On 4/10/20 9:16 AM, Alex wrote:
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had power/network for a while due to some bad storms here.
GROMOS force fields are parametrized assuming all bonds are fixed, so
your constraints should be "all-bonds" not "h-bonds."
Interesting, hopefully that is the problem.
I would also suggest you thoroughly validate the quality of the epoxy
molecule topology against QM data and bulk-phase properties, if possible.
As the ATB folks claim, the parameterization has been performed against a
very high level DFT calculation, especially for the molecules with less
than 50 atoms.
I already have tested the density and it is in agreement with the
experimental value.
Regarding the "comm-grps = " , would you also please kindly let me know
which one you would recommend for this system + plus a small single
molecule called MOL_A which defuses from water inside the epoxy, specially
for the PMF calculation of the Mol_A?
comm-grps = Other SOL ;; (Other = thin_film and Mol_A)
or
comm-grps = system
I saw the conversation with David about this. I have nothing to add that
he hasn't already said.
-Justin
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Justin A. Lemkul, Ph.D.
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Lab: 303 Engel Hall
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