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


From: Andrew Jewett <jewett@...1937...>
Date: Tue, 19 Sep 2017 11:40:19 -0700

Glad you found it.
   For anyone else who stumbles upon this discussion, the .move()
commands are explained in the first couple pages of the
introduction/tutorial chapter at the beginning of the moltemplate
manual.  (At http://moltemplate.org/doc/  Currently, this is chapter
"4", although the numbering may change later.)  Also read the
"coordinate generation" chapter (currently chapter 6).  These are
short chapters, ~7-8 pages long.  A complete list of movement commands
is located in the "Quick Reference" chapter (currently chapter 3.3)
Cheers
Andrew

On Tue, Sep 19, 2017 at 2:37 AM, R. Varsha <varsharani.0909@...24...> wrote:
> Hello Andrew,
>
> Now I got the meaning of that. And I understood about removal of "move"
> also. Now you don't need to explain.
> I am sorry.
>
>
> Thanks
>
> Regards
> Varsha
>
> On Tue, Sep 19, 2017 at 2:04 PM, R. Varsha <varsharani.0909@...24...>
> wrote:
>>
>> Dear Andrew,
>>
>> Thanks a ton to explain about all these things.
>> Here I want to understand some lines in system.lt file.
>>
>> "            wat  = new SPCE  [10].move(0.00, 0.00, 3.45)
>>                                                [10].move(0.00, 3.45, 0.00)
>>                                                [10].move(3.45, 0.00, 0.00)
>>
>>                 na = new NaIon [2].move(0,0,17.25)
>>                                              [2].move(0,17.25,0)
>>                                              [2].move(17.25,0,0)
>>
>>
>>                  cl = new ClIon [2].move(0,0,17.25)
>>                                            [2].move(0,17.25,0)
>>                                            [2].move(17.25,0,0)
>>
>>                 na[*][*][*].move(5.175,5.175,5.6)
>>                 cl[*][*][*].move(12.075,12.075,12.5)         "
>>
>>
>> Here what "move" does.?
>> If I will not mention this then what will happen.? Is this mandatory to
>> mention.?
>> And please explain last two lines specially.
>>
>> Thanks
>>
>> Regards,
>> Varsha
>>
>> On Tue, Sep 19, 2017 at 4:58 AM, Andrew Jewett <jewett@...1937...> wrote:
>>>
>>>  Your most recent question sounds like a VMD question.  I don't know
>>> enough about VMD to answer it.
>>>
>>> Fortunately, perhaps I don't need to.  The issue has nothing to do with
>>> PSF files.  Neither LAMMPS, not moltemplate read or care about PSF files.
>>> You can run your simulations without them.  (I have only ever needed PSF
>>> files to view my molecules in VMD.)
>>>
>>> However if you are adding ions, then you will need to inform LAMMPS and
>>> moltemplate about them.  The simplest way to do that is to modify your
>>> "system.lt" file this way:
>>>  ---- "system.lt" file: ----
>>>
>>> import "spce.lt"
>>> import "ions.lt"
>>>
>>> wat = new SPCE [260]
>>> na = new NaIon [3]
>>> cl = new ClIon [3]
>>>
>>>  ---- end of "system.lt" file ----
>>>
>>> (Again, "3" and "260" are the number of ions and water molecules in this
>>> example.)
>>>
>>>    --- ions.lt ---
>>>
>>> For a working example of the "ions.lt" file, see this link:
>>>
>>> http://moltemplate.org/examples/waterSPCE+Na+Cl/
>>>    ...or if that link is broken, try this one:
>>>
>>> https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_explicit_parameters/waterSPCE%2BNa%2BCl
>>>
>>> The "ions.lt" file contains additional pair_coeff commands to define
>>> Lennard Jones parameters for these atoms.  Later on, as your system gets
>>> more complicated, you may decide it is more convenient to use a canned force
>>> field that already contains definitions for all these atom types by
>>> replacing the "import ions.lt" line with one of these choices:
>>>
>>> import "oplsaa.lt"  #(OPLS boss4.8 force field)
>>> #   -or-
>>> import "gaff.lt"    #(AMBER force field)
>>>
>>> #(...and rename your @atom types accordingly)
>>>
>>>
>>> Cheers
>>> Andrew
>>> More force fields are planned.  Right now, there are two scripts
>>> distributed with moltemplate which have been written to add more force field
>>> support  (tinkerparm2lt.py and emcprm2lt.py) these scripts can convert some
>>> of the other force fields  distributed with TINKER and EMC into moltemplate
>>> format.  But force field conversion can be arduous work, and some force
>>> fields contain terms which are not yet implemented in lammps.
>>>
>>> On Sep 18, 2017 12:18 AM, "R. Varsha" <varsharani.0909@...24...> wrote:
>>>>
>>>> Attachments are here
>>>>
>>>> On Mon, Sep 18, 2017 at 12:42 PM, R. Varsha <varsharani.0909@...24...>
>>>> wrote:
>>>>>
>>>>> Hello Andrew,
>>>>>
>>>>> I have generated lammps data file (system.data) for spc/e water model
>>>>> through moltemplate. And I can visualize that in VMD by topo command which
>>>>> is as follows-
>>>>> in TK console > topo readlammpsdata system.data full
>>>>>
>>>>> Now I want to add ions in that water box. For that first we need pdb
>>>>> and psf files for that system as inputs to autoionize.
>>>>> I have created pdb and psf files in VMD by using following commands-
>>>>> animate write pdb system.pdb
>>>>> animate write psf system.psf
>>>>>
>>>>> These files has been generated successfully.
>>>>> But When I did autoionize to add ions. I got error that my psf file is
>>>>> in charmm format & it should be in x-plor format.
>>>>> I tried other commands also to get x-plor format of psf such as
>>>>> writepsf x-plor system.psf
>>>>> writepsf X-PLOR system.psf
>>>>> writepsf card name "system-xplor.psf" xplor
>>>>>
>>>>> but nothing happened with these commands
>>>>>
>>>>> So first my query is that NAMD and VMD generates psf file in x-plor
>>>>> format by default ..then why my psf file is not created in x-plor format.
>>>>> And secondly how can I convert psf file format from charmm to xplor.
>>>>>
>>>>> Thanks
>>>>>
>>>>> Regards,
>>>>> Varsha
>>>>>
>>>>> On Fri, Sep 15, 2017 at 8:54 AM, Andrew Jewett <jewett@...1937...>
>>>>> wrote:
>>>>>>
>>>>>> 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
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>>>>>> >>>> _______________________________________________
>>>>>> >>>> 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
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>>>>>> >>> _______________________________________________
>>>>>> >>> lammps-users mailing list
>>>>>> >>> lammps-users@lists.sourceforge.net
>>>>>> >>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>>>> >>>
>>>>>> >>
>>>>>> >
>>>>>
>>>>>
>>>>
>>
>