AMBER Archive (2004)

Subject: Re: AMBER: energy conservation with GB !!

From: Dr. Yong Duan (yduan_at_albert.chem.udel.edu)
Date: Sun May 16 2004 - 01:58:25 CDT

This was probably due to SHAKE (and perhaps some "misuse" of it by the
program, not you).
When velocities are assigned, bond constraints were not taken into
account. At NTC=2, bonds connecting H are "SHAKED" and are subtracted from
the total number degrees of fredom. But the velocities assigned were based
on the full 3*N degrees of freedom. So, depends on the number of hydrogens
in the system (actually number of "SHAKED" bonds), you would expect a
higher temperature at 0th step than the one you asked for by TEMPI. After
the SHAKE, the velocities will satisfy the constraints and lose of the
components along the bonds. You would expect a significant change in
temperature (kinetic energy) which is not compensated by the increase in
potential energy and the total energy of the system decreases.

Hope this helps ...

yong

On Sun, 16 May 2004, Pradipta Bandyopadhyay wrote:

> 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
>
>
>
>
> McAfee Scanned !!
>
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