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

[James Starlight]

Justin,

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.

http://img42.imageshack.us/img42/7213/b2armembrane.png

James

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
>> 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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