[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

Peter Kroon p.c.kroon at rug.nl
Thu Aug 17 13:03:17 CEST 2017

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.


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

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