From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Oct 28 2011 - 13:43:51 CDT
You were likely introducing too much energy too fast. What was your
timestep, rate of heating, beginning temperature and ending temperature?
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-0329 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 Liqun Zhang <lxz79_at_case.edu> writes: > Date: Fri, 28 Oct 2011 14:14:36 -0400 > From: Liqun Zhang <lxz79_at_case.edu> > To: namd-l_at_ks.uiuc.edu > Subject: namd-l: question about namd simulation on protein in tip4p water > box > > Dear NAMD users: > > I have a question on namd simulation when running a protein in tip4p water > box. After finishing the minimization steps on the system, I let namd to > heat up the system. It aborted with following error messages: > > REASSIGNING VELOCITIES AT STEP 0 TO 50 KELVIN. > ERROR: Atom 2316 velocity is 57609.7 6314.11 -11224.4 (limit is 6000) > ERROR: Atom 2324 velocity is -32596.9 39272.7 -25582.1 (limit is 6000) > ERROR: Atom 2328 velocity is 5780.04 58819.6 -7693.42 (limit is 6000) > ERROR: Atom 2352 velocity is 28397.3 13055.2 46409.7 (limit is 6000) > > Checking the atom list, I can see that all phantom atoms had the problem of > showing very large velocities. I used namd2.7-b2 edition, and the system was > built using charmm c36a4r1 edition, with tip4p.rtf and tip4p.prm parameters > to restraint the tip4p water. Could I get some help here? thank you very > much. > > Best regards, > > LQZ
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