Dear GROMCS user,
I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on my
local desktop (2*GTX 670 + i7) and everything works as smooth as
possible. The outcomes are very reasonable and match the outcome of the
4.5.5 version without GPU acceleration. On our cluster (M2090+2*Xeon
X5650) I installed the VERSION 4.6-dev-20121120-0290409. Using the same
.tpr file used for runs with my desktop I get lincs warnings that the
watermolecules can't be settled.
My .mdp file looks like:
;
title = ttt
cpp = /lib/cpp
include = -I../top
constraints = hbonds
integrator = md
cutoff-scheme = verlet
;define = -DPOSRES ; for possition restraints
dt = 0.002 ; ps !
nsteps = 100000000 \
nstcomm = 25 ; frequency for center of mass
motion removal
nstcalcenergy = 25
nstxout = 100000 ; frequency for writting the
trajectory
nstvout = 100000 ; frequency for writting the
velocity
nstfout = 100000 ; frequency to write forces to
output trajectory
nstlog = 10000 ; frequency to write the log file
nstenergy = 10000 ; frequency to write energies to
energy file
nstxtcout = 10000
xtc_grps = System
nstlist = 25 ; Frequency to update the neighbor list
ns_type = grid ; Make a grid in the box and only
check atoms in neighboring grid cells when constructing a new neighbor
rlist = 1.4 ; cut-off distance for the
short-range neighbor list
coulombtype = PME ; Fast Particle-Mesh Ewald
electrostatics
rcoulomb = 1.4 ; cut-off distance for the coulomb
field
vdwtype = cut-off
rvdw = 1.4 ; cut-off distance for the vdw field
fourierspacing = 0.12 ; The maximum grid spacing for
the FFT grid
pme_order = 6 ; Interpolation order for PME
optimize_fft = yes
pbc = xyz
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
energygrps = Protein Non-Protein
Pcoupl = no;berendsen
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0
nstpcouple = 5
refcoord_scaling = all
Pcoupltype = isotropic
gen_vel = no;yes
gen_temp = 300
gen_seed = -1
Thanks a lot
Sebastian
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