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

[gupta.rakesh082]

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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