[gmx-users] Setting custom atoms in FF

[Justin Lemkul]

On 4/1/15 4:37 PM, Alex wrote:
> 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

It's a simple convention that works well for biomolecular systems, for which 
GROMACS is principally suited.  It works well in nearly all cases, but clearly 
not here.  If you want to file a feature request, we welcome feedback and input 
on redmine.gromacs.org, but the developers do what they have time for based on 
their interests.  If you want to submit a patch to introduce new functionality, 
great!  Please do; we need contributions from users for things like this.

-Justin

> 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.
>
> Alex
>
>
> 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
>> 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================