[gmx-users] difference in potenital energy on desktop and server run

[Dr. Vitaly Chaban]

Strange.

Sometimes things like this may happen if you incorrectly treat
periodicity between runs.

Without having the system at hand, I cannot say more.


Dr. Vitaly V. Chaban


On Thu, Feb 27, 2014 at 8:16 AM, gupta.rakesh082
<gupta.rakesh082 at gmail.com> wrote:
> EM RUN
>
> Steepest Descents converged to machine precision in 2820 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.9268122e+05
> Maximum force     =  1.9479546e+02 on atom 123
> Norm of force     =  6.3931437e+00
>
> grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
> mdrun -c -v -deffnm min
>
> g_energy -f min.edr -o npt_potenital.xvg
> 10 0
>
> Statistics over 2818 steps [ 0.0000 through 2817.0000 ps ], 1 data sets
> All statistics are over 2225 points (frames)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                   -287434       2800    6986.15   -18110.5
> (kJ/mol)
>
>
>
> NPT RUN
>
> grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr
> mdrun -nt 8 -c -v -deffnm NPT
>
> g_energy -f NPT.edr -o npt_potenital.xvg
> 10 0
>
> Statistics over 10000001 steps [ 0.0000 through 20000.0000 ps ], 1 data sets
> All statistics are over 100001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                    168770       1300    31030.1   -6644.57
> (kJ/mol)
>
> I am surprised to see that at such huge potential energy my simulation box
> is still stable.
>
> Desktop Run
>
> I took generated NPT.gro file in previous run and performed a small 200 ps
> npt simulation on my desktop machine using following commmand.
>
> grompp -f NPT.mdp -c NPT.gro -p cer.itp -o NPTdesktop.tpr
> mdrun --c -v -deffnm NPTdesktop
>
> g_energy -f NPTdesktop.edr -o NPTdesktop_potential.xvg
>
> Statistics over 100001 steps [ 0.0000 through 200.0000 ps ], 1 data sets
> All statistics are over 1001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                   -234831         47    582.555    117.566
> (kJ/mol)
>
> This time potential energy became negative after few ps and converse to
> value around order of ~ -2x 10^5.
>
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> --
> View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813p5014834.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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