[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
Re: [gmx-users] nrexcl = 2 or 3?
On 15/12/11, lq z lqz@gmail.com 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
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 mark.abra...@anu.edu.auwrote: On 15/12/11, *lq z *lqz@gmail.com 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, Yun Shi yunsh...@gmail.com 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 mark.abra...@anu.edu.au wrote: On 15/12/11, lq z lqz@gmail.com 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
