From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Sat May 21 2016 - 17:14:36 CDT
Hello,
Actually, you need to edit quite a lot. Specifically, you need to add
particle definitions and change topology for ALL polar and charged
groups, since in polarizable MARTINI these should contain virtual sites,
just like the polarizable water model does. For example, compare
standard MARTINI parameters for Serine with polarizable ones (given in
GROMACS format, but you should get the main idea):
Standard MARTINI
;;; SERINE
[ moleculetype ]
; molname nrexcl
SER 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P5 1 SER BAS 1 0
2 P1 1 SER SID 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.25 7500
Polarizable MARTINI
;;; SERINE
[ moleculetype ]
; molname nrexcl
SER 1
[ atoms ]
;id type resnr residu atom cgnr charge mass
1 P5 1 SER BB 1 0 72
2 N0 1 SER SC1 2 0 0
3 D 1 SER SC2 3 +0.40 36
4 D 1 SER SC3 4 -0.40 36
[virtual_sites2]
; Site from funct a
2 3 4 1 0.5
[bonds]
; i j funct length force.c.
1 2 1 0.25 7500
[constraints]
; i j funct length
3 4 1 0.28
Also, keep in mind that those files from the NAMD tutorial are for
version 2.0/2.1 of the force field. The polarizable water model was
designed for version 2.2, which contains several changes, especially for
aromatic side chains. Although, in principle, you could just modify the
2.1 version to include polarizability features, it would probably be
better to convert the 2.2 files from the GROMACS format to the
NAMD/CHARMM format.
On 05/21/2016 07:39 PM, Sourav Ray wrote:
> Greetings
>
> 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?
>
> Regards
> Sourav
>
> On Tue, May 17, 2016 at 2:01 AM, Sourav Ray <souravray90_at_gmail.com
> <mailto:souravray90_at_gmail.com>> 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 <jeffcomer_at_gmail.com>
> 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:
> http://jeffcomer.us/downloads.html
>
> 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
>
>
>
-- ******************************************* 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 :fbaltoumas_at_biol.uoa.gr http://biophysics.biol.uoa.gr http://bioinformatics.biol.uoa.gr *******************************************
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:28 CST