Dear all,
I ran a production NVT simulation and found that the fluctuation of potential energy is as large as several hundreds kcal/mol. Is this kind of fluctuation normal? The simulation was in water box. At first I thought this was because the geometry of the frames was not optimized. But after I used Sander to optimize some of the frames with ntmin = 3, the large energy difference was still there. I visualized the trajectory. It seems that this potential energy difference is caused by change of conformations. My calculation is on a metalloenzyme after initial equilibration including constrained minimization, full minimization, and warming up by a short NPT. The input files are attached. If my result is unusual, is there something wrong with my input files? Thank you.
Zhe Li
Input files:
min1.in
Initial minimization solvent + ions
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 1,
igb = 0,
ntr = 1,
cut = 8.0
/
Hold the substrate fixed
500.0
RES 1 464
END
END
min2.in
&cntrl
imin = 1,
maxcyc = 50000,
ncyc = 25000,
ntb = 1,
igb = 0,
ntr = 0,
cut = 8.0
/
eq.in
100ps MD with res
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 2, ntp = 1,
pres0 = 1.0, taup = 2.0
cut = 8.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 2, ig = -1,
nstlim = 50000, dt = 0.002,
ntpr = 1000, ntwx = 2000, ntwr = 2000,
/
Keep substrate fixed with weak restraints
10.0
RES 1 464
END
END
md.in
100 ns MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 1,
cut = 8.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 50000000, dt = 0.002,
ntpr = 10000, ntwx = 10000, ntwr = 10000
ioutfm = 1,
iwrap = 1,
ig = -1,
/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 04 2016 - 15:30:02 PDT
