On Sun, Apr 7, 2013 at 1:58 PM, Shima Arasteh <shima_arasteh2...@yahoo.com>wrote:
> 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. > > I would suggest you take great care to provide accurate information, especially when it is requested of you. I thought I had identified a mistake that would have lead to instability. It turns out that you posted something fictitious and it feels a bit like I wasted my time. If you want free help, make it easy for those who want to help you to do so. > Now, I am wondering what the solution is in such cases of facing such an > error? Would you please let me know your suggestions? > > I see no reason why a system that was previously stable for 10 ns to suddenly become unstable. Monitor energy terms very closely, and try reducing the time step to 1 fs for a period of time. -Justin > 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======================================== > -- ======================================== 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