[gmx-users] elastic restraints in MARTINI simulation

James Starlight jmsstarlight at gmail.com
Wed Mar 23 09:08:10 CET 2016


I am trying to perform 2 MARTINI simulations of several membrane
receptors within membrane i) with eldyn restrains applied on the
protein tetriary structure and ii) unrestrained md. I have no problems
in the i) case but in the ii) my simulation is very unstable under
pruduction run- it begins OK after long period of equilibration but
suddenly is crashed after 20-50ns of C run although I reduced the
integration time-step twisely in comparison to restrained run  (0.005
vs 0.01)

Fatal error:
1 of the 20932 bonded interactions could not be calculated because
some atoms involved moved further apart than the multi-body cut-off
distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see
option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

might another tricks be used here besides elastic restraints consisted
of mostly of md simulation setups e.g switching to the another
termostat (right now martini uses berendsen with gmx 4.5) e.g ussing
of sd integraator instead7

Thanks for help!


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