[gmx-users] g_rdf

[Justin A. Lemkul]

politr at huji.ac.il wrote:
> While trying to search throw mailing list I'm getting the next error 
> "/content/body/p[2]/span, function 'RecordList' failed "

The site is intermittently buggy, although it seems to be working fine now.

> I'm not interested in basic information. I'm using "g_rdf -f xxxx.trr -s 
> topol.tpr -rdf atom" to get rdf of water oxygens around a protein. As a 
> reference group I'm choosing "protein" and as a group I'm using "SOL". 

If you're choosing "SOL" as the the calculation group with "-rdf atom" I don't 
know if that will work.  Typically, you'd create an index group for "OW" atoms 
in water in order to use an atom-based RDF.  You may also be interested in the 
-com option, if you'd like to generate an RDF based on the COM of the protein, 
since the whole molecule is your reference.

> The command line for getting rdf of solute COM I use "g_rdf -f xxxx.trr 
> -s topol.tpr -rdf mol_com". As a reference group I'm choosing "protein" 
> and as a group I'm using "SRB" when SRB is a solute name. So first of 
> all I'm trying to understand if I'm doing the right thing. Second, for 

Seems to be right, aside from the above comment.

> g(r) we need the local density to be divided by the average density in 
> infinite solution (or bulk). How does the algorithm work? I understand 
> that for local density it calculates the number of molecules but what 
> about the bulk or whatever the algorithm uses.

See the manual, section 8.4.

-Justin

> Thanks a lot in advance.
> Regina
> The gromacs version I'm using is 4.0.3
> Justin A. Lemkul wrote:
>> Justin A. Lemkul wrote:
>>>
>>>
>>> politr at fh.huji.ac.il wrote:
>>>> Dear gromacs users,
>>>>
>>>> I want to calculate radial distribution function around my protein. 
>>>> I want to get g_rdf for water molecules (OW) around my protein and 
>>>> g_rdf for COM of some solutes around my protein. The numbers should 
>>>> be averaged over all the frames. I tried to look at the mailing list 
>>>> but there is some error and as a result I can't open it. Can someone 
>>>> help me with it and give me the command I should use.
>>>
>>> The manual and the -h flag should give you the basic information you 
>>> need to run g_rdf.  If there has been "some error" it is useless to 
>>> say so.  What error did you receive?  What was the command line that 
>>> you tried that gave rise to the error?  What Gromacs version are you 
>>> using?
>>>
>>> -Justin
>>>
>>>> Regina
>>>>
>>>>
>>>> ----------------------------------------------------------------
>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>
>>>
>>
> 
>>
>> politr at fh.huji.ac.il wrote:
>>> Dear gromacs users,
>>>
>>> I want to calculate radial distribution function around my protein. I 
>>> want to get g_rdf for water molecules (OW) around my protein and 
>>> g_rdf for COM of some solutes around my protein. The numbers should 
>>> be averaged over all the frames. I tried to look at the mailing list 
>>> but there is some error and as a result I can't open it. Can someone 
>>> help me with it and give me the command I should use.
>>
>> The manual and the -h flag should give you the basic information you 
>> need to run g_rdf.  If there has been "some error" it is useless to 
>> say so.  What error did you receive?  What was the command line that 
>> you tried that gave rise to the error?  What Gromacs version are you 
>> using?
>>
>> -Justin
>>
>>> Regina
>>>
>>>
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>
> 
> 

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

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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