I have performed 5 ns. I have run total 10 jobs, one job is equal to o.5 ns. After 4 ns (md run = 9) my was killed. I started again. When 5 ns simultion completed, I have plotted rmsd graph using cpptraj.
INPUT TRAJECTORIES:
0: 'md_simulation1.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
1: 'md_simulation2.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
2: 'md_simulation3.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
3: 'md_simulation4.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
4: 'md_simulation5.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
5: 'md_simulation6.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
6: 'md_simulation7.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
7: 'md_simulation8.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
8: 'md_simulation9.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box), unknown #frames, start=0 offset=1
9: 'md_simulation10.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box), unknown #frames, start=0 offset=1
Total number of frames is unknown.
TIME: Run Initialization took 0.0015 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
In last two mdcrd.gz files number of frame is unknow, (Orthogonal box), unknown #frames, start=0 offset=1). It effects rmsd plot.
Progress: '+' = 200 iterations.
----- md_simulation9.mdcrd.gz (1-EOF, 1) -----
0
Progress: '+' = 200 iterations.
----- md_simulation10.mdcrd.gz (1-EOF, 1) -----
I can not understand this error. Kindly help me in this regard.
Thank you.
Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.
Contact No:
Office (92-21) 111222292 (Ext 309)
Email ID:
saman.yousufali64.yahoo.com
saman.ali.iccs.edu
|
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Received on Sun Mar 06 2016 - 23:00:03 PST
