On 2011-04-30 14.17, Zoe Hall wrote:
Gmx-users,
I am trying to carry out a simulation of lysozyme in vacuo using the
OPLS-AA forcefield. After energy minimisation, the protein is run for
10ps with position restraints and temperature coupling on. This is
followed by the full production run of 10ns with temperature and
pressure coupling turned off, H bonds are constrained using LINCS and a
time step of 1fs. For vacuum conditions, the periodic boundary
conditions are turned off, and no cut-offs are used. When I carry out
the 10ns simulation the total energy gradually increases, as does the
temperature from 300 to 500K. I presume this is because the temperature
coupling is turned off, however that is what I have noted from the
literature that others do for their vacuum simulations. Can anyone shed
any light on this? Following is my method.
integrator = md
tinit = 0
dt = 0.001
nsteps = 10000000
nstxout = 20000
nstvout = 20000
nstfout = 0
nstlog = 100000
nstenergy = 100000
nstxtcout = 20000
energygrps = Protein
nstcomm = 5
nstlist = 0
ns-type = simple
pbc = no
rlist = 0
coulombtype = Cut-off
rcoulomb = 0
epsilon_r = 2
vdw-type = Cut-off
rvdw =0
Tcoupl = no
tc-grps = Protein
tau_t = 0.1
ref_t = 300
Pcoupl = no
Pcoupltype = Isotropic
tau_p = 1
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes ;
gen_temp = 300.0
gen_seed = -1
constraints = hbonds
constraint-algorithm = LINCS
lincs_order = 4
Thanks,
Zoe
Zoe Hall
Department of Chemistry
Oxford University
_zoe.h...@chem.ox.ac.uk_
Are you sure h-bonds are being constrained, because otherwise the time
step is too large? (maybe you need to write h-bonds). You may need to
increase the constraint accuracy as well. We did all our vacuum calcs in
double precision as well IIRC.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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