[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
> <mailto: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
>     <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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