[gmx-users] topology file for two molecules

[Gavin Melaugh]

Justin

Cheers, I had just posted a more general query prior to you getting
back? It is perhaps not as vague.

Gavin

Justin A. Lemkul wrote:
>
>
> 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
>>>>>>>> -- 
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>>
>>
>