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 ?? 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. > -- 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.