AMBER Archive (2006)

Subject: Re: AMBER: PTRAJ RMS: dumping RMSd vs time data

From: r. a. (
Date: Tue Nov 07 2006 - 00:44:35 CST

Dear Sir
  Thanks for reply. I m also confused. I have 2080 frames for 1040 ps(total simulation).
  total frames is ok but as I found I need to change the time interval in the ptraj command. i changed ptraj command as:
  trajin heat1.crd
  trajin eq1.crd
  trajin md1.crd
  strip :WAT
  rms first mss out rms1.dat time 0.5 @CA,C,N
  atomicflubtuation out rmsf1.dat :1-388 byres
  but the problem of dumping continues.
  I run this simulation.could anyone tell me what causes this dumping?It can be from the intial structure?or any thing else...
  # Heating to 300 K with constant volume
   imin=0, irest=0,
 ntpr=50, ntwr=1000, ntwx=500, iwrap=1,
 ntr=1, ntx=1, tol=0.00001,
 ntb=1, igb=0, ntp=0,
 ntt=3, GAMMA_LN=1.0, tempi=0.0, temp0=300.0,
 nstlim=20000, dt=0.001, cut=10.0,
# keep protein fixed with weak restraint
RES 1 390
  # Initial MD equilibration with constant pressure
 imin=0, irest=1,
 ntpr=50, ntwr=1000, ntwx=500, iwrap=1,
 ntx=7, ntc=2, ntf=2, tol=0.0000001, ntb=2, igb=0,
 ntt=1, tautp=0.2, temp0=300.0,
 ntp=1, pres0=1.0, taup=0.8,
 nstlim=20000, dt=0.001,

  # MD production with constant pressure
 imin=0, irest=1,
 ntpr=50, ntwr=1000, ntwx=500, iwrap=1
 ntx=5, ntf=2, ntc=2, tol=0.00001, ntb=2, igb=0,
 ntp=1, pres0=1.0, taup=0.2,
 nstlim=1000000, dt=0.001,
 ntt=3, gamma_ln=1.0,

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