[gmx-users] g_rdf between bonded and nonbonded groups

[Emily Curtis]

Hi Justin,

Thank you for your help.  I will edit the topology file.  I am running
GROMACS 4.0.7.  I can download the latest version.  The command line I was
using was:

g_rdf -n index -rdf res_com -s full -surf  -o rdf08SEPT10.xvg

Emily


On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis <emilymariecurtis at gmail.com>wrote:

> Hi Justin,
>
> Thank you for your help.  I will edit the topology file.  I am running
> GROMACS 4.0.7.  I can download the latest version.  The command line I was
> using was:
>
> g_rdf -n index -rdf res_com -s full -surf  -o rdf08SEPT10.xvg
>
> Emily
>
> On Wed, Sep 8, 2010 at 4:05 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> Emily Curtis wrote:
>>
>>>
>>>
>>> I would like to calculate the inter- and intra-molecular radial
>>> distribution functions separately.  I have read through g_rdf -h many times
>>> and I have a few questions:
>>>
>>> 1.  I think that I may have to modify a trp file (and not use it for the
>>> simulations) by setting the nrexcl to the number of bonds I would like the
>>> calculation to exclude.  I cannot figure out where in the tpr file I should
>>> add the nrexcl term.  I have tried to sort through the manual to figure out
>>> how to make this modification but I cannot figure it out.  Does anyone have
>>> any suggestions?
>>>
>>>
>> You set nrexcl in the topology, not directly in the .tpr file.
>>
>>
>>  2.  In D.56 g_rdf of the Gromacs manual it says that the option -surf can
>>> be used along with -rdf to only calculate the rdf of a molecule with its
>>> closest neighbor in a set.  Can this option be used for calculating the
>>> intramolecular radial distribution function or am I completely
>>> misinterpreting the manual?  If it can be used how is this done?  I tried to
>>> use it but I get the error message:  Invalid command line argument:
>>> -surf
>>>
>>
>> What is your exact command line?  Which version of Gromacs are you using?
>>  In the latest version I cannot reproduce this error.
>>
>> -Justin
>>
>>
>>
>>> Thank you in advance for any help.
>>>
>>> Emily
>>>
>>>
>> --
>> ========================================
>>
>> 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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