[gmx-users] lipid bilayer equilibriation data

[Rama Gullapalli]

Dear GMX ers,
I had mentioned earlier regarding the equilibriation
problems i was having in terms of the areas. Now i
have been having some more problems of a different
nature. I have run the equilibriation times of a
bilayer in excess of 10 nanoseconds, but my target
tempreature of 323 K has not been attained. Here are
the data for some of the values i have obtained over
the simulation.

Statistics over 2430001 steps [ 5140.0000 thru
10000.0000 ps ], 6 data sets
 
Energy           Average       RMSD      Fluct.   
Drift       Tot-Drift
-------------------------------------------------------------------------------
Temperature      328.596          0          0
6.21023e-06  0.0301817

Pressure (bar)   1.46466    156.762     155.78
-0.0124904   -60.7036

Box-X           5.74551          0          0
-1.70947e-05 -0.083080
3

Box-Y           5.95302          0          0
1.39209e-05  0.0676556
Box-Z  
                8.42456          0          0
2.33379e-06  0.0113422

Density (SI)    1007.46          0          0
0.000367551     1.7863

Heat Capacity Cv:      12.4718 J/mol K (factor = 0)

As you can see, the target tempreature has not been
attained, the areas are completely off, the pressure
is fluctuating quite a bit. I was wondering if you
could give me any insights into this?

I am also attaching the .mdp file of the parameters
which i used for the simulation. I have used NPT
coupling of an anisotropic box. The parameters which i
have used are the from the ffgmx and Dr Tieleman s
website, lipid.itp and dppc.itp.  I sincerely would
appreciate any comments the lipid people would have on
this. Also, i don't understand the RMSD for quite a
few of the quantities is zero, does this mean it is
equilbriated?
Thank you very much for your time.
Sincerely
Regards
Rama

FULL.MDP FILE

;       User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
title               =  Yo
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000000  ; total 10 ps.
nstcomm             =  1
nstxout             =  10000
nstvout             =  10000
nstfout             =  0
nstlog              =  10000
nstenergy           =  10000
nstlist             =  10
ns_type             =  grid
dispcorr            =  enerpres
coulombtype         =  cut-off
rlist               =  1.0
rcoulomb            =  1.4
vdwtype             =  cut-off
rvdw                =  1.8
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  DPPC SOL
tau_t               =  0.1  0.1
ref_t               =  323  323
; Energy monitoring
energygrps          =  DPPC  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          =  anisotropic
tau_p               =  5.0 5.0 5.0 0 0 0
compressibility     =  4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p               =  1.0 1.0 1.0 0 0 0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


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