AMBER Archive (2003)

Subject: AMBER: density equilibrium & harmonic restrain

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Mon Sep 29 2003 - 21:59:50 CDT

Hi all,
I tried to equilibrate my DNA-protein complex in TIP3P solvent
followed the protocol as follows,
%A V. Tsui
%A D.A. Case
%T Calculations of the Absolute Free Energies of Binding between RNA and
Metal
%Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
%J J. Phys. Chem. B
%V 105
%P 11314-11325
%D 2001

However, the solvent density just raises to about 0.85 after 40ps NPT
ensemble, but it raises to about 1.05 while decreasing the harmonic
force constant to a smaller value, like 0.2.
This is my input for 40ps NPT ensemble:
----------------------------------------------------
40ps NPT MD(keep at 300K) T=60.000-100.000

 &cntrl
   imin=0, dt=0.001, ntr=1, ntb=2, nstlim=40000,
   irest=1, ntx=7,
   ntc=2, tol=0.0000001, ntf=1,
   ntt=1, temp0=300.0, tautp=0.5, vlimit=20.0,
   ntp=1, taup=0.02,
   cut=9.0,
   ntpr=50, ntwr=50, ntwx=50,
   nscm=1000, iwrap=1,
 &end
Group input for restrained protein complex
10.0
RES 1 72
END
END
----------------------------------------------------

Thanks for any ideas and help.

Best Regards,
sychen.

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