[gmx-users] Setting custom atoms in FF

Alex nedomacho at gmail.com
Wed Apr 1 22:38:01 CEST 2015

I am not mixing forcefield types, but I am indeed mixing angle types. I
suppose I will adjust my constants so the local derivatives near
equilibrium roughly correspond to what I need while sticking to the rtp
default, I can't see another way around.

I have tremendous respect for you guys, but I too developed a ton of code
for atomistic methods and I do not see the rationale for imposing this
rigidity.  I would understand it, if the code used mathematically
cumbersome potentials, but with all these polynomial springs, the forces
could be done in a switchable manner in a single sweep...

Thanks for clarifying this, Justin. Kind of a crucial point.


On Wed, Apr 1, 2015 at 2:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 4/1/15 4:24 PM, Alex wrote:
>> That is the issue. I AM using -noparam, and x2top is reverting to an
>> incorrect
>> bond type. Which then sets off errors in grompp, because indeed it looks
>> up the
>> bond in ffbonded and sees nothing for the bond type just produced by
>> x2top. As
>> soon as I manually modify bond types in topology, the problem is solved.
> The function type is read from the header of the .rtp.  If you want to
> change the way the force field works, modify that.  If you're mixing types,
> you're out of luck in terms of automation.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
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