[gmx-users] topology file for two molecules

Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Sep 28 14:12:21 CEST 2010




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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