> On Feb 23, 2014, at 3:16 AM, "Ali M. Naserian-Nik" <naseriannik.gmail.com> 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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Received on Sun Feb 23 2014 - 08:00:04 PST
