On 20 August 2011 21:20, Mark Abraham <[email protected]> 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. 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, > > Mark > > > Thank 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 [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 >
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