Quoting sudheer babu <[EMAIL PROTECTED]>: > 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?
I don't see what you're aiming to do. Using an 8-nm cubic box around a roughly 6-nm cubic system will essentially place the bilayer system in the middle of a vacuum. Undoubtedly the water is going to expand into the void. If you were to remove the position restraints from the lipids, I suspect they would move erratically as well. The 6 x 6 x 9 system will also have some vacuum above and below the bilayer system, and water will likely expand into those regions as well, given enough time. -Justin > > 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. > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
