Hi, On Sun, Jul 31, 2016 at 5:21 PM soumadwip ghosh <[email protected]> wrote:
> Hi > In addition to my last query I would like to know whether the sigma > values reported for CHARMM 27 are in Angstrom or in nm. GROMACS conventions are in chapter 2 of the manual. Other conventions you need to find elsewhere. > Similarly, is the > epsilon for atoms in kJ/mol or Kcal/mol? As of now, the values that I got > from the ffnonbonded.itp in CHARMM 27 are 0 for TIP3P water's hydrogen. Is > it right? I generally like to find out how my water model works before I submit my papers. In this case, yes, but Wikipedia or the original literature are good places to start learning. Now if I want to report the graphene-water interaction should I > take the sigma of CA atoms (carbon atoms in graphene) and water hydrogen > and then find the arithmetic mean? Similarly, the geometric mean would give > the epsilon? The description and equations are all in the manual. > Is there anything wrong with this approach.Furthermore, in > ffnonbonded.itp lines are written as below. > > > [ atomtypes ] > ;name at.num mass charge ptype sigma epsilon > C 6 12.01100 0.51 A 0.356359487256 0.46024 > CA 6 12.01100 -0.115 A 0.355005321205 0.29288 > CC 6 12.01100 0.62 A 0.356359487256 0.29288 > CD 6 12.01100 0.000 A 0.356359487256 0.29288 ; > partial charge def not found > CE1 6 12.01100 0.000 A 0.372395664183 0.284512 ; > partial charge def not found > CE2 6 12.01100 0.000 A 0.370613866746 0.267776 ; > partial charge def not found > CM 6 12.01100 0.000 A 0.374177461619 0.46024 ; > partial charge def not found > CP1 6 12.01100 0.02 A 0.405358916754 0.08368 > CP2 6 12.01100 -0.18 A 0.387540942391 0.23012 > CP3 6 12.01100 0.00 A 0.387540942391 0.23012 > CPA 6 12.01100 0.000 A 0.320723538531 0.37656 ; > partial charge def not found > CPB 6 12.01100 0.000 A 0.320723538531 0.37656 ; > partial charge def not found > CPH1 6 12.01100 0.19 A 0.320723538531 0.2092 > CPH2 6 12.01100 0.32 A 0.320723538531 0.2092 > CPM 6 12.01100 0.000 A 0.320723538531 0.37656 ; > partial charge def not found > CPT 6 12.01100 -0.02 A 0.320723538531 0.37656 > CS 6 12.01100 0.000 A 0.391995435982 0.46024 ; > partial charge def not found > CST 6 12.01100 0.000 A 0.278494939291 0.242672 ; > partial charge def not found > CT1 6 12.01100 0.07 A 0.405358916754 0.08368 > CT2 6 12.01100 -0.18 A 0.387540942391 0.23012 > CT3 6 12.01100 -0.11 A 0.367050271874 0.33472 > CY 6 12.01100 -0.03 A 0.355005321205 0.29288 > CT 6 12.01100 0.000 A 0.405358916754 0.08368 ; > partial charge def not found > CT1x 6 12.01100 0.000 A 0.405358916754 0.08368 ; > partial charge def not found > CT2x 6 12.01100 0.000 A 0.358141284692 0.234304 ; > partial charge def not found > CT3x 6 12.01100 0.000 A 0.363486677001 0.326352 ; > partial charge def not found > H 1 1.008000 0.31 A 0.0400013524445 0.192464 > > > For atomtype CA does the sigma and epsilon parameters listed above > correspond to individual CA atoms or is it between a pair? > It's an [atomtype] not a [pairtype]. There's only one type named, so even if the numbers represent a pair of atoms of the same type, I'm sure you can tell me the arithmetic and geometric means of two identical numbers. ;-) Mark > > > Thanks and regards, > Soumadwip Ghosh > Senior Research Fellow > IITB > India > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
