Hi, I have a system that I would like to equilibrate in the NPT ensemble at high temperature, and then, in subsequent equilibration steps, cool down in steps of 50 K. Thus, in the first step, I will use "gen_vel = yes", while in all subsequent steps, I will use "gen_vel = no".
Suppose that I want to run 200 ps at 700 K, 200 ps at 650 K, and 200 ps at 600 K. I have two possible protocols, Protocol 1 and Protocol 2. If you have time, can you please help me see what is the difference between these two protocols? For my application (cooling down a system in steps of 50 K), which protocol do you think is more appropriate? Or do you have any other suggestions? In Protocol 1, both the output configuration (.gro) and the checkpoint (.cpt) resulting from mdrun of the previous step are fed to grompp of the next step (however, I am not appending files, because I want separate .trr files for each step): ***BEGIN PROTOCOL 1*** STEP 1 (700 K, 200 ps): grompp -f a1.mdp -c inputconf.gro -p topology.top -o a1.tpr -po a1out.mdp ;where a1.mdp contains "gen_vel = yes" mdrun -deffnm a1 -cpo a1.cpt -noappend STEP 2 (650 K, 200 ps): grompp -f a2.mdp -c a1.gro -p topology.top -t a1.cpt -o a2.tpr -po a2out.mdp ;where a2.mdp contains "gen_vel = no" mdrun -deffnm a2 -cpo a2.cpt -noappend STEP 3 (600 K, 200 ps): grompp -f a3.mdp -c a2.gro -p topology.top -t a2.cpt -o a3.tpr -po a3out.mdp ;where a3.mdp contains "gen_vel = no" mdrun -deffnm a3 -cpo a3.cpt -noappend ***END PROTOCOL 1*** In Protocol 2, only the output configuration (.gro) resulting from mdrun of the previous step are fed to grompp of the next step: ***BEGIN PROTOCOL 2*** STEP 1 (700 K, 200 ps): grompp -f a1.mdp -c inputconf.gro -p topology.top -o a1.tpr -po a1out.mdp ;where a1.mdp contains "gen_vel = yes" mdrun -deffnm a1 STEP 2 (650 K, 200 ps): grompp -f a2.mdp -c a1.gro -p topology.top -o a2.tpr ;where a2.mdp contains "gen_vel = no" mdrun -deffnm a2 STEP 3 (600 K, 200 ps): grompp -f a3.mdp -c a2.gro -p topology.top -o a3.tpr ;where a3.mdp contains "gen_vel = no" mdrun -deffnm a3 ***END PROTOCOL 2*** Which is preferable? In both protocols, the end velocities of the previous step are used to begin the next step, since the .gro files contain the velocities. However, only in Protocol 1 do I use the checkpoint files to continue the run. Does doing so just cause the energy statistics to be more consistent between steps? Also, if you have time, should I use "continuation = yes" in a2.mdp and a3.mdp? My system does not have any constraints per se; atoms are either frozen (using a freeze group to simulate an immobilized surface) or their bonds are flexible. Thus, I am not really using any constraints, unless freeze groups count as constraints. However, I am not sure what this means as far as what to set "continuation" to in a2.mdp and a3.mdp. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
