[gmx-users] Decreasing of the box size during membrane protein simulation
jmsstarlight at gmail.com
Mon Jan 28 14:30:17 CET 2013
Below you can see graph representation of my system after energy
minimisation ( that case system was filled up with tip3p water using
genbox with slightly increased vdw for C atom ( to 2nm) to prevent
water movement into the membrane.
2013/1/28 Justin Lemkul <jalemkul at vt.edu>:
> 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
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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