Date: Fri, 31 May 2013 05:32:37 -0700 (PDT)
Dear Amber users, I have been recently working on a protein simulation using the GB implicit solvent model (with igb=8), I used the following input parameters pmemd.cuda input &cntrl imin=0,irest=1,ntx=5, nstlim=500000,dt=0.002,ntb=0, ntf=2,ntc=2,tol=0.000001, ntpr=2500, ntwx=2500, ntwr=2500, cut=9999.0, rgbmax=9999.0, igb=8,ntt=0,nscm=0, / For the first 7 ns of the simulation everything seems OK. However, after 7.5 ns of the simulation the protein seems to bend out of shape as seen in the attached file. I also noticed that the protein system seems to move out of the screen .. I plan on centering the molecule during MD runs. Before doing that I just want to make sure that the prameters above are alright.. Any ideas about what might be going wrong here ? Regards, Cenk Andac, M.S., Ph.D. Asst. Professor of Medical Pharmacology Department of Medical Pharmacology School of Medicine, Mevlana University, Konya Turkiye 42003 Cell: +90-(536)-4813012 E-Mail:cenk_andac.yahoo.com Web : http://med.mevlana.edu.tr/personel.asp?ID=1
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