[gmx-users] Pressure Calculation
spoel at xray.bmc.uu.se
Sun Jul 11 08:30:55 CEST 2004
On Sat, 2004-07-10 at 23:49, Farshid Mostowfi wrote:
> Hi david;
> Thanks for your reply. I considered the that factor (16.6) but it didn't work.
> Here is the sample calculations, (g_energy output results are at the bottom
> of the page):
> 2/V(Ekin-Vir(1,1))*16.6 = 2/343(84749.94-211153.88)*16.6 = 6155bar
> I'd appreciate it if you let me know where my mistake is.
The kinetic energy is a tensor as well. The diagonal elements hold the
largest energy, each roughly one third of the number you are using. If
you divide that by three you will find reasonable correspondence to the
> g_energy output results:
> Ekin=84749.94 (Kj/mol)
> V=343 (nm3)
> P= 1114.501 (bar)
> 21153.88 1892.37 -5107.3
> Vir= 1820.15 18818.25 -4488.1
> -5025.92 -4484.56 10246.22
> 719.3521 195.9087 515.1461
> P= 188.9157 920.3499 450.6406
> 507.2669 450.298 1703.802
> On Saturday 10 July 2004 14:16, you wrote:
> > On Sat, 2004-07-10 at 20:44, Farshid Mostowfi wrote:
> > > Hello Everyone;
> > >
> > > I have a problem with pressure calculations. Based on the manual (pp 21,
> > > eq 3.16) the pressure tensor is calculated using the difference between
> > > kinetic energy and virial tensor : P=2/V*(Ekin-Vir)
> > > I extracted the kinetic energy, virial and pressure tensors using
> > > g_energy from energy file, but they don't match and I don't know why.
> > > Is there anybody who can help me with this problem?
> > check units. there is a magic factor 16.6 somewhere.
> > > Thanks in advance.
> > >
> > > Regards,
> > > Farshid
> > > Ph.D student
> > > Mechanical Engineering Dept.
> > > University of Alberta
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users