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Re: [lammps-users] SPC/e water model
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Re: [lammps-users] SPC/e water model


From: "R. Varsha" <varsharani.0909@...24...>
Date: Thu, 14 Sep 2017 11:54:12 +0530

Dear Steve,
I had read that part also. But first I want to do all these things in VMD.


Thanks

On Thu, Sep 14, 2017 at 11:19 AM, R. Varsha <varsharani.0909@...24...> wrote:
Dear Andrew,
I went through moltemplate to create spc/e water model data file by loading the pdb file which I had created in the VMD already.  I got the data file for spc/e water model. But here I am unable to get files related to spc/e water box so that I can see that water box in vmd.

And when I use the first approach that is vmd topotools to generate data file for that water box which is TIP3P, I found some errors in that. I am interested to know that how can I convert this data file into spc/e data in VMD.

On Thu, Sep 14, 2017 at 1:18 AM, Steve Plimpton <sjplimp@...24...> wrote:
I don't know about the VMD part, but on the LAMMPS
side you just need a few different params in your
pair style for SPC/E vs TIP3P,  See Section howto 6.7
thru 6.9.

Steve

On Wed, Sep 13, 2017 at 2:27 AM, Andrew Jewett <jewett@...1937...> wrote:
My impression was that once you have generated the atom coordinates in VMD, you would use Axel's topotools to create the LAMMPS data file and input script with the force field parameters.  Since you choose these force field parameters manually, they could be either TIP3P or SPC/E, or anything else you desire.

Alternatively you could save the coordinated as an .XYZ or .PDB file and load them into moltemplate and then choose SPC/E or TIP3P water.  Those water models are already included with moltemplate, so you don't have to specify the parameters manually.  There's an example/tutorial how to do this included with moltemplate.  Currently, you can also get the files for that example here:
(The URL for these files could change in the future.)

This exact topic is also discussed in chapter 4 of the moltemplate manual.  This is the main introductory chapter, and it is only a few pages long.

I hope this gets you started.
Cheers.

Andrew

On Sep 12, 2017 11:57 PM, "R. Varsha" <varsharani.0909@...24...> wrote:
Hello everyone,

I want spc/e water model for my simulation. I have created a water box in VMD but it is TIP3P by default.
Is there a way to create spc/e water model in vmd.?


Thanks,


Regards
Varsha


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