[gmx-users] Setting custom atoms in FF

[Alex]

I will certainly consider it.

In all honesty, however, the situation is due to the fact that I have
graphene constants that have been calculated a certain way from the Brenner
potential. The problem at hand can be solved without modifying GMX code by
merely calculating proper constants for _all_ angle function types (within
GMX convention). I recall posting a while back about properly
parameterizing graphene, and heard mostly "meh" from the locals (I don't
think you participated in that discussion).

Alex

On Wed, Apr 1, 2015 at 2:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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