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

[Mark Abraham]

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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