Hi gmx-users, I added simulation box by *editconf below mentioned to POPC system downloaded from Tieleman's website, I don't want to add water 1) *editconf -f popc.gro -o popc_box.gro -box 6 6 9 -c this one I followed based on gmx-archives. 2) Then in 2ndcase I used same command but 8 8 8(cubic) instead of 1st case numerical values . After this I did *EM system is fine for both cases when visualise in VMD. when I do *PR I am getting problem in second way of using *editconf rather than first way. I got fine structure in first case (without distortions in water and membrane). In 2nd case displacement of water ( totally there is no cubic structure at all ). Now my doubt is shall I use 1 case output file for my further simulations? or any mistake in my command or pr.mdp file ? while I am using it runs fine. Is it mandatory to add cubic box?
Pls help me I am posting my pr.mdp file(similar parameter for both cases) title = popc restrained define = -DPOSRES_LIPID constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 50 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 pbc = xyz ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = POPC SOL tau_t = 0.1 0.1 ref_t = 323 323 ; Anisotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = anisotropic tau_p = 1.0 1.0 1.0 1.0 1.0 1.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 ; Energy monitoring energygrps = POPC SOL ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 323.0 gen_seed = 173529 ~ Thanks in advance.
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
