[gmx-users] Re:comparison of energy between GROMACS and NAMD

[Sairam Tatikonda]

Hi,
I have performed minimization of ubiquitin  in vaccum both in GROMACS and
NAMD using CHARMM force field .when i have compared the energy values for
first step ,i found that variation in the values

                     NAMD (kcal/mol)                  GROMACS(kcal/mol)
Bond              1929.3647                              1928.57
pro.dihed         256.1007                               345.21
imp dihed         10.8044                                10.797
potential           1295                                    1215
coloumbic       -1483.6554                            -1557.72
LJ                     73.1648                               69.445

Structure
information          NAMD                              GROMACS
atoms                1231                                 1231
bonds                 1237                                 1236
dihedrals            3293                                  3292
Impr dihedrals      204                                    203

Though the number of atoms are same ,i did not understand why there is
variation in number of bonds,angles and dihedrals leading to difference in
energy values.
where i have calculated the coloumbic energy and LJ energy from log file of
GROMACS by adding up short range,long range and 14 terms.is it the correct
way of calculating the total coloumbic and LJ energies to compare  them
with NAMD coloumbic and LJ values.


Any help will be highly appreciated.



Rajitha,
Ph.D student.
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