Hi Justin... Yes I agree my system is behaving absurdly . But I am wondering why !!I have done minimization without any error ..here is the result ... Steepest Descents converged to Fmax < 1000 in 1004 steps Potential Energy = -9.6667906e+05 Maximum force = 9.7920349e+02 on atom 796 Norm of force = 1.7943926e+01 ... I have One gold slab ...with golp parameters ..and amino acid on it ...in box with water and Na , Cl ions ....Freezing is for gold only.... System is not that big . And thing is temperature remain at the value (that is 300K) for few time after some time it start behaving weird . If system is wrong why its working even for one step ??
Thanks and Regards Lovika On Thu, Jun 4, 2015 at 6:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/4/15 8:52 AM, Lovika Moudgil wrote: > >> Hiii....Here is my .mdp file below ... >> >> title = OPLS Lysozyme NVT equilibration >> define = -DPOSRES ; position restrain the protein >> ; Run parameters >> integrator = md ; leap-frog integrator >> nsteps = 2000000 ; 2 * 50000 = 100 ps >> dt = 0.001 ; 2 fs >> ; Output control >> nstxout = 500 ; save coordinates every 1.0 ps >> nstvout = 500 ; save velocities every 1.0 ps >> nstenergy = 500 ; save energies every 1.0 ps >> nstlog = 500 ; update log file every 1.0 ps >> nstxtcout = 500 ; [steps] freq to write >> coordinates >> to xtc trajectory >> xtc_precision = 1000 ; [real] precision to write xtc >> trajectory >> comm_mode = Linear >> comm_grps = Protein Non-Protein ; group(s) for center of >> mass motion removal >> ; Bond parameters >> constraint_algorithm = lincs ; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy >> atom-H bonds) constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> ; 7.3.9 Neighbor Searching >> cutoff-scheme = Verlet >> nstlist = 10 ; [steps] freq to update neighbor >> list >> ns_type = grid ; method of updating neighbor list >> pbc = xyz ; periodic boundary conditions in >> all directions >> rlist = 1.0 ; [nm] cut-off distance for the >> short-range neighbor list >> >> ; 7.3.10 Electrostatics >> coulombtype = PME ; Particle-Mesh Ewald >> electrostatics >> rcoulomb = 1.0 ; [nm] distance for Coulomb >> cut-off >> >> ; 7.3.11 VdW >> rvdw = 1.0 ; [nm] distance for LJ cut-off >> DispCorr = Ener ; apply long range dispersion >> corrections >> >> ; 7.3.13 Ewald >> fourierspacing = 0.12 ; [nm] grid spacing for FFT grid >> when using PME >> pme_order = 4 ; interpolation order for PME, 4 = >> cubic >> ewald_rtol = 1e-5 ; relative strength of >> Ewald-shifted potential at rcoulomb >> ; Temperature coupling is on >> tcoupl = nose-hoover ; modified Berendsen thermostat >> tc-grps = Protein Non-Protein >> tau_t = 0.1 0.1 ; time constant, in ps >> ref_t = 300 300 ; reference temperature, one for each >> group, in K >> ; Pressure coupling is off >> pcoupl = no ; no pressure coupling in NVT >> ; Velocity generation >> gen_vel = yes ; assign velocities from Maxwell distribution >> gen_temp = 300 ; temperature for Maxwell distribution >> gen_seed = -1 ; generate a random seed >> >> ; To keep au surface in place, freeze Au atoms. >> ; The AU group has been defined via make_ndx >> ; to contains all the AU atoms ('a AU'). >> freezegrps = AUS AUB AUI >> freezedim = Y Y Y Y Y Y Y Y Y >> >> >> And in one part of log file.... temperature is getting high..without >> error >> ....and it keeps on increasing ... >> >> Energies (kJ/mol) >> Angle Proper Dih. Ryckaert-Bell. LJ-14 >> Coulomb-14 >> 2.91339e+01 3.23884e-01 8.52437e+00 1.65299e+01 >> 2.68992e+02 >> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. >> Potential >> 5.70551e+05 -6.29186e+03 -8.96225e+05 4.42542e+03 >> -3.27216e+05 >> Kinetic En. Total Energy Conserved En. *Temperature* Pres. DC >> (bar) >> 9.71936e+09 9.71903e+09 2.71970e+19 * 2.35145e+07* >> 0.00000e+00 >> > > Ask yourself whether or not this is even reasonable. A temperature of > 10^7? That's 4000x hotter than the surface of the sun. There's no way > that's real. Your system is physically nonsensical. You'll have to > describe in complete detail what it is you're trying to do, but the > combination of multiple comm-grps, freezing (which is a pretty massive > perturbation in and of itself), restraints, etc. is quite complex and any > number of things could be causing a problem. It could be something as > simple as insufficient minimization and/or bad starting coordinates in > general, but it's a shot in the dark at this point. > > -Justin > > > Pressure (bar) Constr. rmsd >> >> Thanks and Regards >> Lovika >> >> On Thu, Jun 4, 2015 at 5:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 6/4/15 12:39 AM, Lovika Moudgil wrote: >>> >>> Hi...Justin.... Thanks for explaining ...... I just want to ask could >>>> there be any other reasons too?? ...Because I have tried it with PME >>>> too...and still I am not getting desired temperature .... >>>> >>>> >>>> You'll have to provide a full .mdp file and quantitative evidence of >>> what >>> you're seeing. There are plenty of things that could be going on, but >>> I'm >>> not going just blindly guess. >>> >>> >>> -Justin >>> >>> >>> >>>> Thanks and Regards >>>> Lovika >>>> >>>> >>>> On Wed, Jun 3, 2015 at 5:29 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>>> On 6/3/15 3:46 AM, Lovika Moudgil wrote: >>>>> >>>>> Hi...thanks for reply Peter and Mark ....I tried with temperature >>>>> >>>>>> coupling >>>>>> . But things are still same ... >>>>>> >>>>>> Hi ... Mark would you like to explain this factor to me ?? >>>>>> >>>>>> >>>>>> Using a plain cutoff in the condensed phase is outdated methodology >>>>>> >>>>> that >>>>> is very inaccurate. Cutoff artifacts lead to accumulation of heat in >>>>> the >>>>> system. Use something sensible like PME. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> Thanks and Regards >>>>> >>>>> Lovika >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham < >>>>>> mark.j.abra...@gmail.com> >>>>>> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> >>>>>>> Runaway heating is the only useful feature of cutoff electrostatics. >>>>>>> Use >>>>>>> an >>>>>>> actual model physics. >>>>>>> >>>>>>> Mark >>>>>>> >>>>>>> On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon <p.c.kr...@rug.nl> >>>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 02/06/15 09:43, Lovika Moudgil wrote: >>>>>>>> >>>>>>>> Hi everyone >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I am having some problem in my md run .In my system temperature of >>>>>>>>> >>>>>>>>> system >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> is abruptly increasing .I have done nvt for 50 picoseconds ..nd >>>>>>> then >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> using >>>>>>>>> >>>>>>>> >>>>>>>> it for further md simulation .I am not getting any error for this >>>>>>>> >>>>>>>>> temperature increase .....But when I plot temperature graph , >>>>>>>>> >>>>>>>>> temperature >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> is not same as nvt and is very high in md .I am having gold slab >>>>>>> and >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> amino >>>>>>>>> >>>>>>>> >>>>>>>> acid in my system . Mdp file for md run is below ....Is their any >>>>>>>> >>>>>>>>> error >>>>>>>>> >>>>>>>>> in >>>>>>>>> >>>>>>>> >>>>>>>> my mdp file ???what could be the reason for this ???Please suggest >>>>>>>> >>>>>>>>> .... >>>>>>>>> ; Run parameters >>>>>>>>> integrator = md ; leap-frog integrator >>>>>>>>> nsteps = 30000000 ; 2 * 50000 = 100 ps >>>>>>>>> dt = 0.001 ; 2 fs >>>>>>>>> ; Output control >>>>>>>>> ; Output control >>>>>>>>> nstxout = 500 ; save coordinates every 1.0 ps >>>>>>>>> nstvout = 500 ; save velocities every 1.0 ps >>>>>>>>> nstenergy = 500 ; save energies every 1.0 ps >>>>>>>>> nstlog = 500 ; update log file every 1.0 ps >>>>>>>>> nstxtcout = 500 ; [steps] freq to write >>>>>>>>> >>>>>>>>> coordinates >>>>>>>>> >>>>>>>> >>>>>>>> to xtc trajectory >>>>>>>> >>>>>>>>> xtc_precision = 1000 ; [real] precision to write >>>>>>>>> xtc >>>>>>>>> trajectory >>>>>>>>> xtc_grps = System ; group(s) to write to xtc >>>>>>>>> trajectory >>>>>>>>> energygrps = System ; group(s) to write to >>>>>>>>> energy >>>>>>>>> >>>>>>>>> file >>>>>>>>> >>>>>>>> >>>>>>>> ; Bond parameters >>>>>>>> >>>>>>>>> >>>>>>>>> constraint_algorithm = lincs ; holonomic constraints >>>>>>>>> constraints = all-bonds ; all bonds (even >>>>>>>>> heavy >>>>>>>>> atom-H bonds) constrained >>>>>>>>> lincs_iter = 1 ; accuracy of LINCS >>>>>>>>> lincs_order = 4 ; also related to >>>>>>>>> accuracy >>>>>>>>> ; Neighborsearching >>>>>>>>> cutoff-scheme = Verlet >>>>>>>>> ns_type = grid ; search neighboring grid cells >>>>>>>>> nstlist = 10 ; 20 fs, largely irrelevant with >>>>>>>>> Verlet >>>>>>>>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in >>>>>>>>> nm) >>>>>>>>> rvdw = 1.0 ; short-range van der Waals cutoff (in >>>>>>>>> nm) >>>>>>>>> >>>>>>>>> ; Electrostatics >>>>>>>>> coulombtype = cut-off >>>>>>>>> pme_order = 4 ; cubic interpolation >>>>>>>>> fourierspacing = 0.12 ; grid spacing for FFT >>>>>>>>> ; Temperature coupling is on >>>>>>>>> tcoupl = nose-hoover ; modified Berendsen >>>>>>>>> >>>>>>>>> thermostat >>>>>>>>> >>>>>>>> >>>>>>>> tc-grps = Protein AUS AUB AUI SOL NA CL ; two coupling >>>>>>>> >>>>>>>>> >>>>>>>>> groups - >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> more accurate >>>>>>> >>>>>>>> >>>>>>>> tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time >>>>>>>>> constant, >>>>>>>>> >>>>>>>>> in ps >>>>>>>>> >>>>>>>> >>>>>>>> ref_t = 300 300 300 300 300 300 300 ; reference >>>>>>>> >>>>>>>>> temperature, one for each group, in K >>>>>>>>> >>>>>>>>> You have too many temperature coupling groups. (What Not To Do on >>>>>>>>> >>>>>>>> http://www.gromacs.org/Documentation/Terminology/Thermostats) >>>>>>>> I'd stick to one for proteins, and one for the rest. >>>>>>>> >>>>>>>> ; 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 >>>>>>>>> ; Velocity generation >>>>>>>>> gen_vel = yes ; assign velocities from Maxwell >>>>>>>>> >>>>>>>>> distribution >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> gen_temp = 300 ; temperature for Maxwell distribution >>>>>>> >>>>>>>> >>>>>>>> gen_seed = -1 ; generate a random seed >>>>>>>>> >>>>>>>>> ; To keep au surface in place, freeze Au atoms. >>>>>>>>> ; The AU group has been defined via make_ndx >>>>>>>>> ; to contains all the AU atoms ('a AU'). >>>>>>>>> freezegrps = AUS AUB AUI >>>>>>>>> freezedim = Y Y Y Y Y Y Y Y Y >>>>>>>>> comm_mode = None >>>>>>>>> >>>>>>>>> Thanks and Reagrds >>>>>>>>> Lovika >>>>>>>>> >>>>>>>>> >>>>>>>>> Peter >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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. >>> >>> > -- > ================================================== > > 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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