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From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>

Date: Sat, 20 Jun 2015 15:57:34 +0530

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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http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat Jun 20 2015 - 03:30:02 PDT

Date: Sat, 20 Jun 2015 15:57:34 +0530

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat Jun 20 2015 - 03:30:02 PDT

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