please check it....... [ moleculetype ] ; molname nrexcl HOD 3
[ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_116 1 HOD OW 1 -0.8476 2 opls_117 1 HOD HW 1 0.4238 3 opls_805 1 HOD DW 1 0.4238 #ifndef FLEXIBLE ; [ settles ] ; OW funct doh dhh ; 1 0.101 0.16500 ;[ exclusions ] ;1 2 3 ;2 1 3 ;3 1 2 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.102 266292 0.102 266292 [ angles ] ; i j k funct angle force.c. 2 1 3 1 105.7 583 105.7 583 Thanks, Tuhin On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/21/16 3:32 AM, Tuhin Samanta wrote: > >> 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. >> >> > Yes, that's actually rather important; the .top itself just #includes the > .itp and therefore contains no useful information. > > -Justin > > > 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. >>> >>> > -- > ================================================== > > 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? 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