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
reference
/home/vaibhav/vaibhav_data/amber/1fm9_far/1fm9_MD_runs/1fm9_far_equil.restrt
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
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1500000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
------
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
www.niper.nic.in
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Received on Sun Dec 18 2011 - 23:30:02 PST
