Dear Gromacs Users, I have some questions regarding GB-Polarization Energy Calculation with Gromacs. I will be grateful if someone can help me with the answers.
I am trying to calculate GB-Polarization energy for different Protein molecules. I am interested both in energy values with the time required to calculate the Born Radii and Polarization Energy. I am not doing any energy minimization step as the files I am using as input are already minimized. Here is the content of my mdrun.mdp file: constraints = none integrator = md pbc = no dt = 0.001 nsteps = 0 implicit_solvent = GBSA gb_algorithm = HCT sa_algorithm = None And I am using following three steps for all the .pdb files I have: let x is the name of the .pdb file. pdb2gmx -f x.pdb -ter -ignh -ff amber99sb -water none grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr mpirun -np 8 mdrun_mpi -deffnm imd -v -g x.log 1 .Now the running time reported by a log file also includes other times. Its also not clear to me whether the time includes the time for Born Radii calculations. So, to get the GB-energy time I am doing the following: I am also running a simulation with "implicit_solvent" set to "no" and I am taking the difference of these two (with GB and Without GB). Is that a right approach? I also want to be sure that it also includes Born-Radii calculation time. Is there any other approach to do this? 2. I was trying to run the simulations on 192 cores (16 nodes each with 12 codes). But I got "There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 2.90226 nm" error for some pdb files. Can anyone explain what is happening. Is there any restriction on number of nodes can be used? 3. I run the simulations with 1 way 96 (8 nodes each with 12 cores). Its not clear to me from the log file whether Gromacs is able to utilize all the 92 cores. It seems, it is using only 8 nodes. Does Gromacs use both shared and distributed memory parallelism? 4. In the single-point energy calculation "mdrun -s input.tpr -rerun configuration.pdb", is the configuration.pdb mentioned is the original pdb file used on pdb2gmx with -f option? Or its a modified pdb file? I am asking because if I use the original file that does not work always :-( 5. Is there any known speedup factor of Gromacs on multicores? Thanks for your help. Best Regards, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists