[gmx-users] temperature problem

[Peter Kroon]

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