[gmx-users] regarding NVT

[Tsjerk Wassenaar]

Hi Priya,

Does it help if you set

tcoupl = v-rescale

Please read the manual, follow a tutorial properly, and think about what
you're doing and what you get out.

Cheers,

Tsjerk

On Jan 7, 2012 8:54 AM, "priya thiyagarajan" <priya.thiyagarajan09 at gmail.com>
wrote:

hello sir,

i followed lysozyme tutorial to do dynamics for my protein..

but at the end of NVT equilibration, my temperature is  at 243K.. but i set
300K to my mdp file ..

mine is not getting equilibrium condition..

 this is my nvt.mdp file


title           =GROMOS43a1 lipopeptide NVT equilibration
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 100000                ; 2 * 100000 = 200 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 100           ; save coordinates every 0.2 ps
nstvout         = 100           ; save velocities every 0.2 ps
nstenergy       = 100           ; save energies every 0.2 ps
nstlog          = 100           ; update log file every 0.2 ps
; Bond parameters
continuation    = no            ; first dynamics run
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
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = No    ; modified Berendsen thermostat
tc-grps         = DRG   SOL     ; two coupling groups - more accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 300   300     ; reference temperature, one for each
group, in K
; 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
gen_vel         = yes           ; assign velocities from Maxwell
distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed


may i know what is the reason..

initially i did nvt for 100ps but i didnt get equil temperature.
then i increased my time to 200ps.. still i am not getting..




help me with your answer..

Thanking you,
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