[gmx-users] Re: gmx-users Digest, Vol 92, Issue 116
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 22 13:30:01 CET 2011
On 2011-12-22 13:24, Sairam Tatikonda wrote:
> 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.
>
The top file lists all the bonds in order.
I guess the same information must be in the psf file?
>
> Regards
> Rajitha.
>
>
>
>
>
>
> On Thu, Dec 22, 2011 at 4:30 PM, <gmx-users-request at gromacs.org
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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
> <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <E5174BF1-6349-44AE-AD8B-2898CEB50898 at xray.bmc.uu.se
> <mailto: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
> <mailto: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 <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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> End of gmx-users Digest, Vol 92, Issue 116
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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