[gmx-users] Use dihedraltype 4 to allow several multiplicity terms

Justin Lemkul jalemkul at vt.edu
Tue May 5 16:16:27 CEST 2015

On 5/5/15 10:09 AM, Mark Abraham wrote:
> Hi,
> Thanks Justin. If you think it useful, then in the CHARMM36 forcefield.itp
> you could do stuff like
> #if (defined _FF_GROMOS96) || ...
> #error Do not attempt to mix another force field with CHARMM36, it is
> self-contained
> #endif
> getting the magic strings from the other share/top/*/forcefield.itp files.
> Or does this make sense to do generally, e.g. by giving grompp the smarts
> to refuse to #include another forcefield.itp file (or maybe refuse to let
> another distinct _FF_* to be #defined)? That doesn't stop people going
> directly to "#include ffbonded.itp," but you can't save every lemming... :-)

I think it's a hard problem to solve.  There is an intrinsic desire to follow 
patterns and tutorials, all of which #include some parent force field.  What 
CHARMM-GUI does is it generates a CHARMM PSF and then converts it to GROMACS 
format using some in-house scripts.  It then assembles a single force field file 
that has everything the user needs, based on what is present, so effectively a 
subset of the entire force field, suited for the application at hand.

I think users get confused when they just see a listing of .itp files when 
they're using to #include "some.ff/forcefield.itp" at the top of everything that 
pdb2gmx produces, so they try to make it fit :)

I'll think about some generalized safeguards that could be useful, but at some 
point it becomes an unsolvable problem.  Better to think in terms of mechanics 
and "how does this work?" rather than "type this, get this" :)  Part of the 
problem with writing tutorials, everyone thinks everything should fit a script...



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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