[gmx-users] regarding NVT
priya.thiyagarajan09 at gmail.com
Sat Jan 7 08:53:58 CET 2012
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)
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
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)
coulombtype = PME ; Particle Mesh Ewald for long-range
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
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..
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