[gmx-users] question about energy and pressure

[Qiao Baofu]

Hi Mark,

2006/9/22, Mark Abraham <Mark.Abraham at anu.edu.au>:
>
> Qiao Baofu wrote:
>
> What is this "reported data"?



The reported data  are (KJ/mol) : Bond  27;    Angle: 30;  LJ: -27;
electrostatic -530.

Some days ago, I  run again in gromacs but  using all the "reported"
force-field parameters. In the end, I get the similar result as listed in
the first letter.

Have someone compared the energy of gromacs with other software?


> Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 6 data sets
> >
> > Energy                      Average       RMSD     Fluct.      Drift
> > Tot-Drift
> >
> -------------------------------------------------------------------------------
> >
> > Bond                        2869.13    93.6564    93.6562 0.000137548
> > 0.687742
> > Angle                       7303.46     140.13     140.13 0.000189867
> > 0.949334
> > Ryckaert-Bell.          3326.2    97.6245    97.6161 -0.000890977   -
> 4.45489
> > LJ-(SR)                   -7616.62    138.684     138.67 -0.00138166
> > -6.90831
> > Coulomb-(SR)        -22763.2    138.465    138.238 -0.00549019    -
> 27.451
> > Potential                  -64743     219.54    219.203 -0.00842365
> > -42.1182
> >
> > 2. I used the "isotropic!!" pressure coupling, but at the end of the
> > .log file (in the average section), it says:
> >
> >  Pressure (bar)
> >    -2.64364e+01    3.71622e+01     3.00738e+00
> >     3.71622e+01    1.32932e+01   -2.49814e+01
> >     3.00738e+00   -2.49814e+01    1.61609e+01
> >
> > The Pxx, Pyy, Pzz are not equal. Why?
>
> What is the geometry of your system?


It is imidazolium-based material.


PS: The following processes are used:
   1. md1: NTV (nose-hoover for T coupling) 300ps
   2. md2:  NTP (Berendsen for T & P coupling)  T=425K, P=1bar, 500ps,
tau_p=1
   3.  in md3.mdp:  gen_temp  = no      unconstrained-start      = yes
         grompp -e md2.edr  -f md3.mdp  -c md2.gro -p -o
        md3: NTP (nose-hoover for T coupling & Parrillo-rahman for P
coupling) T=425K, P=1bar, 3000ps, tau_p=4
    4. collect data.

g_energy
      Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift

-------------------------------------------------------------------------------
   Pressure-(bar)              1.75443    931.231    931.227 -0.00331938   -
9.95814

In md3.log
   Pressure (bar)
       3.37452e+01   -1.01961e+02    1.77413e+01
      -1.01961e+02   -7.66155e+00   -4.13047e+01
      1.77413e+01   -4.13047e+01   -2.08203e+01

Even though I used the Berendsen P coupling to relax the pressure firstly,
and then use the Parrilo-rahman, the final result of pressure deviates much
from what I want!  After md2 and md3, I both used g_velacc to check the
velocity-corelation function.


Who has such experience? How to solve it?


Mark
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-- 
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
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