[gmx-users] g_hbond

[Erik Marklund]

No. Strike that. The number of contacts is just reported the wrong way. It says "Average number of contacts per timeframe 0.000…" in the terminal but hbnum.xvg says different. Not sure if this applies to your problem.

Erik

Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 15 Jul 2014, at 10:22, Erik Marklund <erik.marklund at chem.ox.ac.uk> wrote:

> Hi,
> 
> I think this may actually be a bug. g_hbond reports zero contacts in cases where I know there are many. Will examine this more thoroughly and file a redmine issue.
> 
> Kind regards,
> Erik
> 
> 
> Erik Marklund, PhD
> Postdoctoral Research Associate
> 
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
> 
> On 14 Jul 2014, at 13:24, mirko busato <busato.mirko at yahoo.com> wrote:
> 
>> thank you very much,
>> I read the manual of g_mindist but seem produce in output only the number of contacts and the minimum distance .
>> 
>> For my problem I would like to know all the atoms involved  (all the contacts) within of 4 Å.
>> 
>> so I can understand which atoms can do salt bridge interactions.
>> 
>> Do you know a way to do this with g_mindist command?
>> Thank you very much,
>> Mirko
>> 
>> 
>> On Monday, July 14, 2014 2:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 
>> 
>> 
>> 
>> 
>> On 7/14/14, 7:44 AM, mirko busato wrote:
>>> Dear Users,
>>> 
>>> I have one question for you. I would  like to  extract some information about salt bridge interactions (without using the gromacs command  g_saltbr  because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer.
>>> 
>>> So I created the two lists of atoms with g_select,
>>> and I made a file index like that:
>>> 
>>> [ N_CRL ]
>>>   300  321  342  363  384  405  426  447  468  489  510  531  552  573  594
>>>   615  636  657  678  699  720  741  762  783  804  825  846  867  888  909
>>>   930  951  972  993 1014 1035 1056 1077 1098 1119
>>> [ OX_ITA ]
>>>   168  181  194  207  220  233  246  259  272  285
>>> 
>>> and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å.
>>> 
>>> in this way:
>>> 
>>> g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4
>>> 
>> 
>> I wouldn't use g_hbond like this; g_mindist -on is more straightforward for 
>> calculating simple contacts.
>> 
>> 
>>> 
>>> I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that:
>>> 
>>> [ OX_ITA ]
>>>   168  181  194  207  220  233  246  259  272  285
>>> [ N_CRL ]
>>>   300  321  342  363  384  405  426  447  468  489  510  531  552  573  594
>>>   615  636  657  678  699  720  741  762  783  804  825  846  867  888  909
>>>   930  951  972  993 1014 1035 1056 1077 1098 1119
>>> 
>>> I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups.
>>> 
>>> Could you help me about it ?
>> 
>> Order of the groups in the index file is irrelevant; it doesn't seem likely that 
>> this is the only issue.
>> 
>> -Justin
>> 
>> -- 
>> ==================================================
>> 
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> 
>> ==================================================
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