AMBER Archive (2004)

Subject: Re: AMBER: Implicit MD simulation

From: Carlos Simmerling (
Date: Thu Jul 01 2004 - 07:07:52 CDT

  Hello all, you need to remove center of mass motion (rotation and
translation). your system is probably translating so
far that the coordinates don't fit the format space.

since you didn't give the amber version, I can't tell you
how to do this. look in the manual, it has details.

  ----- Original Message -----
  From: yen li
  Sent: Thursday, July 01, 2004 7:49 AM
  Subject: AMBER: Implicit MD simulation

  I am trying an implicit solvent molecular dynamics simulation on a protein (input file given). My problem is that after about 12ns, all the coordinates in the restart file becomes '*****' after some sighnificant figures (restart file attached). There is no abnormality observed in the energies in the output file.

  Can somebody help me in figuring out what the problem is?

  Thanking you in advance.



  Input file



          ntx=5, irest=1,

          ntwx=5000, ntpr=200,

          ntf=2, ntb=0, cut=9.0, scee=1.2, igb=1,





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