[gmx-users] v-rescale and conserved energy

[Mikhail Stukan]

Dear gromacs users,

I am running NVT simulations for polarizable (shell particle) water model  (GROMACS version 4.5.1 and 4.5.3 (issue is same in both)) using v-rescale thermostat.
While temperature, potential, kinetic and total energies behave quite well I am failing to obtain constant values for Conserved-Energy. It drifts quite significantly: 1000 kJ/mol/ns with average value 32500 kJ/mol.
I have  noticed that this issue has been already addressed:

http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html

So I tried to switch from  md (leap-frog)  to md-vv integrator, but then temperature went up enormously

According to
http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.html
this issue seems also be know , but I have not found if it  was fixed in 4.5.x version?

Am I doing something obviously wrong? And should Conserved-Energy drift be a real problem if the purpose of the simulation is calculation of the surface tension?

My .mdp file is shown below.

Thank you very much in advance.
Mikhail

===============================
integrator          =  md or md-vv
dt                  =  0.001            ; time step
nsteps              =  20000000                 ; number of steps
comm_mode           =  Linear;Angular           ; Remove center of mass translation and rotation
nstcomm             =  1003                     ; reset c.o.m. motion
nstxout             =  10000            ; write coords
nstvout             =  10000                  ; write velocities
nstxtcout           =  1000                  ; write coords to xtc-trajectory file
nstlog              =  1000                     ; print to logfile
nstlist             =  20                       ; update pairlist
ns_type             =  grid ;simple             ; pairlist method
;================== Polarizable model parameters =======================
emtol               =  0.001              ;the convergency criterion for maximum force
niter               =  50                ;maximum number of iterations for the shell particle optimization
;=================  SHAKE/SETTLE Specification  ===============================
shake_tol            = 0.00001
;=================  Cutt off specification =============================
pbc                 = xyz               ; periodic boundary conditions
optimize_fft        =  yes                      ; perform FFT optimization at start
coulombtype         =  PME
ewald_geometry      =  3dc
rcoulomb            =  1.5 ;1.5                 ; cut-off for coulomb
rlist               =  1.5 ;1.5                 ; cut-off for ns
vdw-type            =  cut-off
rvdw                =  1.5 ;1.5                 ; cut-off for vdw
dispcorr            =  EnerPres
;=======================================================================
Tcoupl              =  v-rescale ;        ; temperature coupling
tc-grps             =  System
ref_t               =  298.15
tau_t               =  0.1
Pcoupl              =  no
;=======================================================================
gen_vel             =  no                       ; generate initial velocities
gen_temp            =  300                      ; initial temperature
gen_seed            =  -1                       ; random seed

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



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