AMBER Archive (2004)

Subject: Re: AMBER: Implicit MD problem

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jul 14 2004 - 11:53:31 CDT

I think the problem is what I suspected and also what dave case
sugested- you are changing the refc reference coordinates each
time, so every time you restart there is a jump in the restraint
energy. this also allows a drift in the structure, it is not the same
as what you would get with 1 long run using a single reference coordinate set.
you should probably keep the same reference coordinates for each run.
carlos

  ----- Original Message -----
  From: yen li
  To: amber_at_scripps.edu
  Sent: Wednesday, July 14, 2004 12:44 PM
  Subject: Re: AMBER: Implicit MD problem

  Hi Carlos,
  For 1 ns of md, the number of steps involved are 500000 with the time step dt=0.002.
  The input file is
  &cntrl
          imin=0,
          ntx=5, irest=1,
          ntwx=5000, ntpr=200,
          ntf=2, ntb=0,dielc=4,cut=300.0,
          ntr=1, nscm=200,
          nstlim=500000,dt=0.002,temp0=300,tempi=300,
          ntc=2,ntt=1,tautp=2.0
   &end
   &ewald
          eedmeth=5,
   &end
  restraint 1
   25.0
  RES 9 17
  RES 22 27
  RES 32 43
  END
  END
  I am also writing the script in which i am repeating the 1ns of the simulation using the above file, so many times as the number of nanoseconds for which i want the simulation.
  1st ns of production phase
  sander -O -i mdprodIm.in -o prot1.out -p prot.top -c eqa.restrt -r prot1.restrt -x prot1mdcrd -ref eqa.restrt
  2nd ns of production phase
  sander -O -i mdprodIm.in -o prot2.out -p prot.top -c prot1.restrt -r prot2.restrt -x prot2mdcrd -ref prot1.restrt
  similarly for more runs.......

  where
            prot.top is the topology file which will be same throughout.
            mdprodIm.in is the input file for the production phase given above which will again be same for each of 1 ns simulation.
            eqa.restrt is the restrt file from the equilibration phase, here it is being used as coordinate file
            prot1.restrt is the new restrt file for 1st ns which will be used as the coordinate file for the 2nd ns of simulation.
            prot1mdcrd is the saved coordinate file.
  I hope now you can follow how exactly i am doing. I'll appreciate your critical remarks.
  Thanks

  Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu> wrote:
    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
      To: amber_at_scripps.edu
      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

       &cntrl
              imin=0,
              ntx=5, irest=1,
              ntwx=5000, ntpr=200,
              ntf=2, ntb=0,dielc=4,cut=300.0,
              ntr=1, nscm=200,
              nstlim=500000,dt=0.002,temp0=300,tempi=300,
              ntc=2,ntt=1,tautp=2.0
       &end
       &ewald
              eedmeth=5,
       &end
      restraint 1
       25.0
      RES 9 17
      RES 22 27
      RES 32 43
      END
      END

      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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