[gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
Hi there, I've been looking at amber ff implementation of gmx 4.5 since I am familiar to Sorin's ffamber works and I am the developer of ACPYPE. I noticed that proper dih are not converted to RB anymore (which's great for understanding) and to accomplish that apparently 2 new funct were added to the gmx code, namely 4 and 9. Needless to say that I couldn't find anything about funct 4 and 9 in the current gmx manual. I would appreciate more information about it. Among other things I would like to know, e.g., what funct 4 would have different from funct 1, since in the seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs. Many thanks, 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 -- gmx-users mailing listgmx-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
RE: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
Hi, Erik was too lazy to document this, I now added it to the manual. Type 4 is identical to type 1, it is only there to distinguish improper from proper dihedrals. Type 9 is identical to type 1, except that multiple entries in dihedraltypes will lead to multiple functions on one dihedral. Berk From: alanwil...@gmail.com Date: Tue, 17 Aug 2010 12:16:16 +0100 To: gmx-users@gromacs.org Subject: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff Hi there, I've been looking at amber ff implementation of gmx 4.5 since I am familiar to Sorin's ffamber works and I am the developer of ACPYPE. I noticed that proper dih are not converted to RB anymore (which's great for understanding) and to accomplish that apparently 2 new funct were added to the gmx code, namely 4 and 9. Needless to say that I couldn't find anything about funct 4 and 9 in the current gmx manual. I would appreciate more information about it. Among other things I would like to know, e.g., what funct 4 would have different from funct 1, since in the seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs. Many thanks, 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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
- Original Message -
From: Alan alanwil...@gmail.com
Date: Tuesday, August 17, 2010 21:24
Subject: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
To: Gromacs gmx-users@gromacs.org
Hi there,
I've been looking at amber ff implementation of gmx 4.5 since I am familiar
to Sorin's ffamber works and I am the developer of ACPYPE.
I noticed that proper dih are not converted to RB anymore (which's great for
understanding) and to accomplish that apparently 2 new funct were added to
the gmx code, namely 4 and 9.
Needless to say that I couldn't find anything about funct 4 and 9 in the
current gmx manual.
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;
}
I would appreciate more information about it. Among other things I would like
to know, e.g., what funct 4 would have different from funct 1, since in the
seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs.
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?
Mark
--
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