Re: [AMBER] Regarding hydrogen bond time correlation function in cpptraj

From: Daniel Roe <>
Date: Sat, 20 Jun 2015 10:53:08 -0600


Although that exact calculation is not implemented directly in cpptraj, the
data sets created via the 'hbond' command 'series' keyword contain the
information that you need. There is one data set created for each hydrogen
bond found containing 1 when the hydrogen bond is present and 0 otherwise.
You would have to do some extra processing to get this information as
'molecules have at least one hydrogen bond' (e.g. check all hydrogen bond
series values at each frame and output 1 if any are 1 - this could be done
using the 'filter' or 'datafilter' commands, assuming you know how many
hydrogen bonds you have), but the raw information is there. The 'lifetime'
command entry in the Amber 15 manual (29.11.12, page 600) has an example of
how to work with data sets from 'hbond series'.


On Sat, Jun 20, 2015 at 4:27 AM, MOHD HOMAIDUR RAHMAN <>

> Dear Amber users
> I want to calculate continuous hydrogen bond time correlation function for
> water molecules in a system. Which is defined as SHB(t) = < h(0) H(t) > /
> <h>. In paper author define two types of hydrogen bond population. The
> variable h(t) is equal to unity when a pair of molecules is hydrogen bonded
> at time t and is zero otherwise and the other variable H(t) is defined as
> H(t) = 1 when two molecules remain continuously hydrogen bonded from time
> t =
> 0 to t or is zero otherwise.
> In cpptraj there is tool to calculate H-bond lifetime and time correlation
> both but I am unable define these variable.
> Could any one help me to how to define these variable in cpptraj.
> Thank you in advance for help.
> Regards
> Rahman
> _______________________________________________
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Jun 20 2015 - 10:00:04 PDT
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