Yes, some letters were transferred by mistakes to email. Yes, I am using charmm36. Also the rvdw_switch was correct the same as you wrote 1.0 in last email.
Now, I am wondering what the solution is in such cases of facing such an error? Would you please let me know your suggestions? Many thanks for your replies. Sincerely, Shima ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, April 7, 2013 4:46 PM Subject: Re: [gmx-users] unstable system 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) 231-9080 http://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
