Hi Jason,
Thank you very much for your reply. But I think for constant force pulling,
I need a linear potential not a parabolic, and r1-r4 must be set to be
around or smaller than the final displacement (r2a-r2). Is it true? If yes,
then how I can change value of r4?
An additional question: What is the role of r4a?
On Sunday, February 23, 2014, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> > On Feb 23, 2014, at 3:16 AM, "Ali M. Naserian-Nik" <
> naseriannik.gmail.com <javascript:;>> wrote:
> >
> > Dear Amber users/developers,
> >
> > I need to increase the distance between two atoms under constant velocity
> > and constant force regime. It seems that I must change the values of r4
> and
> > r4a in the restraint file depending on the final value of the SMD
> distance
> > (r2a) to obtain a parabolic or linear restraint potential. I set these
> > parameters to my desired values in the restraint file, but the output
> file
> > shows that my desired values are ignored by the code and changed to what
> > the code prefers. Here is an example of my restraint file and its output:
> >
> > RST file:
> ------------------------------------------------------------------
> >
> > # SMD under constant velocity
> > &rst iat=379,761, ifvari=1, nstep1=0, nstep2=0, r1=0.0, r2=86.979,
> > r3=86.979, r4=386.979, r1a=125.997, r2a=220.979, r3a=220.979,
> r4a=486.979,
> > rk2=0.125, rk3=0.125, rk2a=0.125, rk3a=0.125, /
> >
> >
> > Output:
> ------------------------------------------------------------------
> >
> > Begin reading energy term weight changes/NMR restraints
> >
> > WEIGHT CHANGES:
> > DUMPFREQ 500 0 0.000000 0.000000 0 0
> >
> > ** No weight changes given **
> >
> > RESTRAINTS:
> > Requested file redirections:
> > DISANG = dist.RST
> > DUMPAVE = F_vs_d
> > LISTIN = POUT
> > LISTOUT = POUT
> > Restraints will be read from file: dist1.RST
> > Here are comments from the DISANG input file:
> >
> > jar option running
> > ******
> >
> > O3' ( 379)-DH ( 761) NSTEP1= 0 NSTEP2=******
> > R1 = -13.021 R2 = 86.979 R3 = 86.979 R4 = 186.979 RK2 = 0.125 RK3 = 0.125
> > R1A= 120.979 R2A= 220.979 R3A= 220.979 R4A= 320.979 RK2A= 0.125 RK3A=
> 0.125
> > Rcurr: 86.979 Rcurr-(R2+R3)/2: 0.000 MIN(Rcurr-R2,Rcurr-R3): 0.000
> >
> > Number of restraints read = 1
> >
> > Done reading weight changes/NMR restraints
> >
> > ------------------------------------------------------------------
> >
> >
> > I use Amber12 with all patches applied. Is there a mistake in my input
> file
> > or it is a bug?
> > I'd be so grateful if anyone could help me on these issues.
>
> No bug and no mistake, it's simply how the steered md code behaves. The r4
> variable is adjusted to make sure the potential is always parabolic.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Feb 23 2014 - 10:00:03 PST
