Re: [gmx-users] nrexcl = 2 or 3?
On 15/12/11, Yun Shi wrote: > Hi Mark, > > I do not quite understand. For example, in amber ff, 1-4 interactions (except > the part from dihedral interactions) are calculated according to non-bonded > parameters and then scaled by 1/2 or 5/6. Yes, see discussion of gen-pairs in manual section 5.7.1 > When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions > excluded from using non-bonded parameters? This is a separate mechanism. Exclusions for non-bonded interactions are applied "on the fly" in mdrun. That doesn't apply to 1-4 parameter generation, but it is necessary for the set of choices of nrexcl, gen-pairs, fudgeXX, [atomtypes], [nonbond_params], [pairtypes] and [pairs] to be consistent. Details vary with the particular force field. Parameters for "bonded" 1-4 interactions (a.k.a. pairs) are generated in grompp according to the rules of the force field - either from the [pairtypes], [pairs] or from scaling depending on the force field and interaction type. Mark > > > > Thanks, > Yun > > > > On Wed, Dec 14, 2011 at 4:33 PM, Mark Abraham wrote: > > > > > > > > > > > > On 15/12/11, lq z wrote: > > > > > Dear GMXers, > > > > > > I need to use charmm ff (same question for amber ffs), and am confused > > > with what value I should give to nrexcl in [ moleculetype ], 2 or 3? > > > > > > > > Whatever value pdb2gmx generates for CHARMM, probably 3. > > > > > > > > > > > > > > > According to the manual (v 4.5), "nrexcl = 3 stands for excluding > > > non-bonded interactions between atoms that are no further than 3 bonds > > > away." In charmm ff, 1-4 interactions are needed and it is "no further > > > than 3 bonds away," > > > > > > > > ... but 1-4 interactions are regarded as bonded interactions. > > > > > > > > > so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. > > > > > > > > Yes, CHARMM has special parameters for some 1-4 interactions, which are > > dealt with seperately. > > > > > > > > > > > > > > > > > > By the way, I did a simple test with a dihedral a-b-c-d. Only a and d > > > have charges. If I use nrexcl =3, no electrostatics energy is reported > > > while the value matches with the one calculated by hand when I set nrexcl > > > to be 2. > > > > > > > > > > > As expected. > > > > > > Mark > > > > -- > > gmx-users mailing listgmx-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 > > > > > > -- gmx-users mailing listgmx-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
Re: [gmx-users] nrexcl = 2 or 3?
Hi Mark, I do not quite understand. For example, in amber ff, 1-4 interactions (except the part from dihedral interactions) are calculated according to non-bonded parameters and then scaled by 1/2 or 5/6. When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions excluded from using non-bonded parameters? Thanks, Yun On Wed, Dec 14, 2011 at 4:33 PM, Mark Abraham wrote: > > > On 15/12/11, *lq z * wrote: > > Dear GMXers, > > I need to use charmm ff (same question for amber ffs), and am confused > with what value I should give to nrexcl in [ moleculetype ], 2 or 3? > > > Whatever value pdb2gmx generates for CHARMM, probably 3. > > > > > According to the manual (v 4.5), "nrexcl = 3 stands for excluding > non-bonded interactions between atoms that are no further than 3 bonds > away." In charmm ff, 1-4 interactions are needed and it is "no further than > 3 bonds away," > > > ... but 1-4 interactions are regarded as bonded interactions. > > > so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. > > > Yes, CHARMM has special parameters for some 1-4 interactions, which are > dealt with seperately. > > > > > By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have > charges. If I use nrexcl =3, no electrostatics energy is reported while the > value matches with the one calculated by hand when I set nrexcl to be 2. > > > As expected. > > Mark > > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] nrexcl = 2 or 3?
On 15/12/11, lq z wrote: > Dear GMXers, > > I need to use charmm ff (same question for amber ffs), and am confused with > what value I should give to nrexcl in [ moleculetype ], 2 or 3? Whatever value pdb2gmx generates for CHARMM, probably 3. > > > According to the manual (v 4.5), "nrexcl = 3 stands for excluding non-bonded > interactions between atoms that are no further than 3 bonds away." In charmm > ff, 1-4 interactions are needed and it is "no further than 3 bonds away," ... but 1-4 interactions are regarded as bonded interactions. > so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. Yes, CHARMM has special parameters for some 1-4 interactions, which are dealt with seperately. > > > > By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have > charges. If I use nrexcl =3, no electrostatics energy is reported while the > value matches with the one calculated by hand when I set nrexcl to be 2. > As expected. Mark -- gmx-users mailing listgmx-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
[gmx-users] nrexcl = 2 or 3?
Dear GMXers, I need to use charmm ff (same question for amber ffs), and am confused with what value I should give to nrexcl in [ moleculetype ], 2 or 3? According to the manual (v 4.5), "nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away." In charmm ff, 1-4 interactions are needed and it is "no further than 3 bonds away," so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have charges. If I use nrexcl =3, no electrostatics energy is reported while the value matches with the one calculated by hand when I set nrexcl to be 2. Your clarification is greatly appreciated. Luke -- gmx-users mailing listgmx-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
