Thanks for the refernce My mdin files (in sequence)
minimization of water or solvent
molecules
&cntrl
imin=1,
ntb=1,
cut=10.0,
maxcyc=100,
ncyc=10,
ntt=0,
ntr=1,
&end
Hold the monomers
fixed
1.0
RES 1
85
END
END
minimization of solvent and solute
&cntrl
imin=1,
ntb=1,
cut=10.0,
maxcyc=100,
ncyc=10,
ntt=0,
&end
heat/dynamics at constant
volume
&cntrl
imin=0,
ntxo=1,
ntrx=1,
cut=10.0,tempi=0.1,
ntpr=500, ntwx=500,
ntwe=500,
nstlim=1000,
temp0=50.0,
dt=0.0005,
ntc=1, ntf=1,
tol=0.00001,
ntx=1,
irest=0,
ntb=1,tautp=1,
ntt=1,
nmropt=1,ntr=1
/
&wt
type='TEMP0', istep1=0, istep2=1000, value1=0.0,
value2=50.0,
/
&wt
type='TEMP0', istep1=1001,istep2=80000,value1=50.0,
value2=50.0,
/
&wt
type='END',
/
GROUP FOR
CONSTRAINTS
1.0
RES 1
85
END
END
heat/dynamics at constant
volume
&cntrl
imin=0,
ntxo=1,
ntrx=1,
cut=10.0,tempi=50,
ntpr=500, ntwx=500,
ntwe=500,
nstlim=1000,
temp0=50.0,
dt=0.0005,
ntc=1, ntf=1,
tol=0.00001,
ntx=1,
irest=0,
ntb=1,tautp=1,
ntt=1,
nmropt=1,ntr=1
/
&wt
type='TEMP0', istep1=0, istep2=100, value1=50.0,
value2=50.0,
/
&wt
type='TEMP0', istep1=101,istep2=1000,value1=50.0,
value2=50.0,
/
&wt
type='END',
/
GROUP FOR
CONSTRAINTS
1.0
RES 1
85
END
END
minimization
&cntrl
imin=1, ntx=1, drms=0.0001,
ntmin=1,
ntrx=1, ntxo=1,
nscm=100,
ntb=1,
ntf=1,
irest=0,
cut=10.0,
ntpr=100, ntwx=100,
ntwe=100,
nsnb=10,
tol=0.0005,
ntc=1,
maxcyc=10,
ncyc=100,
&end
constant pressure
equilibration
&cntrl
imin=0,
ntx=1,
irest=0,
ntxo=1,tempi=50.0,
ntpr=1000, ntwx=1000,
ntwe=1000,
nstlim=10000,tautp=2,
temp0=50.0,
dt=0.001,
nscm=100,
igb=0,ntb=2,ntp=1,
ntt=1,
nsnb=20,ntr=1,
&end
GROUP FOR
CONSTRAINTS
1.0
RES 1
85
END
END
Thanks
Kirtana
On Sun, Dec 4, 2011 at 3:36 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > I attached the output files in my earlier reply.
>
> I rarely open attachments. Mdin files are small and worth comparing
> in proximity to each other.
>
> > My molecule is somewaht
> > similar to plastocyanin as discussed in AMBER tutorial 4 instead of
> copper
> > I have a K+ ion (non -bonded interaction with monomer) , I have non
> bonded
> > parameters in my frcmod file while I construct the solvated box .
>
> By the way, the standard ion vdw parameters are derived for interactions
> with the water model, not the Amber residues and others parameterized
> the same way. I've never seen anyone else stress this fact, but
> here is a paper where it is investigated at length:
>
> Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
> Perturbation Studies. W.S. Ross and C.C. Hardin
> Journal of the American Chemical Society 116, 6070 (1994).
>
> > Is my error related to this intitial structure , I require to have a non
> > bonded ion, how can I work with this in the input files while running
> MD.
>
> A non-bonded ion is fine, see many studies of this. The first step of
> triage is to rule out equilibration errors. Please re-read the below:
>
> > > equilibration at 50K at constant
> > > volume and then I turn on constant pressure equilibration
> >
> > Did you jump the temperature or change the time step between
> > the two? I suggest pasting in all your mdin files to the response.
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Dec 04 2011 - 13:00:03 PST
