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generaitng average structure for RMS calculaitons
#17464 03/13/08 09:15 PM
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Mihir Offline OP
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Hi all
I am trying to calculate RMS fluctuation's in the position of few atoms of polypeptide. After reading trajectory (dcd file) when I use COOY DYNA COMP, it generates average structure over entire trajectory and puts it into comparison set. If I want to calculate RMS fluctuation not over entire trajectory but over some desired small portion of full trajectory, I want to have average structure generated over exactly on that particular portion of full trajectory. Is there any way to generate such an average structure??

Re: generaitng average structure for RMS calculaitons
Mihir #17465 03/13/08 09:57 PM
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Hi Mihir
Use BEGIn int STOP int to limit the portion of your trajectory used for calculating the average structure

ATF

Re: generaitng average structure for RMS calculaitons
Mihir #17466 03/13/08 10:03 PM
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Both COOR DYNA (corman.doc) and the TRAJ commmand within CORREL (correl.doc) support the BEGIN and STOP keywords, which are used to identify the range of integration step numbers to be used.

Re: generaitng average structure for RMS calculaitons
Mihir #17467 03/14/08 03:16 PM
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Thanks for help.
Still a small problem. The trajectory that I am reading is from production run. In production run I restart the trajectory from equilibrium run and write new trajectory for production run. The equilibrium run has 50,000 steps and coordinates are saved every 1000th step. So it has 50 coordinates saved. When I write trajectory for production run I do DYNA LEAP RESTART ...as against DYNA LEAP START for equilibration. So the questions is what is going to be starting number for trajectory in production run? Is the first coordinate going to be saves as 1000th step or 51000??
Also if I want to specify BEGI and STOP in COOR DYNA COMP in RMS claculaitons what will be value for BEGI to start with #1 step in trajectory from production run? Will it be 51000 or 1000?

Re: generaitng average structure for RMS calculaitons
Mihir #17468 03/14/08 03:21 PM
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You can use the TRAJ QUERy command to get the stats for your trajectory.

open unit 20 unform name traj.dcd
traj query unit 20
set begin ?start
set skip ?skip
set nfile ?nfile

etc etc dynamc.doc


Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology
Re: generaitng average structure for RMS calculaitons
Mihir #17469 03/14/08 03:25 PM
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Integration step number is counted from the start of the simulation, independent of the number of files used to store the trajectory.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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