Hi, Please check out the equations and non-bonded combination rules in chapter 4 of the manual, and the units in chapter 2.
Mark On Sat, May 31, 2014 at 2:43 PM, 라지브간디 <ra...@kaist.ac.kr> wrote: > Dear justin, > > Could tell me how do I convert those non-bonded values between CHARMM and > gromos431 ? > > I am unaware of this conversion. > > Thanks in advance. > > On 5/30/14, 11:51 AM, ????? wrote: > > > > Dear justin, > > > > Thank your for your clear answer. > > > > The parameters are specifically written for CHARMM force field based on > the experimental results. > > > > Particularly, charges and non-bonded interaction values for ligand > molecule of CO ( Carbon Monoxide) in Myoglobin are written in literature. > > > > Since Gromos 43a1 has parameter for heme with CO, therefore I asked you > " Is that possible to use only this CO ligand charges and non-bonded values > derive > > > > d from experimental and written in CHARMM ff ?. > > > > In other case, shall I use this CHARMM ff values for CO in CHARMM27/36 > provided by groamcs without doing any conversion ? > > > > Yes, you need to convert the units (CHARMM and Gromacs use different > conventions), but otherwise those parameters can be used directly with > CHARMM27 > or CHARMM36. > > -Justin > > > Thanks in advance. > > > > On 5/29/14, 10:13 PM, ????? wrote: > >> Dear Justin, > >> > >> Thanks for your > >> reply. > >> > >> I am not mixing up the parameter here. > >> What i am trying to do here > >> In order to reproduce the dipole moments of the CO, I have to > >> follow up the specific charges and non-bonded interaction values > specified in > >> literature in CHARMM format ( For C atom, charge -0.75, ?=0.0262 > >> & ? = 3.83) ( For O atom, charge -0.85, ?=0.0262 & ? = > >> 3.83). > > > > "CHARMM format" and "CHARMM force field" are different, so what is the > origin of > > those parameters? Were they developed specifically for CHARMM or some > other > > force field? If these parameters were not specifically designed to be > > consistent within Gromos96 43A1, my original point stands - they cannot > be > > combined with a force field for which they were not self-consistently > derived. > > > >> Could you tell how it can be done? If i cant use them in > >> gromos43a1 ff, possible to use in charmm27 provided by gromacs package? > or it > >> does need any conversion to use in gromacs-charmm27 ff? > >> > > > > Both CHARMM27 and CHARMM36 are fully supported by Gromacs. > > > > -Justin > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.