Dear Amber Users,I have run total 30 ns md simulation and then I have plotted rmsd graph. Number of frames per files is 1000 ps, my rmsd plot y axis end on 60000 ps. I was expected it ends on 30000 ps. I face this problem every time, whenever I run md simulation. Kindly guide me regarding this problem and give me useful suggestion. My production input file in pasted below.
irest=1, ntx=5,
min = 0, ntb = 2, ntp=1,
ntc=2, ntf=2,
ntpr = 5000, ntwx = 500, ntwe = 0,ntwr = 5000,
ntt = 3, gamma_ln = 3.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 500000, dt = 0.002,
cut = 12.0/
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 Wed Mar 16 2016 - 03:00:03 PDT
