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From: yuan bo <yuanbous.yahoo.com>

Date: Sun, 13 Apr 2003 19:34:25 -0700 (PDT)

Dear Amber users

I am simulating protein in mixed solents and saved

trajectory in every 0.2ps for analysis. now I want to

calculate diffusion coefficients of solvent for one

100ps trajectory ( 500=100/0.2 sets data, using Ptraj

program in Amber 6. Manual define diffusion as

follows:

diffusion mask time_per_frame [ average ] [

filenameroot ]

The time_per_frame sepicifies time between frams in

ps. I use " diffusion :WAT 4 average filename" command

to calculate.In figure from filename_r.xmgr, X axis

scale is displayed to be 0-2000. I am a little

confused what meaning is 2000, 2000ps? because x

axis'units is picosecond as mentioned in manual. but I

only calculate 100 ps trajectory. why X axis change

2000(500 sets *4 ps=2000?)? it'unit is still

picosecond? Maybe I don't understand what meaning is

time-per-frame?

Diffusion coefficent can be obtained from the slope

of the line. But I would like to calculate diffusion

coefficent of several intersting solvent molecules.

Howere there is no straight line in filename_r.xmgr

figure but one curve with big fluctuation when I use

method above to calculate. How should I obtain

diffusion coefficient from the such filename_r.xmgr?

Anybody could help me to understand the two problem?

Thanks a lot?

yb

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Received on Mon Apr 14 2003 - 03:53:01 PDT

Date: Sun, 13 Apr 2003 19:34:25 -0700 (PDT)

Dear Amber users

I am simulating protein in mixed solents and saved

trajectory in every 0.2ps for analysis. now I want to

calculate diffusion coefficients of solvent for one

100ps trajectory ( 500=100/0.2 sets data, using Ptraj

program in Amber 6. Manual define diffusion as

follows:

diffusion mask time_per_frame [ average ] [

filenameroot ]

The time_per_frame sepicifies time between frams in

ps. I use " diffusion :WAT 4 average filename" command

to calculate.In figure from filename_r.xmgr, X axis

scale is displayed to be 0-2000. I am a little

confused what meaning is 2000, 2000ps? because x

axis'units is picosecond as mentioned in manual. but I

only calculate 100 ps trajectory. why X axis change

2000(500 sets *4 ps=2000?)? it'unit is still

picosecond? Maybe I don't understand what meaning is

time-per-frame?

Diffusion coefficent can be obtained from the slope

of the line. But I would like to calculate diffusion

coefficent of several intersting solvent molecules.

Howere there is no straight line in filename_r.xmgr

figure but one curve with big fluctuation when I use

method above to calculate. How should I obtain

diffusion coefficient from the such filename_r.xmgr?

Anybody could help me to understand the two problem?

Thanks a lot?

yb

__________________________________________________

Do you Yahoo!?

Yahoo! Tax Center - File online, calculators, forms, and more

http://tax.yahoo.com

Received on Mon Apr 14 2003 - 03:53:01 PDT

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