Dear all,
I am taking some .prmtop and .rst files that worked using AMBER 11, but
am having trouble with maxing out the NONBOND LIST size in Amber 14.
Here is what I am seeing if I cut the nonbonded interactions to 8 Å:
| # of SOLUTE degrees of freedom (RNDFP): 149324.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 149324. NUM_NOSHAKE = 0 CORRECTED RNDFP = 149324.
| TOTAL # of degrees of freedom (RNDF) = 149324.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 15160735
| TOTAL SIZE OF NONBOND LIST = 15160735
Cutoff list exceeds largest sphere in unit cell!!
Big problems with imaging!!
a,b,c = -1244.71951386096 -1184.70414062345
-1127.43981723746
alpha,beta,gamma = 90.0000000000000 90.0000000000000
90.0000000000000
cutlist,sphere = 10.0000000000000 -1778.43173586094
If I leave the cutoff at 16Å, the program crashes because the non-bonded
list is too large. Is there some file that I don't have write access to
that stores NBs? This is a solvated simulation. If this is a simple
problem, great, if not, I can provide more info upon request.
Thanks,
Tom Pochapsky
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Received on Tue May 17 2016 - 12:00:03 PDT
