[gmx-users] Re: gmx-users Digest, Vol 92, Issue 116

[Sairam Tatikonda]

Hi sir,
Thanks alot for your valuable suggestion .

As i was actually searching a way to find out the missing  bond  but i
could not find .can u please suggest  me a way where i can further proceed
to find it.

Thanks in advance.


Regards
Rajitha.






On Thu, Dec 22, 2011 at 4:30 PM, <gmx-users-request at gromacs.org> wrote:

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>   1. Re: Re:comparison of energy between GROMACS and NAMD
>      (David van der Spoel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 22 Dec 2011 09:32:04 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re:comparison of energy between GROMACS and
>        NAMD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <E5174BF1-6349-44AE-AD8B-2898CEB50898 at xray.bmc.uu.se>
> Content-Type: text/plain; charset="us-ascii"
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>
>
> On Dec 22, 2011, at 9:05 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> > 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.
> >
>
> It would be useful to see where the missing bond is, considering that the
> number of atoms is the same.
> In principle there could be a bug in the charmm rtp files for instance.
>
> >>
> >> 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.
> >
> > 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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