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 <jalem...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists