[gmx-users] temperature problem

[Lovika Moudgil]

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.abraham at 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.kroon at 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-request at 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-request at gromacs.org.
>