AMBER Archive (2004)

Subject: Re: AMBER: MD with NTR + NMROPT

From: anshul_at_imtech.res.in
Date: Wed May 12 2004 - 10:07:49 CDT

Dear david,
i am also facing a similar paroblem when I run simulated anealing of my
system. Unlike Martine i am only interested in fixing some of the residues
and not using any distance restraints. Orignally i was usiing the input
with the group information not at the end (like martine) but keeping
nmropt=0, this was my input

&ewald
    eedmeth=5,
 &end
 &cntrl
    imin=0, cut=30, nstlim=30000, ntt=1, ntx=1, irest=0,
    ntpr=200, ntwx=500, ntwe=500, tempi=10,
    ntb=0, ntr=1, dielc=4, vlimit=30, nmropt=1,

 &end
Input for restrained residues (A1-A166)
 2
RES 1 167
END
Input for restrained residues (A182-A276)
 2
RES 182 276
END
END

 &wt type='TEMP0', istep1=0,istep2=15000,value1=10.0,
           value2=500.0, &end &wt type='TEMP0',
istep1=15001,istep2=20000,value1=500.0,
           value2=500.0, &end
 &wt type='TEMP0', istep1=20001,istep2=25000,value1=500.0,
           value2=300.0, &end
 &wt type='TEMP0', istep1=25001,istep2=30000,value1=300.0,
           value2=300.0, &end
 &wt type='TAUTP', istep1=0,istep2=20000,value1=0.5,
           value2=0.2 &end
 &wt type='TAUTP', istep1=20001,istep2=25000,value1=2.0,
           value2=2.0 &end
 &wt type='TAUTP', istep1=25001,istep2=30000,value1=0.5,
          value2=0.2 &end
 &wt type='END' &end

The problem faced with this run is that the temperature of the system does
not rise upto 500K, as desired, but fluctuated near 300K.

Then I read one of your earlier replies in the mail reflector in which
you stated that for such simulations we should be using the nmropt >0 even
if the distance restraints are not used.

After this I used the nmropt=1 and also kept the group information at the
end but now it is not reading the group information and gives error. here
is my new input

&ewald
    eedmeth=5,
 &end
 &cntrl
    imin=0, cut=30, nstlim=30000, ntt=1, ntx=1, irest=0,
    ntpr=200, ntwx=500, ntwe=500, tempi=10,
    ntb=0, ntr=1, dielc=4, vlimit=30, nmropt=1,
  &end
  &wt type='TEMP0', istep1=0,istep2=15000,value1=10.0,
           value2=500.0, &end
 &wt type='TEMP0', istep1=15001,istep2=20000,value1=500.0,
           value2=500.0, &end
 &wt type='TEMP0', istep1=20001,istep2=25000,value1=500.0,
           value2=300.0, &end
 &wt type='TEMP0', istep1=25001,istep2=30000,value1=300.0,
           value2=300.0, &end
 &wt type='TAUTP', istep1=0,istep2=20000,value1=0.5,
           value2=0.2 &end
 &wt type='TAUTP', istep1=20001,istep2=25000,value1=2.0,
           value2=2.0 &end
 &wt type='TAUTP', istep1=25001,istep2=30000,value1=0.5,
           value2=0.2 &end
 &wt type='END' &end
Input for restrained residues (A1-A166)
 2
RES 1 167
END
Input for restrained residues (A182-A276)
 2
RES 182 276
END
END

this is the part of the output file with the error

LOADING THE CONSTRAINED ATOMS AS GROUPS
   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
  &ewald
     GROUP 1 HAS HARMONIC CONSTRAINTS 46.00000
 GRP 1 RES 296 TO 288
 GRP 1 RES 6 TO 6
      ***PROBLEMS WITH GROUPimin 296***** 6 6 -4 0 0 0 0
 0 0 0 0 0*******
 GRP 1 RES 4996 TO 288
 GRP 1 RES 96 TO 96 GRP 1 RES 6 TO 36
 GRP 1 RES 296 TO 6
      ***PROBLEMS WITH GROUP&wt -94***** 0 0 0 0 0 0 0
 0 0 0 0 0*******
     rfree: Error decoding variable 2 2 from:
           value2=500.0, &end

Can you suggest some way out. Is the problem related to temperature rise
related to the value of tautp value? Can you also through some light ont
he use of tautp values ie when should we use a tight coupling and when to
use a loose one.

With regards,
Anshul

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