On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh <shima_arasteh2...@yahoo.com>wrote:
> Hi all, > > I have a system of peptide/POPC/water/ions. The energy minimization and > NVT steps has passed successfully. I ran NPT step for around 10 ns with > restraints of protein and P atoms at first nano seconds and then removing > them gradually. > I tried to go on MDRUN. I did not remove restraint of protein atoms > completely and they are still restrained. When I run the mdrun command, I > get error of "X particles communicated to PME node Y are more than a cell > length out of the domain decomposition cell of their charge group" . > I know this error means an unstable system. When I visualized the written > pdb files, I see some popc hydrogen atoms are broken and located between > two leaflets which are separated by a gap. The protein seems ok, however I > don't get many pdb files to see. > > > As what I see in Diagnosing unstable system web page, > 1. it would be beneficial if one see what part of the system is unstable > in first steps. As I saw, the unstable "POPC hydrogen atoms" are not fine. > 2. The single molecules are supposed to examine in water or vacuum too. I > have passed this step successfully. > 3. I have not ignored any warning during the last steps. > 4. And my mdp files to run md is as follow: > > integrator = md > dt = 0.002 > nsteps = 5000000 > > > ns_type = grid > nstlist = 5 > rlist = 1.2 > rlistlong = 1.4 > rcoulomb = 1.2 > rvdw = 1.2 > pbc = xyz > vdwtype = switch > rvdw_switch = 0.1 > What force field are you using? CHARMM? In any case, the value of rvdw_switch does not make any sense. If you're using CHARMM, it should be 1.0. > ; Parameters for treating bonded interactions > continuation = yes > constraint_algorithm = LINCS NCS / SHAKE) > constraints = all-bonds ) > lincs_iter = 1 > lincs_order = 4 > > ; Parameters for treating electrostatic interactions > coulombtype = PME ; Long range electrostatic interactions > treatment (cut-off, Ewald, PME) > pme_order = 4 ; Interpolation order for PME (cubic interpolation > is represented by 4) > fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using > PME (nm) > > ; Temperature coupling parameters > tcoupl = Nose-Hoover > tc-grps = Protein_POPC Water_and_ions ; Define groups to be > coupled separately to temperature bath > tau_t = 0.5 0.5 ; Group-wise coupling time constant > (ps) > ref_t = 310 310 ; Group-wise reference temperature (K) > > ; Pressure coupling parameters > pcoupl = Parrinello-Rahman > pcoupltype = semiisotropic > tau_p = 2.0 > ref_p = 1.01325 1.01325 > compressibility = 4.5e-5 4.5e-5 > > ; Miscellaneous control parameters > ; Dispersion correction > DispCorr = EnerPres > ; Initial Velocity Generation > gen_vel = no > ; Centre of mass (COM) motion removal relative to the specified groups > nstcomm = 1 y (steps) > comm_mode = Linear > comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the > specified groups > > Would you please let me know if these happen due to an improper > equilibration? Do I need to extend the NPT step? Would that fix it? > > Aside from the above comment, there is nothing particularly wrong about the .mdp file aside from some odd characters here and there, which I will assume are nothing more than quirks of transferring to an email, as they otherwise would have triggered fatal errors in grompp. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
