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 ...
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 22 2011 - 05:30:07 PDT
