Hi Adrian
Thanks for the reply
But do my input and dist. files correspond to stretch it for 1A0 using a parabolic well? So parabolic well is harmonic restraint?
As another question, for pulling under constant force, what does it mean to apply a flatwell potential restraint to the ends of DNA? What I mean is how to set the atoms of the restraint to the two endpoints of the pull? what does it mean? Would you please explain it?
I saw all the related posts in the list, and Daniel Roe once wrote:
Here is an example disang file for pulling between atoms 3 and 992 to a final distance around 208 Ang.:
&rst iat=3,992,0
r1 =206.22, r2 =208.22, r3 =208.22, r4 =210.22, rk2 =0.25, rk3 =0.25
Why does this Disang file mean constant force? so what about the current value?
Thanks in Advance
Ramin
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Tuesday, April 25, 2017 1:01:02 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Stricter convergence Criterion for stretching
Hi
There is no convergence at all in the calculation you sent.
You are asking the system to RUN for a full 6500 steps, and apply a
restraint for that distance to 41A.
It will not stop when it gets to 41, it will stop only after 6500 steps.
That is why you get entries in the DUMPAVE up to 6500
Do not look at the mdinfo file, it is only updated once per minute I
believe.
Look at your mdout file instead.
adrian
On 4/25/17 1:57 PM, Ramin Salimi wrote:
> Dear Amber users
>
> I am trying to stretch my DNA molecule for 1A0 from its current value which is 40A0 to 41A0. So I used nmropt by the application of strict restraint. This restraint consisted of a parabolic well with a force constant of 100 kcal/mol/Å2 using the following dist file:
>
> &rst
> iat=2,382, r1=0, r2=41, r3=41, r4=999, rk2 = 100.0, rk3 = 100.0, /
>
> Is this dist. file correct to apply a parabolic well with that 100 kcal/mol/Å2?
>
> And the mdin file was as such:
>
> &cntrl
> imin = 0, nstlim = 6500, dt = 0.002,
> ntx = 5, tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln=5.0
> ntc = 2, ntf = 2, ntb = 2, ntp = 1,
> ntwx = 100, ntwr = 100, ntpr = 100,
> ntwv = 100, ntwf = 100, ntwe = 100,
> cut = 8.0, ig=-1, ioutfm=1,
> irest = 1, nmropt=1,
>
> &end
> /
> &wt type='DUMPFREQ', istep1=5 /
> &wt type='END' /
> DISANG=dist_nmropt.RST
> DUMPAVE=dist_vs_nmropt
> LISTIN=POUT
> LISTOUT=POUT
> /
>
> When I checked the info file, it showed just 100 steps out of 6500 was completed, which I believe shows it has converged. Is there any way to implement a stricter convergence criterion so it takes longer than just 100 steps?
>
> Also when I check the DUMPAVE file, it shows me the value of the restraint up to step number 6495. If it was cut at step #100 based on the info file, why is it showing the restraint values up to step #6495??
>
> Any help is greatly appreciated
>
> Thanks
>
> Ramin
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Apr 25 2017 - 11:30:02 PDT
