[gmx-users] topology file for two molecules

[Gavin Melaugh]

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.

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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>>
>