2006/9/22, Mark Abraham <[EMAIL PROTECTED]>:
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?
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?
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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