AMBER Archive (2004)

Subject: AMBER: Implicit MD simulation

From: yen li (chem_me2000_at_yahoo.com)
Date: Thu Jul 01 2004 - 06:49:24 CDT

 

 Hello all,

 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.

Bye

 

Input file

&cntrl

        imin=0,

        ntx=5, irest=1,

        ntwx=5000, ntpr=200,

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

        ntr=0,

        nstlim=500000,dt=0.002,temp0=300,tempi=300,

        ntc=2

 &end

                
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