RE: AMBER: nscm in simulation annealing

From: Hu, Shaowen (JSC-SK)[USRA] <"Hu,>
Date: Fri, 13 Apr 2007 10:32:26 -0500

        Thanks for your reply, Dr. Case. I am working on a complex of a
protein subdomain and a 10-base pair duplex DNA, which has 1516 atoms. I
tried to do some simulation annealing with implicit solvent to find some
possible binding modes between them, since currently no high-resolution
structure of the complex is available.
        My input file is following:
        300ps kuc DNA simulated annealing


          imin = 0, irest = 0,

          ntc=1, ntf=1,

          ntpr=500, ntwx=1000,

          ntb = 0, cut = 12.0, rgbmax=12.0,

          igb = 1, saltcon=0.2,

          nstlim = 600000, nscm= 500,

          dt = 0.0005,

          ntt = 3, gamma_ln=1.0,




         &wt type='TEMP0', istep1=0,istep2=100000,

           value1=0.0, value2=300.0


         &wt type='TEMP0', istep1=100001,istep2=200000,

           value1=300.0, value2=400.0


         &wt type='TEMP0', istep1=200001,istep2=300000,

           value1=400.0, value2=500.0


         &wt type='TEMP0', istep1=300001,istep2=400000,

           value1=500.0, value2=500.0


         &wt type='TEMP0', istep1=400001,istep2=500000,

           value1=500.0, value2=300.0


         &wt type='TEMP0', istep1=500001,istep2=600000,

           value1=300.0, value2=300.0



         &wt type='REST', istep1=0,istep2=300000,value1=0.1,

                    value2=0.75 /

         &wt type='REST', istep1=300001,istep2=600000,value1=1.0,

                    value2=1.0, /


         &wt type='END'




        Hold the protein fixed


        RES 21 74



        And my temperature file is attached. If I set nscm=0, the
temperature looks fine. I think it does effect the velocities. If the
removal of the motion of center mass (CM) can not be combined with
Langevin simulation, all my calculation need to redo. My experience is
that, without removal of the motion of CM, the protein and DNA easily
fall apart; but frequently removing the motion of CM (say 500 or 1000),
the complex can form some favorable contacts. If you can refer some
literature, that will be very helpful to me.

        Thank you very much.

        -----Original Message-----
        From: []
On Behalf Of David A. Case
        Sent: Thursday, April 12, 2007 7:05 PM
        Subject: Re: AMBER: nscm in simulation annealing
        On Thu, Apr 12, 2007, Hu, Shaowen (JSC-SK)[USRA] wrote:
> Thank you very much, Dr. Case. I am using AMBER 9. However, I
can not
> find the restriction. With ntt=3, if I did not set nscm=0, the
> value is 1000.
        Yes, but nscm only repositions the center of mass; it does not
modify the velocities. We would need more information about why or how
you think the temperature behavior is odd. Be sure to state what value
of gamma_ln you are using, how big the system is, and how you monitored
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Received on Sun Apr 15 2007 - 06:07:38 PDT
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