AMBER Archive (2004)

Subject: Re: AMBER: Implicit MD problem

From: Carlos Simmerling (
Date: Wed Jul 14 2004 - 08:42:18 CDT

It is very hard to help without seeing the actual files that you used.
If your batches were 1ns, why does this input file say nstlim=500000?
How did you get it to stop at exactly 1ns?
Also, please send the scripts so we can see how you did the restarting
and what was used for the refc for restraints, etc.
Please include them in the mail as plain text, since I do not open Word
documents in email.

  ----- Original Message -----
  From: yen li
  Sent: Wednesday, July 14, 2004 7:01 AM
  Subject: AMBER: Implicit MD problem

  Hello amber users,
  I am doing the md implicit solvent md simulations on a small protein by putting restraints on the helices, using amber7 suite of programs. The input file for the production phase is given below

          ntx=5, irest=1,
          ntwx=5000, ntpr=200,
          ntf=2, ntb=0,dielc=4,cut=300.0,
          ntr=1, nscm=200,
  restraint 1
  RES 9 17
  RES 22 27
  RES 32 43

  I am doing the simulation in baches of 1 ns each.The problem is that the temp v/s runlength, total energy v/s runlength and pot energy v/s run length plots shows kinks or drops at the points where i restart the next batch of the production phase. The plots for the 16 ns are attached.
  Is there any problem in the restarting of the simulation.

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