question about namd simulation on protein in tip4p water box

From: Liqun Zhang (lxz79_at_case.edu)
Date: Fri Oct 28 2011 - 13:14:36 CDT

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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