[gmx-users] Multiple mdp simulations; tinit

David spoel at xray.bmc.uu.se
Tue Jan 27 17:29:01 CET 2004

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 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

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