after a certain point changing r4 won't matter since you will never have
distortions that reach that far.
I think you should check the first energy output (use ntpr=1) in your first
equilibration. The bond value you mention seems very large but I cannot
comment further since I don't know what the input file was for that
particular run, or when it happened, etc.
On Fri, Apr 22, 2011 at 8:24 AM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear Carlos,
> Thank you for an quick reply. As mentioned earlier I
> have used low force constant and very high value of r4. Still I am not able
> to restrain the distance. The input file and rst.dist file are as bellow
>
> filename: eq_v.in
> Heating up the system equilibration stage 1
> &cntrl
> nstlim=5000 dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000, ntwx=5000,
>
> tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
>
> ntb=1, ntp=0,
>
> ntc=2, ntf=2, nmropt=1,
>
> nrespa=2,
> &end
> &wt type='END' /
> DISANG=rst.dist
>
> filename: rst.dist
> #
> # 111 VAL QQG 276 WAT O 1.8
> &rst
> ixpk= 0, nxpk= 0, iat=1735,2946, r1= .00, r2= .00, r3= 1.80, r4=
> 100000.00,
> rk2=0.0, rk3=10, ir6=1, ialtd=1,
> &end
>
> As you can see I have using very large value of r4. Do you want me to even
> go for an higher value of r4?
>
> Another question which I forgot to mention in my earlier mail is about the
> mdout file.
> In the mdout file a line mentioned when we do restrained dynamics
>
> NMR restraints: Bond = 1452.510 Angle = 0.000 Torsion = 0.000
>
> What dose this Bond value gives?
>
> On Fri, Apr 22, 2011 at 7:20 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > You should not use such large force constants. They give high frequency
> > motions, ans in then require short time steps to properly integrate.
> >
> > Why not use a value of 10-100 and set larger r4? You can always use the
> > harmonic oscillator energy equation to estimate the amount of thermal
> > distortion you will get.
> >
> > On Apr 22, 2011 1:13 AM, "nicholus bhattacharjee" <
> > nicholusbhattacharjee.gmail.com> wrote:
> >
> > Dear Carlos,
> > Thank you for your help. I have gone through the
> manual
> > and could understand the restraint energy functions. But I am facing some
> > problems. First of all I have changed to ialtd=1 instead of ialtd=0 since
> > it
> > gives a stiffer value (hyperbolic rather than linear) beyond r4. Now as
> far
> > I could understand We can restrain the distance by either monitoring
> r1->r4
> > values or maximizing rk2 and rk3 values. Since my restrained value is
> very
> > low of around 1.8 A there is low probability of the distance coming to
> > lower
> > value during MD. So if I keep the rst.dist files like bellow
> > &rst
> > ixpk= 0, nxpk= 0, iat= 1735, 2946, r1= 0.1, r2= 0.3, r3= 1.8, r4= 2.3,
> > rk2=0.0, rk3=2000.0, ir6=1, ialtd=1,
> > &end
> >
> > By either giving high rk3 value (as shown above) or by giving high r4
> value
> > I can keep the distance constrained in the desired value of around 1.8A.
> >
> > This was fine with the minimization protocol (both minimization
> > constraining
> > the solute as well as the whole system). But I am unable to run the
> > equilibrium run with this. During equilibration (where I am inceresing
> the
> > temperature from 100K to 300K) we are unable to give very high rk3 value
> as
> > it is showing problem with SHAKE where vlimit exceed. Neither giving very
> > high value to r4 provides a desired result i.e. I am unable to restrain
> the
> > desired distance. I am confused what should I do next. Kindly suggest
> some
> > solution.
> >
> > On Mon, Apr 18, 2011 at 9:33 AM, Carlos Simmerling <
> >
> > carlos.simmerling.gmail.com> wrote:
> >
> > > I don't think you should use the script- what you were doing ...
> > _______________________________________________
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> >
>
>
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
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Received on Fri Apr 22 2011 - 05:30:09 PDT
