[gmx-users] Multiple mdp simulations; tinit

[David]

On Tue, 2004-01-27 at 11:31, Martina Bertsch, PhD wrote:
> 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?
give it a gro file, it will read the stuff from the trr file later on.


> 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
se above
> 
> 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?
> 
At the last time step the energies are computed, but the positions are
not integrated. The starting time should thus be the same as the ending
time of the previous sim.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++