This is the input for my simulations:
Constant pressure constant temperature production (50ns) - FIRST (with
random seed number)
&cntrl
nstlim=25000000, dt=0.002
ntx=1, irest=0
ntpr=1000, ntwr=50000, ntwx=1000, ioutfm=1
tempi=300.0, temp0=300.0, ntt=3, gamma_ln=2.0,
ntb=1, cut=8.0, ntr=1, ntc=2, ntf=2,
nrespa=1, nscm=1000, iwrap=1,ig=-1,
&end
On Mon, Sep 11, 2017 at 12:34 PM, Chayya Bhargac <chayyachemistry.gmail.com>
wrote:
> 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?
>
>
> ------------------------------------------------------------
> --------------------
>
> 4. RESULTS
>
> ------------------------------------------------------------
> --------------------
>
>
> | # 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 - 11:00:02 PDT
