[gmx-users] Decreasing of the box size during membrane protein simulation

[Justin Lemkul]

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

-- 
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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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