On 10/1/18 9:25 PM, paul buscemi wrote:
Alex,
Thanks for your feedback.
So far the critters seem to be compliant, align when they should with H
bonding, crumple when they should, and grommp’s major complaint is when I
forget to adjust the number of residues. But I am unseasoned in MD and
following the discussions on gmx-users you come to realize that there is more
to MD than just good looks. Another set of eyes would do no harm. I’ll do
some more vetting and if the polymers react appropriately in polar and
non-polar solvents, I will set it loose.
There are two separate things to be considered: (1) whether your
procedure works for generating a topology and (2) whether the parameters
applied are physically valid. I usually have disclaimers in my tutorials
that the user should not simply assume that my parameters for things are
correct or necessarily best for any given system, but that the protocol
itself is robust.
-Justin
Best
Paul
On Oct 1, 2018, at 1:25 PM, Alex <nedoma...@gmail.com> wrote:
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..
Alex
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?
Thanks
Paul
-----Original Message-----
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Alex
Sent: Sunday, September 30, 2018 12:44 AM
To: gmx-us...@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.
Alex
On 9/29/2018 8:58 PM, paul buscemi wrote:
Alex,
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.
Thanks,
Paul
On Sep 27, 2018, at 5:47 PM, Alex <nedoma...@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.
Alex
On Thu, Sep 27, 2018 at 4:11 PM paul buscemi <pbusc...@q.com> wrote:
Alex,
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.
Regards
Paul
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