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 ; 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? Thanks in advance. I appreciate your suggestions. Sincerely, Shima -- 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
