[gmx-users] Fwd: About g_energy analysis

[rama david]

---------- Forwarded message ----------
From: rama david <ramadavidgroup at gmail.com>
Date: Fri, Mar 30, 2012 at 8:31 PM
Subject: About g_energy analysis
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


Hi Gromacs users ,

I have 4 molecule in system, I am study how are they interacting ,
I did NPT,  equilibration , for 1 ns with following MDP file..

title        = gromacs
define        = -DPOSRES    ; position restrain the protein
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 500000        ; 2 * 50000 = 100 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    = yes        ; Restarting after NVT
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        = 0.9        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 0.9        ; short-range electrostatic cutoff (in nm)
vdw-type        = Cut-off
rvdw        = 1.4        ; 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        = V-rescale    ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more
accurate
tau_t        = 0.1    0.1    ; time constant, in ps
ref_t        = 310     310    ; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
pcoupltype    = isotropic    ; uniform scaling of box vectors
tau_p        = 2.0        ; time constant, in ps
ref_p        = 1.0        ; reference pressure, in bar
compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = no        ; Velocity generation is off


 I used G96 53a6 force field , with spc water model

So I check system equilibriation I check press with g_energy
avg press = 1.17   avg density = 985.588

Is system is equilibrated ??
And what other parameter are imp to check ???

I am new in these field so please all suggestion are welcome ..


Thank you in advance ...
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120330/98d2ef2e/attachment.html>