On 4/15/16 5:20 AM, gozde ergin wrote:
Dear all, I simulate the NaCl solution to estimate the osmotic pressure. My salt concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules. I use CHARMM36 ff with NBFIX correction. After the simulation I extract the z-coordinates of restraint ions and use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic pressure. Actually I try to get the similar results as Lou&Roux 2010 study. However my osmotic pressure results are on the line of ideal solution osmotic pressure as shown equation in below; P = cRT (Van’t Hoff equation) but not the similar result with experiments.
What values do you actually get? How do they compare with the values from the Roux paper? Are you remembering to divide by 2*area in your calculation (since you have two walls)?
Is there anyone here that get the same trend as me for osmotic pressure calculation? Or is there something that I miss? Here is my .mdp file; define = -DPOSRES integrator = md dt = 0.002 nsteps = 2500000 ; ; Output control nstxout = 2000 nstvout = 2000 nstlog = 2000 nstenergy = 2000 ; Bond parameters continuation = no ; constraint_algorithm = shake ; h constraints = all-bonds ; a shake_tol = 0.0001 ; Neighborsearching ns_type = grid ; nstlist = 5 ; rlist = 1.1 ; rcoulomb = 1.1 ; rvdw = 1.1 ;
These nonbonded settings are wrong. The values for CHARMM36 are well established and you should not deviate from them.
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM -Justin
; Electrostatics coulombtype = PME ; pme_order = 4 ; fourierspacing = 0.16 ; tcoupl = berendsen tc-grps = System tau_t = 1.0 ref_t = 300 ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling pcoupltype = semiisotropic ; uniform scaling of x-y-z box vectors tau_p = 2.0 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure (in bar) compressibility = 0 4.5e-5 ; isothermal compressibility, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 300 ; temperature for velocity generation gen_seed = -1 ; random seed ; COM motion removal ; These options remove COM motion of the system nstcomm = 10 comm-mode = Linear comm-grps = System
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