[gmx-users] force field not found
nedomacho at gmail.com
Mon Oct 1 20:25:55 CEST 2018
I don't really work much with small organics or polymers (angle
descriptions should be quite important there), so my review would be at
the level of what the good old grumpy robot grompp already does. If you
are sure of the parameters and your tests are coming out okay, given
some criteria, I say why not share it..
On 10/1/2018 11:46 AM, pbuscemi wrote:
> Alex, Justin,
> I've managed to make and run polymers using Avogadro ,modifying the n2t, then creating the top using x2top under 54a7 ff. The method may be useful for others but before presenting it to the user group, it should be reviewed so that glaring mistakes/concepts are revised. If you think it worthwhile, would either of you be agreeable to reviewing the process?
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Alex
> Sent: Sunday, September 30, 2018 12:44 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] force field not found
> Yeah, if it is missing bonded parameters, you can always try to find
> something similar, at least with OPLS-AA -- don't really know about the
> other ff.
> On 9/29/2018 8:58 PM, paul buscemi wrote:
>> I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3 pdb model. oplsaa works fine, but not 54a7 FF generating the erro “ cannot find forcefield for C “ Th two CH3’s do not cause the error found but the fourteen CH2’s.
>> In the ffbonded.itp bond angle types i see CH2-S-CH3 , C-CH2-C and CH2-S_S, but not C-CH2-C. Can I add a new atomas ga 5_55 by anology or hunt for the correct parameters ? (I’ m trying his now )
>> I am assuming the n2t nor the rtp do not have to be modified since x2top does not rely on the rtp. This is a fairly basic but essential task, and would surly like to master it.
>>> On Sep 27, 2018, at 5:47 PM, Alex <nedomacho at gmail.com> wrote:
>>> Never dealt with TiO2, but the path to parameterizing forcefields for
>>> solid-state structures in MD is becoming more and more straightforward,
>>> e.g., J. Phys. Chem. C 2017. 121(16): p. 9022-9031.
>>> On Thu, Sep 27, 2018 at 4:11 PM paul buscemi <pbuscemi at q.com> wrote:
>>>> There are so many important reactions / applications in which protein
>>>> polymer interactions play a role that the ability to generate of
>>>> polymers should be part of gromacs repertoire. I’ll keep plugging away on
>>>> this and report to the community if I can break the code - other than
>>>> using the very good but terribly expensive commercial programs. I would
>>>> not doubt that many have already accomplished this this task, but it is not
>>>> well tracked within this group.
>>>> I might not approach a Molysulfidnitride substrate , ( making turbine
>>>> blades ??) but TiO2 is indeed another surface very popular with proteins.
>>>> Most every nitinol surface is essentially TiO2. If you have some pointers
>>>> on that, I’m listening.
>>>> Thank you again for the assist.
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