AMBER Archive (2004)

Subject: AMBER: Implicit MD problem

From: yen li (
Date: Wed Jul 14 2004 - 06:01:39 CDT

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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