[gmx-users] Problem with running local pressure routine under Gromacs 3.0.2

[George Khelashvili]

Dear users,

I am experimenting with local pressure routine available under Gromacs 
3.0.2. I wanted to use re-run option on already converged trajectory. My 
trajectory has been generated by gromacs 3.2.1 version using lincs as a 
constraint, and in NPT ensemble, with PME.
Now when I tried local pressure, I needed to switch to shake since it 
does not accept lincs, and to cut-off from PME. So I have modified my 
mdp files accordingly. However on the very first step I receive shake 
error "Inner product between old and new vector <= 0.0!". I had no 
problems previously running the same membrane under lincs. I 
experimented with reducing the time-step from 2fs to 1fs and even down 
to 0.5fs but it does not make a difference.
I would appreciate if somebody can suggest what can be the reason for 
the error. Below I attach my mdp file:

title               =  membrane simulation
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
constraint_algorithm = SHAKE
shake_tol           = 0.0001
unconstrained-start=no
integrator          =  md
dt                  =  0.002
tinit               = 0.0
nsteps              = 6000
nstcomm             =  100
nstxout             =  1000
nstvout             =  1000
nstxtcout = 0
xtc_precision = 1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  5
ns_type             =  grid
coulombtype         = cut-off
rlist               =  1.0
rcoulomb            =  1.8
rvdw                =  1.8
userreal1           =  0.1
fourierspacing = 0.15
pme_order = 6
ewald_rtol = 1.E-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
;Tcoupl              =  berendsen
Tcoupl              =  nose-hoover
tc-grps             =  DMPC     SOL
tau_t               =  0.2      0.2
ref_t               =  308.0    308.0
; Energy monitoring
energygrps          =  DMPC SOL
; Isotropic pressure coupling is now on
;Pcoupl              =  berendsen
Pcoupl              =  Parrinello-Rahman
Pcoupltype          =  semiisotropic
tau_p               =  1.0 1.0
compressibility     =  4.5e-5 4.5e-5
ref_p               =  1.01325 1.01325
; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  308.0
gen_seed            =  712349
pbc = xyz

Thank you in advance,

George

-- 
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
gek2009 at med.cornell.edu
Phone: 1-212-746-6539
Fax:   1-212-746-6226