 ps;
4) Equilibration at 500 K for 200 ps;
5) Cooling from 500 to 400 K in 10 ps;
etc.

 I wrote 3 mdp files: heat.mdp, equilibrate.mdp and cool.mdp, as well as 
a script which reuses them by changing the ref_t and tinit parameters 
after each phase. I would like to input the coordinates and velocities 
from the last step of the heat phase (the last frame in heat.trr) as the 
starting structure for the equilibration phase, but when I run:

grompp -f equilibrate.mdp -t heat.trr -n index.ndx -p MT1.top -o eq600.tpr

I get an error:

"...calling /lib/cpp...
processing topology...
Generated 135 of the 1081 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
processing coordinates...
Fatal error: conf.gro does not exist"

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?

If I just use the -c flag to select the gro file corresponding to that 
frame (e.g., MT1_post_heat.gro), I can run grompp and mdrun, but then I 
should turn gen_vel on in each phase. Am I right? If I do so, will I 
still be able to concatenate the trr and edr files from different 
phases, provided that their time stamps are different?

Or is it better to do:

 grompp -f equilibrate.mdp -t heat.trr -c MT1_post_heat.gro -n index.ndx 
-p MT1_vac.top -o eq600.tpr

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?

Best wishes,
Martina