Re: Coarse-grained simulation with Polarizable Water crashing

From: Sourav Ray (
Date: Mon May 16 2016 - 15:31:14 CDT

Thanks a lot!

This clarifies every issue I had with polarizable water, I didn't bother
about the "exclude" command to be frank. I was worried about how to include
the TP TW exclusion and to apply PME to the martini system.

Seems I will have to build NAMD (something that I will try for new).
Anyway, I figured out why the system was crashing so frequently. I had put
the K value as close to ~60 instead of ~11 used by yourself (also had to
edit parameter and topology files for first time!) and apparently it is not
suitable for low "langevindamping". Now the simulation is off the ground,
but will definitely implement your suggestions and build the NAMD.


On Mon, May 16, 2016 at 10:34 PM, Jeff Comer <> wrote:

> Hi,
> It is not simple to correctly implement Martini polarizable water in
> NAMD. I've put up some information on my webpage that might help:
> The problem you are having is likely due to the fact that you are not
> excluding nonbonded interactions between the WM and WP particles of
> the polarizable water. Martini uses "exclude 1-2", but there are
> supposed to be exclusions between these two particles (see the
> official Gromacs input martini_v2.2P.itp), which are not directly
> connected by a bond. An easy way to make this exclusion is to add a
> bond between the WM and WP particles with a very small spring constant
> (I use 1e-20). If you use 0.0, NAMD will ignore the bond and not
> include the exclusion, so you have to use something small but nonzero.
> Specific exclusions can also be specified in the psf, but the format
> is really strange.
> Another issue with implementing the Martini polarizable water in NAMD
> is that the bonds are supposed to be rigid. This requires altering the
> NAMD source code. You need to make NAMD think that the WM and WP
> particles are hydrogen atoms so that rigid bonds will be enforced. To
> do this, find the line in Molecule.C that says
> } else if (atoms[atom_number-1].mass <=3.5) {
> and change it to
> } else if (atoms[atom_number-1].mass <=3.5 || strcmp(atom_type,"D")==0 ) {
> Here I'm assuming that the type of the WM and WP particles is "D" as
> in the official Martini Gromacs input.
> You also have to comment out the "splitPatch" line (see below) in
> SimParameters.C. With Martini, you should be using "exclude 1-2", for
> which NAMD forces you to use "splitPatch position" regardless of
> whether you put "splitPatch hydrogen" in the config file. Maybe
> someone else can tell me why this is and whether I'm breaking
> something by commenting this out.
> else if (!strcasecmp(s, "1-2"))
> {
> exclude = ONETWO;
> //splitPatch = SPLIT_PATCH_POSITION;
> }
> Also you need to comment out the following line in SimParameters.C if
> you want to use PME with Martini water, which is explored a little bit
> in the original Yesylevskyy et al. paper. If you're using polarizable
> Martini water, you probably have a highly charged system and care
> about things like ion distributions. For this PME gives better
> results.
> //NAMD_die("Do not use Particle Mesh Ewald with Martini. Set: PME off");
> Other things required for correct implementation:
> # Martini
> martiniDielAllow on
> cosAngles on
> martiniSwitching on
> dielectric 2.5
> Regards,
> Jeff

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