Dear Carlos,
Thank you for the reply. I think I should play more
with the input values to get an optimum result. I will get back to you
hopefully with a positive result next time. By the way you dint reply to my
last question. What dose Bond value in the following line of mdout file say
NMR restraints: Bond = 1452.510 Angle = 0.000 Torsion = 0.000
Thank you once again.
On Fri, Apr 22, 2011 at 8:27 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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)
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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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 - 06:00:03 PDT
