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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Received on Tue Apr 25 2017 - 11:00:04 PDT
