Well, 20-30 fs is fine with Martini. But you may have to take care
initially, and start with a smaller time step.
Cheers,
Tsjerk
On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
@Justin,
Fmax=8.0226669e+00
OK, that looks good.
the system includes protein, lipid, water, ion Cl-
em.mdp file is
integrator = steep
tinit = 0.0
dt = 0.02
nsteps = 50000
nstcomm = 1
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = no
pcoupl = no
gen_vel = no
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
equi.mdp file is
integrator = md
tinit = 0.0
dt = 0.03
Does a smaller time step work? I know the whole point of a MARTINI
simulation is to use a 20-40 fs time step, but in my (very very limited)
experience, nothing over 20 fs is consistently stable. Perhaps others
with
better experience can offer pointers.
-Justin
nsteps = 3000000
nstcomm = 1
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps =
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein DSPC Ion_W
tau_t = 1.5 1.5 1.5
ref_t = 310 310 310
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 3.0 3.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
Thanks so much for any help !
Regards,
KT
On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
Thank Tsjerk so much !
But after being minimized 50000 steps and equilibrated 90 ns, there
are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does
not
achieve balance.
Should i carry out more many steps for minimization ? or minimize
many
times ? to get more equilibrated system.
I would say that 50000 steps of minimization is far more than is
normally
necessary. What Fmax do you achieve at the end of EM? What is in the
system? What is in your .mdp file? Systems can randomly crash if the
model
physics breaks due to incorrect .mdp settings or an unstable topology.
-Justin
On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <
tsje...@gmail.com
wrote:
Hi KT,
This is caused by another problem. Your system blew up. Check
messages
before this one, and check the log for LINCS warnings.
Cheers,
Tsjerk
On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <
kieuthu2...@gmail.com
wrote:
Dear All,
My MD simulation has an error
Warning: Only triclinic boxes with the first vector parallel to the
x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
I searched on Gromacs-errors web, but i did not see this error.
How can i fix it ?
Thanks and regards,
KT
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