[gmx-users] regarding NVT equilibration
priya.thiyagarajan09 at gmail.com
Fri Jan 6 10:48:36 CET 2012
i am following lysozyme tutorial for my dynamics.
when i go for equilibration first we need to do NVT. there i set 300K ...
At the end of NVT when i check my temperature using my edr file i am not
getting equilbrium temp..
it showed 239K one time and sometime 329K like this..but not around 300K..
then when i changed my time (by changing number of steps)also i am not
getting equilibrium temp.
how can i attain equilibrium..
pls help me with your answer..
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)
Is it correct if i proceed with that wrong temperature file..
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users