<br><br><div class="gmail_quote">On 20 August 2011 21:20, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 20/08/2011 8:02 AM, Elisabeth wrote:
<blockquote type="cite">Dear experts,<br>
<br>
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. <br>
<br>
P = 50 bar > NPT rho= 0.344 experimental density ~ 0.54<br>
P 100 > NPT rho= 0.43 experimental density ~
0.55<br>
<br>
densities become more accurate for P >100 bar. <br>
<br>
P 500 > rho= 0.56 experimental density ~ 0.61<br>
<br>
I thought maybe you have some idea on how this inaccuracy can be
improved.<br>
</blockquote>
<br></div>
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.<br></div></blockquote><div><br>Hello Mark,<br><br>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.<br>
<br>BTW: I am using version 4.5.4<br><br>Thank you,<br><br> <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div bgcolor="#FFFFFF" text="#000000">
<font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">Thank you in advance for your invaluable help.<br>
Best,<br>
<br>
<br>
; Bonds<br>
constraints = none <br>
constraint-algorithm = lincs<br>
<br>
; Run control <br>
integrator = md <br>
dt = 0.001 <br>
nsteps = 5000000 <br>
nstcomm = 100 <br>
<br>
; Output control<br>
nstenergy = 100 <br>
nstxout = 100 <br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 <br>
nstxtcout = 1000 <br>
<br>
; Neighbor searching<br>
nstlist = 10 <br>
ns_type = grid <br>
<br>
; Electrostatics/VdW <br>
coulombtype = Shift <br>
vdw-type = Shift <br>
rcoulomb-switch = 0 <br>
rvdw-switch = 0.9 <br>
<br>
; Cut-offs<br>
rlist = 1.25 <br>
rcoulomb = 1.0 <br>
rvdw = 1.0 <br>
<br>
; Temperature coupling <br>
Tcoupl = v-rescale <br>
tc-grps = System <br>
tau_t = 0.1 <br>
ref_t = 425 <br>
<br>
; Pressure coupling<br>
Pcoupl = berendsen <br>
Pcoupltype = isotropic <br>
tau_p = 1 <br>
compressibility = 3.5e-5 <br>
ref_p = 100 <br>
<br>
; Velocity generation <br>
gen_vel = no;yes <br>
gen_temp = 425 <br>
gen_seed = 173529 <br>
<br>
<br>
<br>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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