From: Karteek Bejagam (karteek4_at_vt.edu)
Date: Fri Dec 30 2016 - 18:14:17 CST
Hello Jeff,
I have modified the NAMD code as suggested and built it again.
Now, I could see the bonds are constrained. Thanks a lot for the
suggestions.
I have an additional question with the martini FF.
I have simulated the trajectory and determined the dielectric constant
using the formula ( from the fluctuations of dipole moment).
Dielectric constant comes around 16.6 instead of ~64. I was wondering do
we need to multiply with a factor of 4 (equivalent of AA water molecules).
I could able to see the dipole moment distribution coming out consistent
with that of paper, so there may be any problem in determining the
dielectric constant.
Do we need to multiply the factor of 4?
Thanks in advance,
Karteek
On Thu, Dec 22, 2016 at 2:24 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Hey, Karteek, I was also doing this to use Martini polarizable water.
> The files I use and a description of what to do is at:
>
> http://jeffcomer.us/downloads.html
>
> For posterity, I'll paste some of the details below:
>
> Easy Modifications for Martini Polarizable Water
>
> 1. Make NAMD think that the WP and WM particles are hydrogen (both WP
> and WM have type D in my parameter file)
>
> Change the following line in Molecule.C
> } else if (atoms[atom_number-1].mass <=3.5) {
> to
> } else if (atoms[atom_number-1].mass <=3.5 || strcmp(atom_type,"D")==0 ) {
>
> 2. splitPatch line SimParameters.C
> else if (!strcasecmp(s, "1-2"))
> {
> exclude = ONETWO;
> //splitPatch = SPLIT_PATCH_POSITION;
> }
>
> 3. Enable PME and martiniSwitching
> //NAMD_die("Do not use Particle Mesh Ewald with Martini. Set: PME off");
>
>
> The NAMD options that I'm using are:
> # Martini
> martiniDielAllow on
> cosAngles on
> martiniSwitching on
> dielectric 2.5
>
> # Electrostatics
> # PME is optional for polarizable Martini
> pme on
> pmeGridSpacing 1.2
>
> # Integration
> rigidBonds all
> timestep 25
> nonBondedFreq 1
> fullElectFrequency 1
> stepsPerCycle 10
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website: http://jeffcomer.us
>
>
> On Thu, Dec 22, 2016 at 10:00 AM, Karteek Bejagam <karteek4_at_vt.edu> wrote:
> > Thanks Jeff,
> >
> >
> > I am simulating polarizable CG martini model, where we need to constrain
> two
> > bonds from the central bead. Whose mass are 24 each.
> >
> > I am looking such bonds in my simulations.
> >
> > Thanks
> > Karteek
> >
> > On 22 Dec 2016 10:38, "Jeff Comer" <jeffcomer_at_gmail.com> wrote:
> >>
> >> Hi Karteek,
> >>
> >> NAMD only applies rigid bonds to hydrogen atoms. It decides what is
> >> hydrogen based on mass. If you want to rigidify other bonds, you can
> >> either reduce the atom's mass to something greater than 1.0 and less
> >> than 3.5 or alter the code that decides whether the atom is hydrogen
> >> or not. See the line "} else if (atoms[atom_number-1].mass <=3.5) {"
> >> in Molecule.C. You can change it to something like the following for
> >> to get atoms named "X..." to be identified as hydrogen:
> >>
> >> } else if ( atoms[atom_number-1].mass <=3.5 ||
> >> atomNames[atom_number-1].atomname[0] == 'X' )
> >>
> >> I've only done this for atoms with a single bond. I'm not sure it
> >> works for other geometries.
> >>
> >> Regards,
> >> Jeff
> >>
> >> –––––––––––––––––––––––––––––––––––———————
> >> Jeffrey Comer, PhD
> >> Assistant Professor
> >> Institute of Computational Comparative Medicine
> >> Nanotechnology Innovation Center of Kansas State
> >> Kansas State University
> >> Office: P-213 Mosier Hall
> >> Phone: 785-532-6311
> >> Website: http://jeffcomer.us
> >>
> >>
> >> On Wed, Dec 21, 2016 at 11:00 PM, Karteek Bejagam <karteek4_at_vt.edu>
> wrote:
> >> > Dear NAMD users,
> >> >
> >> > I would like to constrain a bond that does not involve hydrogen.
> >> >
> >> > I have tried to use "rigidBonds all" but it fails.
> >> >
> >> > Can anyone help me to figure out any way to constrain the bond?
> >> >
> >> > I was looking for algorithms like SHAKE/RATTLE/SETTLE to constrain a
> >> > bond.
> >> >
> >> > Thanks in advance,
> >> >
> >> > Karteek
>
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