On 21/08/2011 2:08 PM, Elisabeth wrote:
On 20 August 2011 21:20, Mark Abraham <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:On 20/08/2011 8:02 AM, Elisabeth wrote:Dear experts, I am intending to calculate the equilibrium density of a pure hydrocarbon at different pressures , at 425 K. The normal boiling point of the liquid is around 350 K. For pressures below 100 bar densities I am getting from NPT is in accurate. I start form a structure which is compressed to above 0.6 g/cm3 density but since temperature is high density goes than to the values below. P = 50 bar > NPT rho= 0.344 experimental density ~ 0.54 P 100 > NPT rho= 0.43 experimental density ~ 0.55 densities become more accurate for P >100 bar. P 500 > rho= 0.56 experimental density ~ 0.61 I thought maybe you have some idea on how this inaccuracy can be improved.These could reflect limitations in the model you are using (which almost certainly wasn't parametrized upon data like this). Your integration time step is twice as large as is commonly used in the absence of constraints. Also, be sure you are measuring your density only after equilibration, not an average that includes the equilibration period - and describe that method so people here know you're making such sensible measurements. Hello Mark,Thank you for your comment. Densities are equilibrated. I am not sure what you mean by limitations in the model.
Parameters are not magic truth values. They're empirical values that have been observed to replicate some experimental or computational results - almost invariably room temperature and atmospheric pressure. It is not necessarily known how well they reproduce other conditions - increasing temperature and pressure may well lead to those parameters modelling some alternative reality. Taking a small test system and systematically trialling small increases in temperature and/or pressure from "normal" will tend to reveal such trends. Such results may indicate the need for different parametrization. This is typically expensive in computer and human time.
Mark
I actually fixed the density and tried NVT using the experimental density at 298 and found a full agreement between vaporization heat of the liquid and that reported in the original OPLS paper. Once I try to obtain the density using NPT this inaccuracy in densities appear. I have been using 1 fs dt with berendsen barostat for 5 ns and collected data over the last 1 ns ( there are about 2500 atoms in the system). So now I am going to follow your instruction and try dt of 0.5 fs for another 5ns along with cpt files from previous barostat trial (berendsen). I will get back to you to report the results soon.BTW: I am using version 4.5.4 Thank you, MarkThank you in advance for your invaluable help. Best, ; Bonds constraints = none constraint-algorithm = lincs ; Run control integrator = md dt = 0.001 nsteps = 5000000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = Shift vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ; Cut-offs rlist = 1.25 rcoulomb = 1.0 rvdw = 1.0 ; Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 425 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 3.5e-5 ref_p = 100 ; Velocity generation gen_vel = no;yes gen_temp = 425 gen_seed = 173529-- gmx-users mailing list gmx-users@gromacs.org <mailto: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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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