The topology file for my system --------- HOD System like that ---
#include "oplsaa.ff/forcefield.itp" ; Include hod topology #include "hod.itp" [ system ] ;Name HOD [ molecules ] ; Compound #mols HOD 102 .mdp file is like that ----- (FOR Energy minimization) ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 0.1 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 200000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none For Equilibritaion (NVT) title = NVT equilibration of W10 RM cpp = /lib/cpp include = -I../top integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 10000 = 20 ns dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.1 ns nstvout = 100 ; save velocities every 0.1 ns nstenergy = 100 ; save energies every 0.1 ns nstlog = 100 ; update log file every 0.1 ns ; Bond parameters continuation = yes ; continuation from previous run constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT optimize_fft = yes ; Temperature coupling is on tcoupl = Berendsen ; modified Berendsen thermostat tc-grps = System ; two coupling groups - more accurate tau_t = 1.0 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution Please take a look . I am getting the error like that ------ 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. If you want I can send you my .itp file also. Tuhin On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/20/16 1:20 PM, Tuhin Samanta wrote: > >> I have done the energy minimization many times by taking previously >> minimized structure. >> >> > A box of water should be basically impossible to break. Either your .mdp > or topology has problems. Since you've provided neither, there's not much > anyone can do to help you. The diagnostic walkthrough that Mark linked is > the best source of figuring it out. Short of that, provide us with your > input topology and .mdp (copied and pasted if small enough for an email, or > linked to a file-sharing service otherwise). > > -Justin > > > >> >> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >> >> Hi, >>> >>> On Wed, 20 Apr 2016 19:04 Tuhin Samanta <samantatuhin1...@gmail.com> >>> wrote: >>> >>> Thank Mark for your suggestion. >>>> >>>> I was trying to resolve the problem -------- >>>> " 4 particles communicated to PME node 4 are more than 2/3 times the >>>> cut-off out of the domain decomposition cell of their charge group in >>>> dimension x. >>>> This usually means that your system is not well equilibrated." >>>> >>>> First of all I have done the energy minimization for long times for >>>> >>> proper >>> >>>> equilibriuation. >>>> >>>> >>> Then what did you change? You may need to be more gentle. >>> >>> Secondly by changing rcut and PME mesh girding I have tried a lot. But >>> it's >>> >>>> showing same error message. >>>> >>>> >>> Those suggestions are made for perhaps improving performance, which is >>> unrelated to your error. They just both happen to use the word PME... >>> >>> So can you please tell me any specific solution for this problem. >>> >>>> >>>> >>> They're all at >>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up >>> >>> Mark >>> >>> Thanking you, >>> >>>> Tuhin >>>> >>>> >>>> On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham <mark.j.abra...@gmail.com >>>> > >>>> wrote: >>>> >>>> Hi, >>>>> >>>>> The information message and the actual error are separated in your log >>>>> >>>> file >>>> >>>>> with a bunch of punctuation because they're logically separate. >>>>> >>>>> Anyway, there should also have been a link to >>>>> http://www.gromacs.org/Documentation/Errors which suggests some >>>>> >>>> strategies >>>> >>>>> for this issue. >>>>> >>>>> Mark >>>>> >>>>> On Wed, 20 Apr 2016 09:00 Tuhin Samanta <samantatuhin1...@gmail.com> >>>>> wrote: >>>>> >>>>> Hello , >>>>>> >>>>>> My system involves water molecules in a box of 5x5x5 nm3. When I was >>>>>> >>>>> doing >>>>> >>>>>> the simulation for energy minimization I got n error message -- >>>>>> >>>>>> The optimal PME mesh load for parallel simulations is below 0.5 >>>>>> and for highly parallel simulations between 0.25 and 0.33, >>>>>> for higher performance, increase the cut-off and the PME grid >>>>>> >>>>> spacing >>> >>>> >>>>>> 4 particles communicated to PME node 4 are more than 2/3 times the >>>>>> >>>>> cut-off >>>>> >>>>>> out of the domain decomposition cell of their charge group in >>>>>> >>>>> dimension >>> >>>> x. >>>>> >>>>>> This usually means that your system is not well equilibrated. >>>>>> >>>>>> I have changed the cut off and grid spacing but still it's showing >>>>>> >>>>> the >>> >>>> error message. I know it is the problem with the parallelization. >>>>>> >>>>> Also >>> >>>> I >>>> >>>>> have gone through the user forum's discussion. So can anyone please >>>>>> suggest me how to get rid of that problem. >>>>>> >>>>>> >>>>>> Thank you so much. >>>>>> Best regards, >>>>>> Tuhin >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>> >>>>> or >>> >>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>> >>>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.