[gmx-users] regarding NVT equilibration

[Justin A. Lemkul]

priya thiyagarajan wrote:
> 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)
> 
> 

Your .mdp file does not even specify any temperature coupling information, so 
you're not doing NVT.  I'd suggest you refer to some tutorial material to 
understand how to carry out such processes.

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

No.  It is never a good idea to blindly push forward when you get a result you 
know to be invalid.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================