Dear Adrian,
Thank you very much for your reply. Your solution works! But could you
please say how I can calculate the input force to obtain a displacement vs.
force diagram?
On Sunday, February 23, 2014, Adrian Roitberg <roitberg.ufl.edu> wrote:
> do not use the jar option, just use nmropt
>
> On 2/23/14 12:48 PM, Ali M. Naserian-Nik wrote:
> > 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<javascript:;>>
> wrote:
> >
> >>
> >>> On Feb 23, 2014, at 3:16 AM, "Ali M. Naserian-Nik" <
> >> naseriannik.gmail.com <javascript:;> <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
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
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>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu <javascript:;>
> 352-392-6972
>
>
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Received on Sun Feb 23 2014 - 12:00:02 PST
