According to the advice of Professor David, I recalculate my system by
using a small force constant. However, it seems that it doesn't work.
My system includes a dsDNA and a CNT. I wish to fix the CNT. The
following is my input files and the change of the coordinates of one
CNT atom.
Fist step:
Minimization input file, MIN1.in
Initial minimization / position restraints on DNA_CNT
&cntrl
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=100, ntwx=0, ntwv=0, ntwe=0,
ntf=1, ntb=1,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=1, maxcyc=1000, ncyc=5000,
ntmin=1, dx0=0.01, dxm=0.5, drms=0.0001,
nscm=0,
t=0.0, dt=0.002,
tempi = 300.0, temp0 = 300.0, ntt = 0,
vlimit=20.0,
ntc=1, tol=0.0005,
/
Hold the DNA and CNT fixed
20.0
RES 1 25
END
END
MD simulation input file, MD1.in
Initial minimization / position restraints on DNA_CNT
&cntrl
nmropt =1,
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=500, ntwx=500, ntwv=0, ntwe=0,
ntf=2, ntb=2,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=0, nstlim=12500,
nscm=0,
t=0.0, dt=0.002,
tempi = 100.0, temp0 = 300.0, ntt = 1,
ig = 71277, heat=0.0, tautp =0.2, vlimit=20.0,
ntp =1, pres0=1.0, taup=1.0, npscal=1,
ntc=2, tol=0.00001,
/
&wt
type='TEMP0', istep1=0, istep2=500,
value1=100.0, value2=300.0,
/
&wt
type='TEMP0', istep1=500, istep2=12500,
value1=300.0, value2=300.0,
/
&wt
type='END',
/
Hold the DNA and CNT fixed
20.0
RES 1 25
END
END
Result: the coordinates of C10 in CNT after 1ps MD simulation is
(38.576, 25.732, 11.424), the final coordinates of the C10 is (38.119,
25.438, 11.069) after 25ps MD simulation run.
Second Step:
Minimization input file, MIN2.in
Initial minimization / position restraints on DNA_CNT
&cntrl
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=100, ntwx=0, ntwv=0, ntwe=0,
ntf=1, ntb=1,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=1, maxcyc=1000, ncyc=5000,
ntmin=1, dx0=0.1, dxm=0.5, drms=0.0001,
nscm=0,
t=0.0, dt=0.002,
tempi = 300.0, temp0 = 300.0, ntt = 0,
ig = 71277, heat=0.0, tautp =0.2, vlimit=20.0,
ntc=1, tol=0.0005,
/
Constraints on DNA
10.0
RES 1 24
END
Hold CNT fixed
20.0
RES 25
END
END
MD simulation input file, MD2.in
Initial minimization / position restraints on DNA_CNT
&cntrl
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=500, ntwx=500, ntwv=0, ntwe=0,
ntf=2, ntb=2, dielc =1.0,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=0, nstlim=10000,
nscm=0,
t=0.0, dt=0.002,
tempi = 300.0, temp0 = 300.0, ntt = 1,
ig = 71277, heat=0.0, tautp =0.2, vlimit=20.0,
ntp =1, pres0=1.0, comp=44.6, taup=1.0, npscal=1,
ntc=2, tol=0.00001,
/
Constraints on DNA
10.0
RES 1 24
END
Hold CNT fixed
20.0
RES 25
END
END
Result: the coordinates of C10 in CNT after 1ps MD simulation is
(38.134, 25.414, 11.05), the final coordinates of the C10 is (37.455,
25.076, 10.565) after 20ps MD simulation run.
Third Step:
Minimization input file, MIN3a.in
Initial minimization w/ position restraints on DNA_CNT, 9.0 cut
&cntrl
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=200, ntwx=0, ntwv=0, ntwe=0,
ntf=1, ntb=1,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=1, maxcyc=1000, ncyc=5000,
ntmin=1, dx0=0.1, dxm=0.5, drms=0.0001,
ntc=1, tol=0.0005,
/
Constraints on DNA
5.0
RES 1 24
END
Hold CNT fixed
20.0
RES 25
END
END
Minimization input file, MIN3b.in
Initial minimization / position restraints on DNA_CNT, 9.0 cut
&cntrl
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=500, ntwx=0, ntwv=0, ntwe=0,
ntf=1, ntb=1,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=1, maxcyc=1000, ncyc=5000,
ntmin=1, dx0=0.1, dxm=0.5, drms=0.0001,
ntc=1, tol=0.0005,
/
Constraints on DNA
0.0
RES 1 24
END
Hold CNT fixed
20.0
RES 25
END
END
MD simulation input file, MD3.in
Initial minimization / position restraints on DNA_CNT, 9.0 cut
&cntrl
nmropt =1,
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=500, ntwx=500, ntwv=0, ntwe=0,
ntf=2, ntb=2,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=0, nstlim=10000,
t=0.0, dt=0.002,
tempi = 100.0, temp0 = 300.0, ntt = 1,
ig = 71277, heat=0.0, tautp =0.2, vlimit=20.0,
ntp =1, pres0=1.0, comp=44.6,
ntc=2, tol=0.00001,
/
&wt
type='TEMP0', istep1=0, istep2=1000,
value1=100.0, value2=300.0,
/
&wt
type='TEMP0', istep1=1000, istep2=10000,
value1=300.0, value2=300.0,
/
&wt
type='END',
/
Hold the CNT fixed
20.0
RES 25
END
END
Result: the coordinates of C10 in CNT after 1ps MD simulation is
(37.414, 25.063, 10.423), the final coordinates of the C10 is (36.462,
24.642, 9.711) after 20ps MD simulation run.
The final step:
MD simulation input file, MD4.in
Initial minimization / position restraints on DNA_CNT, 9.0 cut
&cntrl
ntx=7, irest=1, ntrx=1, ntxo=1,
ntpr=1000, ntwx=1000, ntwv=0, ntwe=0,
ntf=2, ntb=2, dielc =1.0,
cut=9.0, nsnb=10,
ibelly=0, ntr=1,
imin=0, nstlim=1000000,
nscm=0,
t=0.0, dt=0.002,
tempi = 300.0, temp0 = 300.0, ntt = 1,
ig = 71277, heat=0.0, tautp =0.2, vlimit=20.0,
ntp =1, pres0=1.0, comp=44.6, taup=2.0, npscal=1,
ntc=2, tol=0.00005,
/
Hold CNT fixed
20.0
RES 25
END
END
Result: the coordinates of C10 in CNT after 2ps MD simulation is
(36.429, 24.601, 9.644), the final coordinates of the C10 is (26.660,
19.652, 1.688) after 300ps MD simulation run.
According to the user's manual of Amber 8 "Please note: in general you
will need to equilibrate the temperature to something like the final
temperature using constant volume (ntp=0) before switching on constant
pressure simulations to adjust the system to the correct density.", I
change the NTB = 2 and NTP =1 as NTB=1 and NTP=0 in the input files of
MD1.in, MD2.in and MD3.in, but keep NTB = 2 and NTP =1 in the input
file of MD4.in. In this case the coordinates of C10 are:
MD1 simulation: the coordinates after 1ps simulation are (38.726,
25.826, 11.551), and the coordinates are (38.686, 25.799, 11.530)
after 25ps run.
MD2 simulation: the coordinates after 1ps (38.765, 25.782, 11.541) and
the coordinates after 20ps (38.647, 25.761, 11.511)
MD3 simulation: the coordinates after 1ps (38.743, 25.790, 11.507) and
the coordinates after 20ps (38.655, 25.934, 11.563)
MD4 simulation: the coordinates after 1ps (38.564, 25.856, 11.508) and
the coordinates after 300ps (26.650, 19.707, 1.661)
What should I do? Does the density of water in Solvatebox affect it?
Thank you very much for your kind help.
On 5/2/05, David A. Case <case.scripps.edu> wrote:
> On Mon, May 02, 2005, george Chen wrote:
> >
> > I have a question about the MD simulation by using Amber 8. I want to
> > fix one of the molecules. Then I use NTR = 1 in the MD input file. In
> > the case NTB=1 and NTP=0 (NVT condition), the change of the
> > Coordinates of the atoms within the fixed molecule is minor. However,
> > in the case NTB=2 and NTP=1 (NPT condition), the change of the
> > coordinates of the atoms is significant.
>
> What do you catergorize as significant? The restraints will allow small
> changes in coodinates, but this should rarely be a problem.
>
> > Hold the DNA and CNT fixed
> > 500.0
>
> This is way too big a force constant. Try something about 100 times smaller.
>
> ...good luck....dac
>
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Received on Tue May 03 2005 - 21:53:00 PDT
