On 1/28/13 2:45 AM, James Starlight wrote:
Dear Gromacs Users!
I'm simulating membrane receptor embedded in the explicit membrane
using charmm36 ff.
My simulation setup consist of
; Compound #mols
Protein 1
iso 1
POPC 228
SOL 11713
NA 66
CL 70
I've done short nvt and npt equilibration using sd1 integrator as the
thermostat and Parrinello-Rahman barostat
; Temperature coupling
; tcoupl = no ; modified Berendsen thermostat
tc-grps = Protein_LIG POPC SOL_Na_Cl
tau_t = 2 2 2 ; time constant, in ps
ref_t = 310 310 310 ; reference
temperature, one for each group, in K
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = semiisotropic
tau_p = 5
ref_p = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5
refcoord_scaling = com
during analysis of the 50ns production run trajectory I noticed
significant decrease of my box size on Z dimension (looks like my
system was compressed): from 10 to 6 nm. How I could avoid such
compression ?
Assuming the membrane is in the x-y plane, the result suggests you had void
space within the water layer that got compressed during NPT. Fill the voids
before starting.
-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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