[gmx-users] Re: g_analyze

bharat gupta bharat.85.monu at gmail.com
Mon Nov 11 07:30:23 CET 2013


thank you informing about g_rdf...

Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??


On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/10/13 8:38 PM, bharat gupta wrote:
>
>> But trjorder can be used to calculate the hydration layer or shell around
>> residues ... Right ??
>>
>>
> Yes, but I also tend to think that integrating an RDF is also a more
> straightforward way of doing that.  With trjorder, you set some arbitrary
> cutoff that may or may not be an informed decision - with an RDF it is
> clear where the hydration layers are.
>
> -Justin
>
>
>
>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/10/13 8:30 PM, bharat gupta wrote:
>>>
>>>  Thanks for your reply. I was missing the scientific notation part. Now
>>>> everything is fine.
>>>>
>>>> Regarding trjorder, it doesn't measure h-bonds but gives the water
>>>> nearest
>>>> to protein.
>>>>
>>>>
>>>>  I wouldn't try to draw any sort of comparison between the output of
>>> trjorder and g_hbond.  If you want to measure H-bonds, there's only one
>>> tool for that.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> 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
>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==================================================
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