You shouldn't use PRODRG, well the default output at least (e.g. see
http://pubs.acs.org/doi/abs/10.1021/ci100335w).
The ATB is generally pretty good, and although it might not be perfect
here (e.g. as you have sugars in your structure which have been pretty
heavily optimised in different variants of the GROMOS force field; see
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24229/abstract and
http://pubs.acs.org/doi/abs/10.1021/ct300479h amongst other papers), I'd
be pretty surprised that the topology is causing LINCS warnings/crashes.
If it were me, I'd definitely simply the situation to begin with and
look at one of your surfactants in water. This will help you ensure your
starting structure is fine and also allow you to determine exactly what
bit of the system is causing the crashes.
Cheers
Tom
On 18/08/17 14:10, edesantis wrote:
Hi,
thank you for both your suggestions,
as Tom, I also think that the structure of the surfactant could be
modified by the presence of other surfactants in the aggregate form,
maybe it is not and only the non bonded parameters can have a role in
the formation of the aggregates (I am quite a beginner of these kind
of simulation...)
anyway my all atomistic simulation has double purpose,
firstly, since it was the first time I used an ATB created topology, I
wanted to see if the topology well reproduced the aggregations of
these kind of surfactants,
and secondly, I want to use the bonds and angles distribution to
parametrize my Martini model, and see again if also the Martini model
can reproduce similar aggregates to those seen in the aa simulation
I've tried to continue the simulation using dt=0.00182 ps and after a
while there are lincs warnings, so it smells like a bad
parametrization of the all-atomistic topology, as Tom said.
till now I've always simulated standard proteins, so I don't know how
to parametrize the force field for these small molecules, I am now
trying PRODRG (once I have the token to use it), if you have other
suggestion are welcome....
for gromos sugar ff, do you have any reference??
for what concern the needed to introduce this kind of molecules,
I think it is quite necessary, these surfactants, use to solubilize
the proteins in the crystal, are forming micelles around them and,
since the final goal of my Martini simulation is the reproduce the
diffuse scattering in the crystals, I think it is quite important to
reproduce all the crystal components in order to have a system that is
more similar to the real condition.
thank you again
Emiliano
On 2017-08-18 14:22, Thomas Piggot wrote:
Hi Peter,
I'd imagine that in particular the CG angle parameters between beads
may well be different if you determined them by mapping on to a single
one of these surfactants in water, compared to mapping onto an
ensemble of structures in an aggregated state as the hydrophobic
chains would try to 'fold up' and bury themselves away from the water.
I haven't actually tried this though, that's just how I think it would
probably be. Nice and easy to test anyway, if Emiliano really does
need to parameterise this molecule.
Cheers
Tom
On 18/08/17 09:04, Peter Kroon wrote:
Hi Tom,
thanks for your thoughts :)
I want to respond to your sampling argument: I figured that a
surfactant
in solution is "more free" to sample conformations due to sterics than
one in an aggregated state, and that sampling would therefore be
faster.
Your point of sampling the bonded conformations from a solvated vs an
aggregated state is a powerful one though (then again, shouldn't the
difference in aggregated state vs solvated state come from the
non-bonded parameters? i.e. the bonded parameters should be the same
for
both).
Peter
On 17-08-17 21:10, Piggot T. wrote:
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: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
Peter Kroon [p.c.kr...@rug.nl]
Sent: 17 August 2017 12:03
To: gromacs.org_gmx-users@maillist.sys.kth.se
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
--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
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