Hi Peter/Emeliano,
I'm not sure I agree with some of what Peter says, but I guess it's probably a
matter of taste. If it were me, I'd definitely want my atomistic simulations to
behave properly before trying to develop CG parameters based upon these
simulations. I know that the coarse-graining will lose some of the detail, but
I'd want all of the detail in the atomistic simulations to be as accurate as
possible to hopefully develop reasonable CG parameters with the appropriate
detail lost but the underlying, correct, behaviour retained. You cannot be sure
of this in your case here.
As for the sampling in the atomistic simulations, I guess you mean you could
run one in a box a lot quicker as the system is smaller? With 50, you obviously
have more surfactants in there to give you a lot more data for the
parameterisaton and as a larger simulation size should scale better, you
probably will get better sampling (in terms of stats) with the 50 in a box
setup. Plus you get to also check, as Emeliano said, that the atomistic
simulations behave sensibly and aggregate/form micelles, etc. (whatever this
surfactant does). You can also look for differences in the CG bonds/angles
depending upon what state the molecule is in (solvated, aggregated, etc.). For
this specific case, I guess this may not matter if it's only one bound to a
protein though.
Anyway, regarding the original post, I would firstly ask is it really necessary
to have this molecule in the simulations? I couldn't tell from the post why
this was wanted to be included. Is it an important ligand, or is it just in the
experimental structure as an artefact of the crystallisation
conditions/procedure (which I suspect is quite likely)? If it's the latter,
there is no need to go to all this effort. As for the LINCS warnings, it's hard
to exactly say without seeing the topology/starting structure. It could well be
that the ATB topology for things like the sugars isn't that great (the GROMOS
sugar force fields are heavily optimised for things like dihedrals), or it
could potentially be an issue with the starting structure of the system. If it
were me, I would likely make the atomistic parameters manually through
combining the building blocks available within the GROMOS force field.
Cheers
Tom
________________________________________
From: [email protected]
[[email protected]] on behalf of Peter Kroon
[[email protected]]
Sent: 17 August 2017 12:03
To: [email protected]
Subject: Re: [gmx-users] surfactants simulation topology generation with
Automated Topology Builder and lincs warnings
Hi Emeliano,
since you're just going to use the atomistic simulation to get some
parameters for your CG model, I don't think the differences will be
significant --- the approximations your are going to make in CG will be
larger anyway. I would even argue you'll be better off if you run just
one surfactant in water to get your bonded parameters, rather than 50,
since sampling will be better.
For further validation of your Martini model, you can (should) look at
some more macroscopic properties as well, such as dimerization free
energy and partition free energy.
Peter
On 17-08-17 11:18, edesantis wrote:
dear gromacs users,
I have a problem in the simulation of a surfactant, Octyl Glucose
Neopentyl Glycol, that is present in protein crystals.
my goal is to have a coarse grained model for this surfactant with
Martini ff.
to do that I have to generated an all atomistic simulation to use as a
reference to build the Martini topology.
I've downloaded the pdb file https://www3.rcsb.org/ligand/37X of the
surfactant and since there is not an existent ff for the all atom
simulation, I've generated it from ATB web site
(https://atb.uq.edu.au/) for gromos 53a6 united atoms parameters set.
I've built a cubic box of 7 nm of side, I've put inside the box 50
surfactant molecules and then I've solvated it with spc water.
then after a minimisation with the sd both in vacuum and in the
presence of the solvent, I proceeded with a md in the NVT ensemble,
with dt=0.002 ps
the problem is that I received several lincs warnings and the
simulation stops.
so I've decreased the dt to 0.0015 ps and the simulation ends without
problem, I've continued it increasing the dt to 0.0018 for 20ns, and
than to 0.00183 ps and there are not any kind problem.
but when I try to increase dt to 0.00186 the lincs warning problems
came again.
watching the simulation movie with vmd, I can see that the surfactants
form an aggregate (as they should do), and it seems to me that there
is not an apparent weird behavior.
should I have to continue to increase the dt with small increments
(i.e. 0.0002ps at each run) or can I just trust to the results I have
(angles and bonds distributions) using the dt=0.00183 ps??
could the problem of the lincs warning arise from the generation of
the topology with ATB??
thank you in advance
Emiliano
