On 6/18/13 10:12 PM, Neha wrote:
Hi,
Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.
Please post a full .mdp file; partial .mdp files are rarely useful.
-Justin
Justin Lemkul wrote
On 6/18/13 3:13 PM, Neha wrote:
Hi everybody!
I am trying to simulate a lipid membrane at zero pressure and at a range
of
temperatures. I am using a bilayer from the Martini website. I was having
a
problem with the Parinello-Rahman barostat so I switched to Berendsen and
am
also keeping the height of the box constant otherwise it grows
uncontrollably. However my runs keep crashing, giving the error of atoms
having moved too far beyond the cut-off distance. I have attached part of
my
mdp file, and would love any suggestions as to how to alter it to get
more
fruitful runs. I am still really new to Gromacs and want to make sure I
am
not doing something completely wrong.
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 325 325
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0 1.0
compressibility = 5e-6 0.0
ref_p = 0.0 0.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 325
gen_seed = 473529
Please let me know!
What happens if you set ref_p to 1.0? I don't understand the use of zero
pressure; your system is expanding out into a vacuum and that's likely why
the
z-dimension is expanding uncontrollably. Water diffuses faster than the
lipids,
so the z-dimension expands faster than x-y does.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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