Hi<br>I just saw the article "Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density" published in Journal of Computational Chemistry, Vol. 19, No. 10, 1179]1186 (1998). It gives 0.985 for SPC at 25 C with different setup... perhaps 0.978 is not so bad?<br>
<br><br><br><br><br><div class="gmail_quote">On Wed, Dec 28, 2011 at 9:34 AM, Theodora García <span dir="ltr"><<a href="mailto:theodoraaagarcia@gmail.com">theodoraaagarcia@gmail.com</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">
Thank you very much for your advice... I have tried including dispcorr = enerpres in my mdp file and the density increased a bit in a timescale of 5 ns but it is still far from the value expected for pure water. These are the new results:<br>
<br>Statistics over 2500001 steps [ 0.0000 thru 5000.0000 ps ], 3 data sets<br>All averages are exact over 2500001 steps<div class="im"><br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br></div>
Temperature 298 2.67563 2.67534 2.70867e-05 0.135433<br>Volume 126.133 0.529594 0.529323 1.17324e-05 0.0586622<br>Density (SI) 978.114 4.10621 4.10412 -9.08266e-05 -0.454133<br>
Heat Capacity Cv: 12.4733 J/mol K (factor = 8.06157e-05)<br>Isothermal Compressibility: 5.40447e-05 /bar<br>Adiabatic bulk modulus: 18503.2 bar<br><br>I guess I should get 1000 g/cm^3<br><br>Any other suggestion?<div class="HOEnZb">
<div class="h5"><br>
<br><br><br><br><div class="gmail_quote">On Tue, Dec 27, 2011 at 6:23 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</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>On 2011-12-27 17:57, Theodora García wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear all<br>
I am starting some MD simulations aimed to calculate the volume of a<br>
solute in water as a function of the concentration. First I ran a<br>
simulation of a box with 4124 SPC water molecules (similar number of<br>
molecules that will be later used with my solute) for which I got the<br>
following results after ~7.5 ns:<br>
</blockquote>
<br></div>
dispcorr = enerpres<div><div><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
Statistics over 3762001 steps [ 0.0000 thru 7524.0005 ps ], 3 data sets<br>
All averages are exact over 3762001 steps<br>
<br>
Energy Average RMSD Fluct. Drift<br>
Tot-Drift<br>
------------------------------<u></u>------------------------------<u></u>-------------------<br>
Temperature 298 125.156 125.156 1.9202e-05<br>
0.144476<br>
Volume 126.908 53.2917 53.2917 5.61522e-06<br>
0.0422489<br>
Density (SI) 972.142 408.201 408.201 -4.30887e-05<br>
-0.324199<br>
Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389)<br>
Isothermal Compressibility: 0.543909 /bar<br>
Adiabatic bulk modulus: 1.83854 bar<br>
<br>
Why am I obtaining so low density? The density seems to be constant over<br>
that timescale.<br>
<br>
This is my mdp file:<br>
<br>
constraints = all-bonds<br>
integrator = md<br>
dt = 0.002<br>
nsteps = 2500000<br>
<br>
nstxout = 5000<br>
nstvout = 50000<br>
nstenergy = 1000<br>
nstxtcout = 5000<br>
energygrps = SOL<br>
nstlist = 5<br>
<br>
ns_type = grid<br>
rlist = 1.2<br>
rcoulomb = 1.2<br>
rvdw = 1.2<br>
coulombtype = PME<br>
fourierspacing = 0.15<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
<br>
Tcoupl = nose-hoover<br>
tau_t = 0.1<br>
tc-grps = SOL<br>
ref_t = 298<br>
<br>
Pcoupl = Parrinello-Rahman<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
pcoupltype = isotropic<br>
<br>
gen_vel = yes<br>
gen_temp = 298<br>
gen_seed = -1<br>
<br>
<br>
Thanks in advance for any help...<br>
<br>
<br>
</blockquote>
<br>
<br></div></div><span><font color="#888888">
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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</font></span></blockquote></div><br>
</div></div></blockquote></div><br>