[gmx-users] regarding NVT equilibration

[priya thiyagarajan]

hello sir,
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)
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)



Is it correct if i proceed with that wrong temperature file..

Thanking you,
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