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From: <brmeher.iitg.ernet.in>

Date: Sat, 17 Nov 2007 12:10:31 +0530 (IST)

Dear AMBER users,

I want to calculate generalized order

parameters (S2) of each

amino residues (N-H vector) by molecular

dynamics simulation and

compare it to order parameters derived from

NMR experiment.

However before that, we need to calculate the

auto time

correlation function for the vector. I performed the same

in ptraj and

find one ouput containing the information like as

follows:

Auto-correlation functions,normal type

***** Correlation functions *****

Time <P2>

0.000 1.000

1.000 0.894

2.000

0.891

3.000 0.884

4.000 0.881

5.000 0.882

6.000 0.880

7.000 0.874

8.000 0.883

9.000 0.884

10.000

0.880

.

.

.

*>From the above
*

output we have the P2 values.

My question is that,how to calculate

S2 from the P2 values.

Can any one help in this regard ?

with regards

Biswa Ranjan Meher

Research Scholar,

IIT Guwahati, Assam-781039

Biswa Ranjan Meher

Research Scholar,

IIT

Guwahati, Assam-781039

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Received on Sun Nov 18 2007 - 06:07:56 PST

Date: Sat, 17 Nov 2007 12:10:31 +0530 (IST)

Dear AMBER users,

I want to calculate generalized order

parameters (S2) of each

amino residues (N-H vector) by molecular

dynamics simulation and

compare it to order parameters derived from

NMR experiment.

However before that, we need to calculate the

auto time

correlation function for the vector. I performed the same

in ptraj and

find one ouput containing the information like as

follows:

Auto-correlation functions,normal type

***** Correlation functions *****

Time <P2>

0.000 1.000

1.000 0.894

2.000

0.891

3.000 0.884

4.000 0.881

5.000 0.882

6.000 0.880

7.000 0.874

8.000 0.883

9.000 0.884

10.000

0.880

.

.

.

output we have the P2 values.

My question is that,how to calculate

S2 from the P2 values.

Can any one help in this regard ?

with regards

Biswa Ranjan Meher

Research Scholar,

IIT Guwahati, Assam-781039

Biswa Ranjan Meher

Research Scholar,

IIT

Guwahati, Assam-781039

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Nov 18 2007 - 06:07:56 PST

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