I am preparing a protein in solvent box (TIP3P water) for MD simulations. I am
seeing some strange behavior during the equilibration steps. After initial
minimization steps, I am doing short MD runs to rescale the box and remove the
"vacuum bubbles". For this I am first performing a constant volume MD run with
slow heating, which is followed by a constant pressure MD run. After the
constant volume MD run I notice that most of the water molecules gather at the
center of the box with few scattered on the outside. This problem continues
with constant pressure MD and the system looks very inhomogeneous. The before
and after snapshots are available at the following locations:
Before MD : http://linus.ornl.gov/MD/before.gif
After const. Vol. MD : http://linus.ornl.gov/MD/after_const_T.gif
(slow heating to 300K)
After const. Press MD : http://linus.ornl.gov/MD/after_const_P.gif
(const. T = 300K)
If anybody can help me find out where the problem is, I would really appreciate
it. Attached are the input files (more information can be found at :
http://linus.ornl.gov/MD/)
============= mdinp for const. volume MD run =================
&cntrl
imin=0, irest=0, ntx=1, nmropt=1,
ntt=1, tempi=100.0, temp0=300.0, tautp=1.0,
ntb=1, ntc=1, ntf=1, nsnb=10,
nstlim=20000, dt=0.001
ntwe=50, ntpr=25, ntwx=500,
cut=10.0, ntr=1,
&end
&wt
type='TEMP0', istep1=0, istep2=5000,
value1=100.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=5000, istep2=20000,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
&end
Apply restraints to the solute atoms
500.0
RES 1 168
END
END
=============================================================
================== mdinp for const. volume MD run ===========
&cntrl
imin=0, irest=0, ntx=5,
ntt=1, tempi=300.0 temp0=300.0, tautp=1.0,
ntb=2, ntp=1, taup=1.0,
ntc=1, ntf=1, nsnb=10,
nstlim=30000, dt=0.001
ntwe=50, ntpr=25, ntwx=500,
cut=10.0, ntr=1,
&end
Apply restraints to the solute atoms
500.0
RES 1 168
END
END
=====================================================================
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Received on Wed Sep 11 2002 - 12:38:36 PDT
