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

edesantis edesantis at roma2.infn.it
Thu Aug 17 11:18:35 CEST 2017

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 
the problem is that I received several lincs warnings and the simulation 
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 

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 De Santis

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