Re: Equivalent of gromacs' "rdd" option

From: Marlon Sidore (
Date: Mon Jul 25 2016 - 10:44:48 CDT

I am currently using restarts in order to keep simulating despite the
crashes actually, as it sometimes runs for quite a long time (10 to 600ns).

I will look into gromacs (with the preliminary colvars) or how to add LINCS
to NAMD, thanks. It would indeed be a lot more handy to use gromacs for
this ~~

The temperature is set to 325K to avoid the freezing of the CG water. The
system also has antifreeze particles, so I could probably lower this indeed
- Marrink & al usually run these temperatures if they don't have the
antifreeze particles (for example in their paper for the
cyanobacteria/plant membrane).

Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille

2016-07-25 17:26 GMT+02:00 Fotis Baltoumas <>:

> Also, I just noticed, you use a temperature of 325 K (52 Celsius). Is
> that high temperature necessary, for instance? If not, try using a more
> "normal" temperature like 300 or 310 K. If lipid phase transitions is what
> you're worried about, keep in mind that MARTINI lipids generally have lower
> melting temperatures.
> On 07/25/2016 06:08 PM, Fotis Baltoumas wrote:
> Hi,
> Unfortunately, I don't know of any workarounds. Theoretically, you could
> edit the part of the source that contains the rigidBonds function (that's
> where the SHAKE/RATTLE constraints algorithm is) and add LINCS-like code,
> but that would require more advanced knowledge of the NAMD code than what I
> can offer.
> You could try fooling around with the force magnitudes you use in the
> elastic network or the colvars code, maybe that would fix things somewhat--001a113cd19a0fcced053877aab6--

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