Dear Amber users,
I am trying to run a NVT simulation on AMBER.
When I try running the simulation with sander,
it doesn't run and I get an error (shown below).
But when, I run the same using pmemd, it runs to
completion. What could be the reason for this?
------------------------------------------------------------
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4. RESULTS
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| # of SOLUTE degrees of freedom (RNDFP): 245702.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 245702. NUM_NOSHAKE = 0 CORRECTED RNDFP = 245702.
| TOTAL # of degrees of freedom (RNDF) = 245702.
---------------------------------------------------
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 = 5358049
| TOTAL SIZE OF NONBOND LIST = 20966528
vlimit exceeded for step 4; vmax = 44.2390
vlimit exceeded for step 5; vmax = 1010.7098
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 6 1 3
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
With pmemd it works perfectly fine and I the simulation goes to completion.
Thanks.
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Received on Mon Sep 11 2017 - 10:00:02 PDT
