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 ? Thanks for help James -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
