Re: Coarse-grained simulation with Polarizable Water crashing

From: Sourav Ray (
Date: Sat May 21 2016 - 11:39:42 CDT


My apologies for the late query, I observed the values of most of the pair
non-bonded interactions are different from those given in the NAMD martini
tutorial. My concern is, is there any need to change the bonded parameters
and dihedrals too as I work with protein molecules?


On Tue, May 17, 2016 at 2:01 AM, Sourav Ray <> wrote:

> 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.
> Regards
> Sourav
> 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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