[gmx-users] topology file for two molecules

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi Justin
> 
> I Did the following and it worked. You were right about using one atom
> types directive. If you don't mind I have another query. In all my
> topology files to date (one molecule type), I have always listed the
> atomtypes in the [atomtypes] directive, and used the set up in
> [defaults] below. Is this all that is required for the calculation of
> the LJ energies. I have never used a pair list, a pair types directive
> or a nonbond_params directive. From the output I still get LJ energies
> but I am slightly confused by all the different options.
> 

I can't give a better explanation than what is already in the manual, 
specifically section 5.3.3 ([nonbond_params] and whether or not you need it). 
Whether or not you need [pairs] depends on the underlying mechanics of the force 
field you're using.  See section 5.3.5.

-Justin

> parameter level
> [defaults]
> ; nbfunc    comb-rule     gen-pairs        fudgeLJ     fudgeQQ
>      1         3              yes            0.5         0.5
> 
> [atomtypes]
> ;type     mass           charge      ptype     sigma(nm)    
> epsilon(kjmol-1)
>    CB     12.011000      0.000000       A      0.355000      0.292880
>    CA     12.011000     -0.115000       A      0.355000      0.292880
>    HC      1.008000      0.115000       A      0.242000      0.125520
>    CU     13.019000      0.265000       A      0.350000      0.334720
>    NU     14.007000     -0.597000       A      0.325000      0.711280
>    CH     13.019000      0.332000       A      0.385000      0.334720
>    C3     15.035000      0.000000       A      0.390500      0.732200
>    CT     12.011000     -0.180000       A      0.350000      0.276144
>    HH      1.008000      0.060000       A      0.250000      0.125520
> 
> #include "tertpentane.itp"
> #include "methylcage.itp"
> 
> ;System level
> [system]
> ;the name of this system
> cage and pentane
> 
> [molecules]
> ; moleculename     number
>  tertpentane          1
>  methylcage           1
> 
> 
> Justin A. Lemkul wrote:
>>
>> Gavin Melaugh wrote:
>>> Hi Justin
>>>
>>> Cheers. I have attached my pentane itp file. The cage itp is formatted
>>> the same. In the examples there never seems to be [atom types] included.
>>> I have included it. Does it seem O.K?
>>>
>> You only need to use an [atomtypes] directive if you're introducing
>> new atom types into the force field.  I don't know if it's necessary. 
>> I also don't know if these sections can be discontinuous (i.e., one
>> section present in cage.itp, another in tertpentane.itp).  Try the
>> approach I sent you and see.  If you get fatal errors, then you may
>> have to assemble a single [atomtypes] directive and put it either in
>> the first .itp file you #include, or before any of the #includes in
>> the .top (since #include really just means "cut-and-paste the stuff
>> here," it works the same).
>>
>> -Justin
>>
>>> Gavin
>>>
>>> Justin A. Lemkul wrote:
>>>> Gavin Melaugh wrote:
>>>>> Hi Mark.
>>>>>
>>>>> I have looked this up, but I am a little uncertain. Does one of the
>>>>> topologies have to be included within the other as an .itp file. If so
>>>> No.  You #include .itp files to simply add molecules within a .top; it
>>>> would be very rare to #include an .itp within an .itp (although it can
>>>> be done).  For your case, your .top is simple:
>>>>
>>>> #include (force field)
>>>>
>>>> #include "cage.itp"
>>>> #include "pentane.itp"
>>>>
>>>> [ system ]
>>>> My system
>>>>
>>>> [ molecules ]
>>>> Cage    1
>>>> Pentane 1
>>>>
>>>>> do I only define the [defaults directive] in the .top file i.e. I take
>>>>> it I don't include this directive in the .itp file as well.
>>>>>
>>>> The [defaults] directive is provided by whatever force field you
>>>> #include.  If you're using some custom parameters, then it needs to be
>>>> defined once (and only once) at the top of your .top file.  Otherwise,
>>>> you'll get fatal errors from grompp.
>>>>
>>>> -Justin
>>>>
>>>>> Cheers
>>>>>
>>>>> Gavin
>>>>>
>>>>> Mark Abraham wrote:
>>>>>> Look up the include file mechanism on the webpage.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> ----- Original Message -----
>>>>>> From: Gavin Melaugh <gmelaugh01 at qub.ac.uk>
>>>>>> Date: Tuesday, September 28, 2010 19:04
>>>>>> Subject: [gmx-users] topology file for two molecules
>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>>>>
>>>>>>> Hi all
>>>>>>>
>>>>>>> I want to run a simulation of one tert-pentane molecule inside one
>>>>>>> organic cage molecule. I have the topology files for both
>>>>>>> molecules but
>>>>>>> obviously I only need one .top file as the input for grompp.
>>>>>>> What is the
>>>>>>> most convenient way of having both topologies in one file?
>>>>>>>
>>>>>>> Many Thanks
>>>>>>>
>>>>>>> Gavin
>>>>>>> -- 
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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