From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Thu Dec 22 2016 - 13:24:30 CST
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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