Deal all, I am trying to build up my alkane system to calculate the surface tension a fixed pressure. Here are the steps:
1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v However, I am not clear about the setting of pressure coupling and compressibility. I guess I need to use 0 compressibility in Z with isotropic option? Please advise me on the settings and details of these calculations. I am going to compare the surface tension and density profiles at several different pressures. Thank you in advance :) Below is the md.mdp contents: pbc = xyz integrator = md dt = 0.001 nsteps = 20000000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100;1 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = Shift vdw-type = Shift rcoulomb-switch = 1 rvdw-switch = 1 ;0.9 ; Cut-offs rlist = 1.35 rcoulomb = 1.1 ;1.1 rvdw = 1.1 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 425 * * *Pcoupl = berendsen* *Pcoupltype = isotropic * *tau_p = 1 0.5 * *compressibility = 3.5e-5 3.5e-5 0* *ref_p = 50 10** * gen_vel = no gen_temp = 500.0 gen_seed = 173529 constraints = none constraint-algorithm = lincs -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists