AMBER Archive (2005)

Subject: AMBER: How to fix the atom in NPT case?

From: george Chen (georgemdchen_at_gmail.com)
Date: Mon May 02 2005 - 13:19:54 CDT

Dear Amber User,

I have a question about the MD simulation by using Amber 8. I want to
fix one of the molecules. Then I use NTR = 1 in the MD input file. In
the case NTB=1 and NTP=0 (NVT condition), the change of the
Coordinates of the atoms within the fixed molecule is minor. However,
in the case NTB=2 and NTP=1 (NPT condition), the change of the
coordinates of the atoms is significant. The reason maybe is that the
box size change according to the pressure, so the coordinates of the
atom change. Then how can we fix the Position of the atom in the NPT
condition? Thank you very much.

  

 The following is my input file!!!

 Initial md with position restraints
  &cntrl

    nmropt =1,
    ntx=1, irest=0, ntrx=1, ntxo=1,
    ntpr=500, ntwx=500, ntwv=0, ntwe=0,

    ntf=2, ntb=2,
    cut=9.0, nsnb=10,

    ibelly=0, ntr=1,

    imin=0, nstlim=12500,
    nscm = 1000,
    t=0.0, dt=0.002,

    tempi = 100.0, temp0 = 300.0, ntt = 1,
    ig = 71277, heat=0.0, tautp =0.2, vlimit=20.0,

    ntp =1, pres0=1.0, comp=44.6, taup=1.0, npscal=1,

    ntc=2, tol=0.00005,
  /

 &wt
   type='TEMP0', istep1=0, istep2=500,
                  value1=100.0, value2=300.0,
  /
 &wt
   type='TEMP0', istep1=500, istep2=12500,
                  value1=300.0, value2=300.0,
  /
 &wt
   type='END',
  /
 Hold the DNA and CNT fixed
 500.0
 RES 1 14
 END
 END
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