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-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 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 <sp...@xray.bmc.uu.se> > Subject: Re: [gmx-users] Re:comparison of energy between GROMACS and > NAMD > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <e5174bf1-6349-44ae-ad8b-2898ceb50...@xray.bmc.uu.se> > Content-Type: text/plain; charset="us-ascii" > > > > On Dec 22, 2011, at 9:05 AM, Mark Abraham <mark.abra...@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 > > > > -- > > This message has been scanned for viruses and > > dangerous content by MailScanner, and is > > believed to be clean. > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111222/818a5c0c/attachment-0001.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 92, Issue 116 > ****************************************** >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists