On 12/22/2011 6:16 PM, Sairam Tatikonda wrote:
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
In GROMACS, that energy is based on the result of the first EM step. To
do a "single-point" energy calculation, do a zero-step MD run, or use
mdrun -rerun.
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
It seems clear that you have a difference in the .psf and .top
topologies you are generating, so any further comparison is not profitable.
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
<http://terms.is> it the correct way of calculating the total
coloumbic and LJ energies to compare them with NAMD coloumbic and LJ
values.
You will have to read the documentation for each code carefully in order
to do calculations that compute the same things. There are lots of
details you will have to get exactly right.
Mark
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