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Re: [lammps-users] Fwd: Moltemplate Execution
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Re: [lammps-users] Fwd: Moltemplate Execution


From: "R. Varsha" <varsharani.0909@...24...>
Date: Thu, 28 Sep 2017 15:21:33 +0530

And yes Andrew now I am running this execution in cluster. Therefore, It will not take that much time for me.

On Thu, Sep 28, 2017 at 3:18 PM, R. Varsha <varsharani.0909@...24...> wrote:
Dear Andrew,

Thanks a lot for your response.
First I tried with pdb file to take atom's coordinates and time I didn't mention "move" command in the script (system.lt)
But when I received the output file (system.data), I found some errors in atom's coordinates. The reason of this is - that pdb file was incorrect which I used.
So I tried it with "move" command so that I can get atom's coordinates in the moltemplate itself.
I have not any choice if I will remove "move" command from system.lt .

Please help me out. I would be always thankful to you.

Thanks & Regards,
Varsha

On Thu, Sep 28, 2017 at 5:45 AM, Andrew Jewett <jewett@...1937...> wrote:
Dear Varsha

   move() commands appear in many of the moltemplate examples so far,
but it sounds like you don't need them.  Remove the lines containing
.move() in your system.lt file:

  --- explanation ---

   If you are reading the coordinates of your molecules from a file,
then just use:

  ---- "system.lt" ----
wat = new SPCE [446]

kions = new KIons [9]

clions = new ClIons [9]

... and make sure that the coordinates of the kions and clions appear
AFTER the coordinates of you water molecules.  (Your PDB, XYZ, or .RAW
file should contain coordinates in the same order the "new" commands
appear in your system.lt file.)

    If you are -not- reading the coordinates from a file, then the
.move() commands are necessary to control the position of each
molecule and prevent them from overlapping (which they do by default).

  --- speed issues ---

   The number of copies of each molecule is the product of the number
in each [] bracket following the "new" command.  (This is similar to
multidimensional arrays in C++).
So in your "system.lt" file, you requested moltemplate to create
446000 (446x10x10x10) SPCE (water) molecules, 72 (9x2x2x2) "ClIon" and
"KIon" "molecules"(atoms).  That's why it's taking so long (and using
so much memory).  (Even so, I am somewhat ashamed that a system with
1.5 million atoms currently takes moltemplate 2 hours.  If more people
are simulating these large systems, then I'll devote more effort in
making moltemplate run faster.)

Cheers
Andrew

On Tue, Sep 26, 2017 at 3:28 PM, R. Varsha <varsharani.0909@...24...> wrote:
> ---------- Forwarded message ----------
> From: "R. Varsha" <varsharani.0909@...24...>
> Date: 22 Sep 2017 13:55
> Subject: Moltemplate Execution
> To: "LAMMPS Users Mailing List" <lammps-users@...42...e.net>
> Cc:
>
> Hello all,
>
> I wanted to create lammps data file for spc/e water model with ions via
> moltemplate.
> When I executed this for small no. of water molecules I found some errors in
> system.lt file. (snapshot has attached as 22 sept.png).
>
> And one another issue I am facing that is for large no. of water molecules
> (2089) the file generation is with held from 2 hours. It is not progressing
> further. (22sept 41.png)
>
> Please help me in this regard.
>
>
> Thanks.
>
>
> Regards
> Varsha
>
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