LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] SPC/e water model
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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


From: Andrew Jewett <jewett@...1937...>
Date: Thu, 14 Sep 2017 20:24:13 -0700

On Wed, Sep 13, 2017 at 10:49 PM, 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.

If you have already installed moltemplate, then all you need to do is

1) Create a file "system.lt" with these contents:

 ---- "system.lt" file: ----

import "spce.lt"

wat = new SPCE [260]

 ---- end of "system.lt" file ----

(In this example, "260" is the number of water molecules in the PDB
file you created by vmd.  Change it for your PDB)

2) Then run moltemplate this way:

moltemplate.sh -pdb YOURFILE.pdb system.lt

That's all there is to it.

This works because several of the most popular force fields (like
"oplsaa.lt" and "gaff.lt") and water models ("spce.lt" and
"tip3p_2004.lt") are included in a subdirectory that moltemplate.sh
looks in whenever it can't find a file you requested.  If you get the
chance, you really should take a look at the contents of the the
"spce.lt" file (in the "force_fields" subdirectory).  It includes the
settings that Steve mentioned.  For one thing you may need to modify
the "spce.lt" file if later you want to mix SPC/E water with molecules
that use a slightly different (but equivalent) pair_style.  (For
example, the OPLSAA force field uses pair_style lj/cut/coul/long
instead of lj/charmm/coul/long, currently used by default in spce.lt.
The "force_field_OPLSAA/waterSPCE+methane/moltemplate_files/"
directory has a customized version of "spce.lt" for use with OPLSAA.)

Unfortunately, you would not even know these files exist or where to
find them if you installed moltemplate the easy way using:

pip install moltemplate

...all of the examples and documentation will be omitted or hidden
from view.  I'm not sure how to handle this issue.  If I start getting
a lot more questions like this, I'll remove the pip/pypi installation
option.

Cheers

Andrew

> 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:
>>>
>>> https://github.com/jewettaij/moltemplate/tree/master/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile
>>> (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
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> lammps-users mailing list
>>>> lammps-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> lammps-users mailing list
>>> lammps-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>
>>
>