Hi,
If you're having trouble minimizing your system, you may want to try
the protocol outlined here:
https://aip.scitation.org/doi/abs/10.1063/5.0013849
I have a script that implements this protocol for Amber:
https://github.com/drroe/AmberMdPrep
Feel free to give it a try, but be aware that it's still fairly rough
around the edges, so use with caution.
-Dan
On Sat, Sep 19, 2020 at 5:54 AM Jisha B <jisha.b.k0511.gmail.com> wrote:
>
> Dear all,
> I am dealing with a large system of protein-RNA-DNA. I have minimized the
> system. But when I started the heating stage where I have to increase the
> temperature from 0K to 100K, it is stuck at
>
> 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 = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 101843086
> | TOTAL SIZE OF NONBOND LIST = 101843086
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -1363415.9230 EKtot = 0.0000 EPtot =
> -1363415.9230
> BOND = 2311.6832 ANGLE = 4410.0196 DIHED =
> 19869.1201
> 1-4 NB = 5810.6688 1-4 EEL = 39862.6725 VDWAALS =
> 207873.5245
> EELEC = -1643553.6116 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.6217E-04
>
> It has been in this stage for last one hour. My input for heating is
> Heating Equilibration - constant volume
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10.0,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 100.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 100000, dt = 0.002
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
> When I repeated the simulation, I got the error vlimt exceeded error. How
> to solve this?
>
> --
> Jisha
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Received on Wed Sep 23 2020 - 04:00:02 PDT
