Dear Justin, Thank you for your reply. It is a protein carbohydrate system. Including the solvent, the number of atoms is 43499. I have minimized the system for 200 ps followed by NPT and NVT simulations for 200 ps respectively
Below is the .mdp file. ; VARIOUS PREPROCESSING OPTIONS title = REMD Simulation define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md-vv ; velocity verlet algorithm - tinit = 0 ; dt = 0.002 ; timestep in ps nsteps = 5000000 ; simulation-part = 1 ; Part index is updated automatically on checkpointing comm-mode = Linear ; mode for center of mass motion removal nstcomm = 100 ; number of steps for center of mass motion removal comm-grps = Protein_Carb Water_and_Ions ; group(s) for center of mass motion removal ; ENERGY MINIMIZATION OPTIONS emtol = 10 ; Force tolerance emstep = 0.01 ; initial step-size niter = 20 ; Max number of iterations in relax-shells fcstep = 0 ; Step size (ps^2) for minimization of flexible constraints nstcgsteep = 1000 ; Frequency of steepest descents steps when doing CG nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS nstxout = 50000 ; Writing full precision coordinates every ns nstvout = 50000 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 5000 ; Writing to the log file every step 10ps nstcalcenergy = 100 nstenergy = 5000 ; Writing out energy information every step 10ps nstxtcout = 2500 ; Writing coordinates every 5 ps xtc-precision = 1000 xtc-grps = Protein_Carb Water_and_Ions ; subset of atoms for the .xtc file. energygrps = Protein_Carb Water_and_Ions ; Selection of energy groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; nblist update frequency- ns-type = Grid ; ns algorithm (simple or grid) pbc = xyz ; Periodic boundary conditions: xyz, no, xy periodic-molecules = no rlist = 1.4 ; nblist cut-off rlistlong = -1 ; long-range cut-off for switched potentials ; OPTIONS FOR ELECTROSTATICS coulombtype = PME ; Method for doing electrostatics rcoulomb = 1.4 ; epsilon-r = 1 ; Relative dielectric constant for the medium pme_order = 10; ; OPTIONS FOR VDW vdw-type = Cut-off ; Method for doing Van der Waals rvdw-switch = 0 ; cut-off lengths rvdw = 1.4 ; DispCorr = EnerPres; Apply long range dispersion corrections for Energy and Pressure table-extension = 1 ; Extension of the potential lookup tables beyond the cut-off fourierspacing = 0.08 ; Spacing for the PME/PPPM FFT grid ; GENERALIZED BORN ELECTROSTATICS gb-algorithm = Still ; Algorithm for calculating Born radii nstgbradii = 1 ; Frequency of calculating the Born radii inside rlist rgbradii = 1 ; Cutoff for Born radii calculation gb-epsilon-solvent = 80 ; Dielectric coefficient of the implicit solvent gb-saltconc = 0 ; Salt concentration in M for Generalized Born models ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = -1 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA - default -1 ; Temperature coupling tcoupl = nose-hoover nsttcouple = 10 ; nh-chain-length = 10 tc-grps = Protein_Carb Water_and_Ions ; Groups to couple separately tau-t = 10 10; Time constant (ps)- ref-t = 270.0 270.0; reference temperature (K) ; pressure coupling pcoupl = no ;- ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 270.0 gen-seed = 173529 ; OPTIONS FOR BONDS continuation = yes ; constrain the start configuration constraints = all-bonds constraint-algorithm = lincs ; Type of constraint algorithm- lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Thank you for your help. Nisha On Thu, Jun 30, 2016 at 6:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/30/16 8:46 AM, NISHA Prakash wrote: > >> Dear all, >> >> I have conducted a 10ns REMD simulation for a protein ligand complex with >> the temperature range - 270 to 350 K, however the temperature distribution >> plot of the replicas show that the sampling has occurred at higher >> temperatures as well that is beyond 350K - >> Below is an excerpt from the temperature xvg file >> >> >> @ title "Gromacs Energies" >> @ xaxis label "Time (ps)" >> @ yaxis label "(K)" >> @TYPE xy >> @ view 0.15, 0.15, 0.75, 0.85 >> @ legend on >> @ legend box on >> @ legend loctype view >> @ legend 0.78, 0.8 >> @ legend length 2 >> @ s0 legend "Temperature" >> 0.000000 0.000000 >> 10.000000 350.997864 >> 20.000000 353.618927 >> 30.000000 350.068481 >> 40.000000 353.921753 >> 50.000000 359.485565 >> 60.000000 353.463654 >> 70.000000 352.015778 >> 80.000000 350.657898 >> 90.000000 351.927155 >> 100.000000 354.539429 >> 110.000000 354.287720 >> 120.000000 349.436096 >> 130.000000 352.960541 >> 140.000000 351.631317 >> 150.000000 354.217407 >> 160.000000 350.185852 >> 170.000000 350.294434 >> 180.000000 350.980194 >> 190.000000 350.914429 >> .... >> .... >> 470.000000 349.224060 >> 480.000000 350.819458 >> 490.000000 348.541748 >> 500.000000 350.393127 >> 510.000000 398.775208 >> 520.000000 444.802856 >> 530.000000 470.899323 >> 540.000000 466.652740 >> 550.000000 465.600677 >> 560.000000 469.225555 >> 570.000000 470.548370 >> 580.000000 470.011566 >> 590.000000 470.643951 >> 600.000000 472.433197 >> 610.000000 470.451172 >> 620.000000 469.991699 >> 630.000000 469.073090 >> 640.000000 467.259521 >> 650.000000 464.561798 >> 660.000000 468.416901 >> 670.000000 468.754913 >> 680.000000 469.259613 >> 690.000000 467.641144 >> 700.000000 468.542328 >> >> >> Temperature coupling was done using Nose hoover algorithm. >> >> Does this imply the sampling is wrong or insufficent? >> Any help / suggestion is appreciated. >> >> > How large is your system, and what is it? What were your (full) .mdp > settings? The fact that your temperature started at 0 K and ramped up > suggests that you did not equilibrate prior to the run, did not generate > appropriate velocities, or did not continue properly. The sudden jump in > temperature later suggests instability, and could be due to incorrect > settings. N-H allows for large oscillations, but I wouldn't expect a > stable system to that degree. > > -Justin > > -- > ================================================== > > 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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