Use this
rms mass reference out 1fm9_far_H-12_backbone_time time 2.0 :
278-288.CA,C,N
> 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
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
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Received on Mon Dec 19 2011 - 04:00:02 PST
