Re: [gmx-users] potential energy in implicit solvent simulations

[Per Larsson]

Hi

It seems that the non-polar energy term has gone missing, and does not get 
included in the print-out. 

While adding it back again properly  I found some other issues that I need to 
check before committing. The total potential energy should be correct. 

/Per

16 sep 2010 kl. 17:47 skrev "Ehud Schreiber" :

> Can you explain this situation?
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[gmx-users] potential energy in implicit solvent simulations

[Ehud Schreiber]

Dear GROMACS users,

 

I am conducting energy minimization with an implicit solvent, using
GROMACS version 4.5.1 at double precision.

The minimization provides the minimal potential energy I'm interested
in, but I also wanted to see the contributions to it.

I therefore used g_energy_d and picked the potential energy itself (no.
10) together with what I thought are its constituents (no. 1-9).
However, those contributions do not sum to the potential energy. There
is also a term #Surf*SurfTen (no. 30) but it is printed as zero. 

 

Can you explain this situation?

 

The relevant part of g_energy_d's output for a certain example is the
following:

 

# This file was created Thu Sep 16 16:51:26 2010

# by the following command:

# g_energy_d -s em2.tpr -f em2.edr -o em2.potential_energy.xvg 

#

# g_energy_d is part of G R O M A C S:

#

# GROningen Mixture of Alchemy and Childrens' Stories

#

@title "Gromacs Energies"

@xaxis  label "Time (ps)"

@yaxis  label "(kJ/mol), (bar nm)"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "Bond"

@ s1 legend "Angle"

@ s2 legend "Proper Dih."

@ s3 legend "Ryckaert-Bell."

@ s4 legend "GB Polarization"

@ s5 legend "LJ-14"

@ s6 legend "Coulomb-14"

@ s7 legend "LJ (SR)"

@ s8 legend "Coulomb (SR)"

@ s9 legend "Potential"

@ s10 legend "#Surf*SurfTen"

0.00  179.387112  1063.328043   64.818404  2220.374294
440.027560  3580.261354  12299.937527  -3164.489764  -44972.543752
-27990.3807600.00

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