AMBER Archive (2004)

Subject: AMBER: energy conservation with GB !!

From: Pradipta Bandyopadhyay (pradipta_b_at_mail.jnu.ac.in)
Date: Sun May 16 2004 - 01:27:01 CDT

Hi,

  I am doing generalized born calculation for a peptide + few water
system. I am using AMBER 7.

I am doing constant energy simulation (NTT =0). The first question is
- what is the relationship between NVE MD with periodic boundary conditions and GB with constant energy?

While doing the NTT=0 (with GB) the first few lines of the output is like this:

NSTEP = 0 TIME(PS) = 13.020 TEMP(K) = 475.14 PRESS = 0.0
 Etot = -379.5578 EKtot = 116.6084 EPtot = -496.1662

NSTEP = 1 TIME(PS) = 13.021 TEMP(K) = 362.58 PRESS = 0.0
 Etot = -407.1830 EKtot = 88.9832 EPtot = -496.1662

NSTEP = 2 TIME(PS) = 13.022 TEMP(K) = 312.76 PRESS = 0.0
 Etot = -415.3095 EKtot = 76.7579 EPtot = -492.0673

after NSTEP =2 the energy is more or less conserved. I am generating
the initial velocities random.ly ( I have the input file below). Is it nornal
that it needs 2 steps to come to the conserved energy?

input file
-------------------------------------------------
&cntrl
   IREST = 0, ibelly= 0,
IG=125074,
   NTX = 1,
   IGB=1,
   NTB = 0,
   NTT = 0, TAUTP = .5,
   TEMPI = 300.0,
   TEMP0 = 300.0,
   DTEMP = 0.0, NTP = 0,
   NSTLIM= 200, DT = .001,
   NTC = 2,
   NTF = 2,
   NTPR = 1, NTWX = 5,NMROPT =0,
   NTR=0
 &end
----------------------------------------

                  Pradipta

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