Re: Equivalent of gromacs' "rdd" option

From: Fotis Baltoumas (
Date: Fri Jul 22 2016 - 11:05:50 CDT


The quick answer is no, there isn't any equivalent of -rdd in Namd. But
you could try replicating its effect by fooling around with parameters
that determine the system partition size, such as "margin" (manually set
its value in the configuration file, start with low values and increase
until the crashes stop). Although, until you give us your configuration
parameters and the actual error you get, I cannot be of more help.

Having said that, it should be pointed out that the NAMD version of
protein topology/parameters of MARTINI is problematic at best. The main
issue is that, since NAMD doesn't implement any equivalent for LINCS
(constraints for all bonds, not just those of hydrogens), all bond
constraints were modeled as regular bonds but with very high force
constant values, which leads to a lot of crashes when timesteps of 20 fs
or above are used. If you're using such a value, try lowering the
timestep to 10 fs and see if that solves your issue. Most crashes I
have had when using MARTINI with NAMD to simulate proteins were solved
by doing that (the lipid parameter implementation was more successful
since no constraints needed to be defined).

Hope that helps

On 07/22/2016 06:12 PM, Marlon Sidore wrote:
> Hello,
> I am simulating membrane proteins with the martini forcefield in NAMD but
> have been struggling with random crashes from the beginning of this journey

Fotis A. Baltoumas
Phd Candidate, Bioinformatics Postgraduate Programme
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
email :

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