Dear all,
I want to simulate collagen model peptides and I am trying to decide cutoff
for non bonded interactions. Below I have results from the last step of a
1000 step minimisation. Using 8A instead of 12A results in approx. 50%
reduction in time.
I am just wondering if I should go on with 8A for my MD simulations. I want
to do rather long MD runs (~50ns) and reducing time by 1/2 will be great. I
will be using PME for dynamics.
The solute in a water-box was created using
solvateoct model TIP3PBOX 12.0 iso
And initial box length is ~78 Angstroms
Thanks for your time.
Lekpa.
FINAL RESULTS (8 Angstroms)
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -1.3648E+05 7.3686E-01 3.8736E+01 C 163
BOND = 10407.9190 ANGLE = 118.6558 DIHED =
216.6186
VDWAALS = 25559.3125 EEL = -174199.3822 HBOND =
0.0000
1-4 VDW = 57.2821 1-4 EEL = 1333.9180 RESTRAINT =
29.7503
EAMBER = -136505.6763
Total time = 424 secs
FINAL RESULTS (10 Angstroms)
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -1.3602E+05 3.0467E-01 1.5727E+01 C 235
BOND = 10261.5540 ANGLE = 118.1092 DIHED =
215.6671
VDWAALS = 24964.1168 EEL = -173000.0875 HBOND =
0.0000
1-4 VDW = 57.1944 1-4 EEL = 1333.7586 RESTRAINT =
26.3831
EAMBER = -136049.6874
Total time = 610 secs
FINAL RESULTS (12 Angstroms)
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -1.3625E+05 8.0374E-01 8.0853E+01 H1 15842
BOND = 10293.9982 ANGLE = 118.2531 DIHED =
215.6771
VDWAALS = 25345.4841 EEL = -173644.0830 HBOND =
0.0000
1-4 VDW = 57.2408 1-4 EEL = 1333.7694 RESTRAINT =
26.8284
EAMBER = -136279.6604
Total time = 904 secs
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Received on Wed Apr 13 2011 - 10:00:05 PDT
