Hi, That depends. If you have explicit parameters in the dihedral section then 1 and 9 are equivalent. If grompp has to look up parameters in the dihderaltypes section there will be difference when multiple parameter lines are present the same atom types for a dihedral type 9.
Berk From: alanwil...@gmail.com Date: Fri, 20 Aug 2010 14:41:33 +0100 To: gmx-users@gromacs.org CC: gporte...@mmb.pcb.ub.es Subject: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber Hi there, Now I have some results that I hope to clear this matter about dihe funct 4 and 9 (specially the latter). Please see: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx >From my understanding (and results), where dihe funct 4 or 9, replacing both >with 1 changes nothing in tot pot energy for amber force fields. I don't know about charmm here, but I thought amber dihe parameters were sort multiple terms and as far as I remember, the need to convert proper dihe to RBs was necessary for early versions of gromacs 3.x, am I right? Best, Alan On 18 August 2010 22:01, Alan <alanwil...@gmail.com> wrote: Hi Berk and Mark, Erik was too lazy to document this, I now added it to the manual. Is this manual available even via git? When funct 4 and 9 appeared? in gmx 4.5? Type 4 is identical to type 1, it is only there to distinguish improper from proper dihedrals. So for amber impr. dih. only, if I put 1 instead of 4 I for my GAFF generated ligand it would do the same thing, right? I ask that for the grace of compatibility with gmx 4.0.x. Type 9 is identical to type 1, except that multiple entries in dihedraltypes will lead to multiple functions on one dihedral. This one is more difficult to get. I know about multiple entries in CNS, Charmm and Amber. I was even trying to convert amber99bsc0 new dih parameters to gromacs and I was using funct 1. However I didn't have Amber to validate, and now I have Amber11, I don't have time for the moment. Sounds like funct 9 is to not only pave the way for Charmm, but may help to address properly the bsc0 parameters, right? But I need to understand this better. Converting amber's proper dih. param. to gromacs 4.0.x was done by making these dih. to be RB. However amb2gmx.pl converts everything to proper (using funct 1) -- acpype is smarter here. So in gmx 4.0.x proper dih. funct 1 was never able to interpret multiple entries on one dihedral? Now on Mark: Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git commit a7c597c778351f by Erik, whose message was Added support for dihedraltype 9, which allows multiple terms for proper dihedrals. By listing a dihedral with type 9, grompp will now scan the force field to see if there are multiple terms on _adjacent_ lines listed in the dihedraltypes section, and in that case add them all. A code snippet in src/kernel/toppush.c reads if(ft == 9) { /* Previously, we have always overwritten parameters if e.g. a torsion with the same atomtypes occurs on multiple lines. However, CHARMM and some other force fields specify multiple dihedrals over some bonds, including cosines with multiplicity 6 and somethimes even higher. Thus, they cannot be represented with Ryckaert-Bellemans terms. To add support for these force fields, Dihedral type 9 is identical to normal proper dihedrals, but repeated entries are allowed. */ bAllowRepeat = TRUE; ft = 1; } So amb2gmx.pl never worked properly here? For example, I have this for DNA with amber99bsc0: ; treated as usual propers in GROMACS since Phase angle diff from 0 or 180 degrees; i j k l func phase kd pn 2 3 6 23 1 190.98 4.92892 1 ; O5'- C5'- C4'- C3' 2 3 6 23 1 295.63 0.38535 2 ; O5'- C5'- C4'- C3' 2 3 6 23 1 348.10 4.02848 3 ; O5'- C5'- C4'- C3' 28 29 32 33 1 31.80 0.77480 1 ; O3'- P- O5'- C5' 28 29 32 33 1 351.96 5.25733 2 ; O3'- P- O5'- C5' 28 29 32 33 1 357.25 1.48473 3 ; O3'- P- O5'- C5' So, this would only work if funct was 9 and not 1 as above? The way it is, the last line of a sequence dih. is overwriting the 2 previous one, ignoring them completely? >From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it can >be seen that dihedraltypes 4 and 1 call the same evaluation function. Perhaps >Erik can confirm this. src/gmxlib/ifunc.c did suggest to me that something is not quite right... def_bonded ("PDIHS", "Proper Dih.", 4, 3, 3, eNR_PROPER, pdihs ), def_bonded ("RBDIHS", "Ryckaert-Bell.", 4, 6, 6, eNR_RB, rbdihs ), def_bonded ("FOURDIHS", "Fourier Dih.", 4, 4, 4, eNR_FOURDIH, rbdihs ), def_bonded ("IDIHS", "Improper Dih.", 4, 2, 2, eNR_IMPROPER,idihs ), def_bonded ("PIDIHS", "Improper Dih.", 4, 3, 3, eNR_PROPER, pdihs ), If PIDIHS is an improper dihedral with the functional form of a proper dihedral, should it not use eNR_IMPROPER? I definitely need to run my validations myself, but any words here would be helpful. Many thanks you all. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
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