normal extended simulation

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1 year 3 weeks ago #7637 by cm
extended simulation was created by cm
i have run 1 micro second simulation of a martini protein cg in a water box.the simulation has comleted 1 microseconds without any error.(following this tutorial " cgmartini.nl/index.php/tutorials-general-introduction/proteins ")

grompp -f martini_v2.x_new-rf.mdp -c equilibration.gro -p system.top -o dynamic.tpr
mdrun -deffnm dynamic -v
from this i have obtained
dynamic.tpr,dynamic.xtc,dynamic_prev.cpt,dynamic.log,dynamic.gro,dynamic.edr,
dynamic.cpt

Now i want to run for another 1 microsecond simulation starting from this point.I am using this command
grompp -f martini_v2.x_new-rf.mdp -c dynamic.gro -t dynamic.cpt -p system.top -o dynamic.tpr
and then
mdrun -deffnm dynamic1 -v
i just to want to know is this correct for further simulation of martini protein cg in gromacs.

thank you......

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1 year 3 weeks ago - 1 year 3 weeks ago #7638 by riccardo
Replied by riccardo on topic extended simulation
You should use something like this (with -c you provide the last snapshot of the previous simulation as your starting configuration):

grompp -f martini_v2.x_new-rf.mdp -c dynamic.gro -p system.top -o dynamic1.tpr

mdrun -deffnm dynamic1 -v

the -deffnm flag tells mdrun to look for a *tpr* file called "dynamic1".
Last edit: 1 year 3 weeks ago by riccardo.

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1 year 3 weeks ago #7639 by cm
Replied by cm on topic extended simulation
thank you for your quick reply.
grompp -f martini_v2.x_new-rf.mdp -c dynamic.gro -t dynamic.cpt -p system.top -o dynamic1.tpr (i have just miss print dynamic1.tpr by dynamic.tpr)
now is this correct

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1 year 3 weeks ago #7640 by riccardo
Replied by riccardo on topic extended simulation
As I wrote in my previous message, you don't need "-t dynamic.cpt". For the rest, it is okay.

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1 year 3 weeks ago #7641 by cm
Replied by cm on topic extended simulation
thank you so much for your suggestion.

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