[Openmd-users] (no subject)

[Dan Gezelter]

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
*************************************************************