Hi Necmettin,
A few notes here. Firstly it is best to run a small number of steps say nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is going wrong and visualize the trajectory.
Also, tempi=600 is hot - that may causes issues - especially if your system is not well equilibrated first.
Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable potential function. I would not recommend going above ntf=2,ntc=2 for anything other than debugging.
If changing to ntc=2,ntf=2 does not fix things then look carefully at your structure - it may not be well enough minimized, it may have structural deficiencies etc. Visualizing for and ntwx=1 run will help here.
The parameters may also be suspect since this is not a regular amino / nucleic acid - where did you get the parameters from?
All the best
Ross
> On Feb 25, 2016, at 00:48, necmettin pirinccioglu <pirincn.gmail.com> wrote:
>
> Dear All,
> I have been running MD for diphosphoric acid anion with the following input
> but I get the error message below. Helps will be welcomed!
>
> INPUT
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=250000, dt=0.002,
> ntc=4, ntf=4,
> ntt=1, tautp=0.5,
> tempi=600.0, temp0=600.0,
> ntpr=500, ntwx=500,
> ntb=0, igb=0,
> cut=999
> /
>
> ERROR MESSAGE!!!
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 1
> | TOTAL SIZE OF NONBOND LIST = 1
> vlimit exceeded for step 369; vmax = 22.0998
> vlimit exceeded for step 373; vmax = 54.3352
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1 1 2
>
> --
> Necmettin Pirinccioglu (BSc, PhD)
> Department of Chemistry
> University of Dicle
> 21280 Diyarbakir
> TURKEY
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Received on Thu Feb 25 2016 - 01:30:03 PST
