[Openmd-users] (no subject)

[Dan Gezelter]

Dear Tanni,

  Copper is also an FCC metal, with a lattice constant of 3.597 angstroms, so if you are following the instructions here:  

http://openmd.org/building-and-equilibrating-a-gold-nanoparticle-in-openmd

the gold lattice constant (4.08) would be replaced by 3.597.

You’ll also need to modify the starting file with the molecule definition to use copper instead of gold:

<OpenMD>
  <MetaData>
molecule{
  name = “Cu";
  atom[0]{
    type = “Cu";
    position(0.0, 0.0, 0.0);
  }
}

component{
  type = “Cu";
  nMol = 1;
}

forceField = "SC";
forceFieldFileName = "SuttonChen.QSC.frc";
  </MetaData>
</OpenMD>



> On May 20, 2017, at 9:19 AM, tanni bhattacharjee <tanni222byc at gmail.com> wrote:
> 
> IF I WANT TO CREATE COPPER NANOPARTICLE WHAT ARE THE PRAMETER WHICH I SHOULD CHANGE?
> 
> 
> On Fri, May 19, 2017 at 8:55 PM, tanni bhattacharjee <tanni222byc at gmail.com> wrote:
> thanks!it worked
> 
> On Fri, May 19, 2017 at 6:56 PM, Dan Gezelter <gezelter at nd.edu> wrote:
> Dear Tanni,
> 
> It looks like the directory where openmd was installed is not in your path.  By default, it will install all of the relevant binaries in /usr/local/openmd/bin, so you'll need to add this directory to your path:
> 
> If you are using bash, ksh or sh as your shell:
> 
> export PATH=$PATH:/usr/local/openmd/bin
> 
> If you are using tcsh or csh as your shell
> 
> setenv PATH ${PATH}:/usr/local/openmd/bin
> 
> The correct path command can be added to the relevant startup file .cshrc (for csh and tcsh) or .profile (for sh and ksh) or .bash_profile (for bash).
> 
> Best regards,
> 
>   --Dan Gezelter
> 
> 
> > On May 18, 2017, at 11:14 PM, tanni bhattacharjee <tanni222byc at gmail.com> wrote:
> >
> > thanks!actually i have tried to install openmd but i think it is not installing.will you tell me whether i am doing all the steps correctly
> > 1.curl -o openmd-2.4.1.tar.gz http://openmd.org/releases/openmd-2.4.1.tar.gz
> > 2.tar zxf openmd-2.4.1.tar.gz
> > mkdir build
> >
> > 3.cd build
> > cmake ../openmd-2.4.1
> >
> > 4.make
> >
> >
> > 5.make -j 4
> >
> >
> > 6.umask 0022; sudo make install
> >
> > after this when i tried   this example                 openmd ar864.omd its showing  error  No command 'openmd' found, did you mean:
> >  Command 'openmx' from package 'openmx' (universe)
> >
> >
> >
> >
> >
> >
> >
> > On Thu, May 18, 2017 at 11:23 PM, Dan Gezelter <gezelter at nd.edu> wrote:
> > Dear Tanni,
> >
> >  You might want to take a look at the example here:  http://openmd.org/building-and-equilibrating-a-gold-nanoparticle-in-openmd/
> >
> > Notably, steps 4->6 show how to  set up parameters to assign initial velocities and run the program using openmd.
> >
> > Best regards,
> >
> >  --Dan Gezelter
> >
> >
> > > On May 18, 2017, at 6:52 AM, tanni bhattacharjee <tanni222byc at gmail.com> wrote:
> > >
> > >
> > > ---------- Forwarded message ----------
> > > From: tanni bhattacharjee <tanni222byc at gmail.com>
> > > Date: Thu, May 18, 2017 at 4:18 PM
> > > Subject:
> > > To: openmd-users at openmd.org, openmd-developers at openmd.org
> > >
> > >
> > > hello users!
> > >
> > > i want to create gold nanoparticle.will you please tell me the steps how should i proceed.i am completely new in openmd.
> > >
> > > after creating my initial structure as pdb or xyz how can i processed further?
> > > what is the command to run omd file?
> > >
> > >
> > >
> >
> >
> >
> > *************************************************************
> >  J. Daniel Gezelter
> >  Professor and Director of Undergraduate Studies
> >  Department of Chemistry and Biochemistry
> >  251 Nieuwland Science Hall
> >  University of Notre Dame
> >  Notre Dame, IN 46556-5670
> >
> >  gezelter at nd.edu | (574) 631-7595 | http://gezelterlab.org
> > *************************************************************
> >
> >
> 
> 
> 
> *************************************************************
>  J. Daniel Gezelter
>  Professor and Director of Undergraduate Studies
>  Department of Chemistry and Biochemistry
>  251 Nieuwland Science Hall
>  University of Notre Dame
>  Notre Dame, IN 46556-5670
> 
>  gezelter at nd.edu | (574) 631-7595 | http://gezelterlab.org
> *************************************************************
> 
> 
>