On Dec 22, 2011, at 9:05 AM, Mark Abraham <[email protected]> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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