[AMBER] RMDS vs. time problem

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Mon, 19 Dec 2011 12:37:35 +0530

Dear Amber community member,
I'm having trouble calculating RMSD vs time.
I have done successfully RMSD vs frames.

The 3ns MD input file and input for ptraj are given below.
Please suggest what modifications will give me RMDS values vs. time.

Ptraj input file
trajin /home/vaibhav/vaibhav_data/
amber/1fm9_far/1fm9_MD_runs/1fm9_far_3nMD_1.mdcrd 15 1500 1


rms mass reference out 1fm9_farallbackbone_time '.CA,C,N' time 0.5

rms mass reference out 1fm9_far_H-12_time ':278-288' time 0.5

rms mass reference out 1fm9_far_H-12_backbone_time ':278-288 & .CA,C,N'
time 0.5
I tried using time 1.0 and time 2.0.
Without time command it gives RMSD vs. frame which is OK for my purpose

3nd MD input file
3ns MD 1fm9_far complex
  cut=8.0, ntb=2, ntp=1, taup=2.0,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,

Thank you all.
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
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Received on Sun Dec 18 2011 - 23:30:02 PST
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