normal .mdp options for Martini simulations with GMX 5.0

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3 years 1 week ago #5442 by James Starlight
.mdp options for Martini simulations with GMX 5.0 was created by James Starlight
Hello,

I just tried to use all mdp options provided in the Martini tutorials with the last gromacs on my local cluster and obtained below errors

NOTE 1 : ./mdp/minimization.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# NOTE 2 [file ./mdp/minimization.mdp]: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off and vdw_modifier=Force-switch ERROR 1 [file ./mdp/minimization.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported NOTE 3 [file ./mdp/minimization.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. ERROR 2 [file ./mdp/minimization.mdp]: Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier. NOTE 4 [file ./mdp/minimization.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Could someone provide me with valid electrostatics parameters for such GMX version assuming that I performing CG MD of membrane protein. Thanks!![file ./mdp/minimization.mdp, line 20]:
./mdp/minimization.mdp did not specify a value for the .mdp option
"cutoff-scheme". Probably it was first intended for use with GROMACS
before 4.6. In 4.6, the Verlet scheme was introduced, but the group
scheme was still the default. The default is now the Verlet scheme, so
you will observe different behaviour.

Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#

NOTE 2 : Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off and vdw_modifier=Force-switch ERROR 1 [file ./mdp/minimization.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported NOTE 3 [file ./mdp/minimization.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. ERROR 2 [file ./mdp/minimization.mdp]: Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier. NOTE 4 [file ./mdp/minimization.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Could someone provide me with valid electrostatics parameters for such GMX version assuming that I performing CG MD of membrane protein. Thanks!![file ./mdp/minimization.mdp]:
Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off
and vdw_modifier=Force-switch


ERROR 1 : With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported NOTE 3 [file ./mdp/minimization.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. ERROR 2 [file ./mdp/minimization.mdp]: Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier. NOTE 4 [file ./mdp/minimization.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Could someone provide me with valid electrostatics parameters for such GMX version assuming that I performing CG MD of membrane protein. Thanks!![file ./mdp/minimization.mdp]:
With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported


NOTE 3 : You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. ERROR 2 [file ./mdp/minimization.mdp]: Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier. NOTE 4 [file ./mdp/minimization.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Could someone provide me with valid electrostatics parameters for such GMX version assuming that I performing CG MD of membrane protein. Thanks!![file ./mdp/minimization.mdp]:
You have set rlist larger than the interaction cut-off, but you also have
verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.


ERROR 2 : Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier. NOTE 4 [file ./mdp/minimization.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Could someone provide me with valid electrostatics parameters for such GMX version assuming that I performing CG MD of membrane protein. Thanks!![file ./mdp/minimization.mdp]:
Explicit switch/shift coulomb interactions cannot be used in combination
with a secondary coulomb-modifier.


NOTE 4 : The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Could someone provide me with valid electrostatics parameters for such GMX version assuming that I performing CG MD of membrane protein. Thanks!![file ./mdp/minimization.mdp]:
The switch/shift interaction settings are just for compatibility; you
will get better performance from applying potential modifiers to your
interactions!


Could someone provide me with valid electrostatics parameters for such GMX version assuming that I performing CG MD of membrane protein.


Thanks!!

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3 years 2 days ago #5448 by riccardo
For parameter files to run Martini with GMX 5.0, please see:
cgmartini.nl/index.php/force-field-parameters/input-parameters
(check the publication for details)

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5 months 1 day ago #7844 by bart
I think it doesn't matter in the EM step if you use steepest decent. I always thought it only looks at the interaction energies, but motion isn't actually propagated (therefore there are no velocities). As soon as you start to use an integrator this will start to matter.

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5 months 7 hours ago #7856 by riccardo
Does your system run normally after this minimization? If so, there's no need to bother about why you don't get lower forces at the end of the energy minimization.

If it does not run (i.e., it crashes), take a look (VMD or similar) at your system to check whether there are parts of the system which could give rise to such forces (e.g., overlapping or too close beads) and try to fix that.

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