[gmx-users] temperature problem

[Mark Abraham]

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
>
>
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