I think that my complex has been moving out of the octahedron water box
(TIP3PBOX) during the simulation, it looks like part of the complex goes
out of the box at many points. Are there any parameters in my input files
that I should try adjusting?
Here are the settings that I used for my input files
--complex initial minimization solvent + ions
&cntrl imin = 1,maxcyc = 3000,ncyc = 1500,ntb = 1,ntr = 1,cut
= 10.0/
Hold the Protein + DNA fixed
100.0
RES 1 153
END
END
--complex initial minimization solvent + ions
&cntrl imin = 1,maxcyc = 5000,ncyc = 2500,ntb = 1,ntr = 1,cut
= 10.0/
Hold the Protein + DNA fixed
25.0
RES 1 153
END
END
--Complex minimization for whole system without restraint
&cntrl imin = 1,maxcyc = 5000,ncyc = 2500,ntb = 1,ntr = 0,cut
= 10.0/
--complex: 20ps MD with res on the protein + DNA complex
&cntrl
imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10.0,
ntr = 1, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0,ntt
= 3, gamma_ln = 1.0, nstlim = 10000, dt = 0.002, ntpr = 10000, ntwx =
10000, ntwr = 10000,
/
Keep DNA fixed with weak restraints
10.0
RES 1 153
END
END
--complex: 80ps MD with 0.5 Kcal res on protein + DNA complex
&cntrl
imin = 0, irest = 1, ntx = 7, ntb = 1, cut = 10.0,
ntr = 1, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0, nstlim = 40000, dt = 0.002, ntpr = 40000,
ntwx = 40000, ntwr = 40000 ig = -1
/
Keep Protein + DNA fixed with weak restraints
0.5
RES 1 153
END
END
--complex: 200ps of MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0, ig = -1,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 100000, ntwx = 10000, ntwr = 100000
/
Sincerely,
*Syeda Amna Arshi*
*Ph.D. Scholar*
Multidisciplinary Centre For Advanced Research and Studies
Jamia Millia Islamia
Delhi-110025
Ph.no: 7737638065
[image: Image result for save world by plant][image: Image result for save
world by plant white background]
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 20 2020 - 23:30:03 PST
