On 9/1/13 1:17 PM, Nidhi Katyal wrote:
Even after giving same cutoff radius of 0.35nm in both, I am getting around
400 contacts per timeframe with mindist but 0 contacts with g_hbond.
What version of Gromacs are you using?
-Justin
On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/1/13 1:08 PM, Nidhi Katyal wrote:
The two groups are: protein and cosolvent molecules. With g_mindist -on ,
I am getting values of around 6500 per timeframe. But then why g_hbond
giving different results.
Are you using the same cutoff radius for both?
-Justin
On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/1/13 12:50 PM, Nidhi Katyal wrote:
Hello,
I would like to calculate number of contacts between two groups, for
which
I am using following command:
g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 50000
I am getting 0 as the output. But when I am calculating number of
hydrogen
bonds between the same two groups by using the above command without
contact option I am getting 5.2 as the output.
My question is wouldn't number of contacts be higher than number of
hydrogen bonds since hydrogen bonds are subset of contacts.
In theory, but something might be failing. What are the groups you are
choosing? What is your expected outcome? What does the output of
g_mindist -on give you?
-Justin
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Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
20 Penn St.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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