try setting ntpr to a smaller value (even 1) to get more detail about
what's going wrong before the NaN.
also what is the initial coordinates? the vdw energy drops, was it
minimized first using the same parameters?
once you get that resolved, you might want to make sure temp0 is defined
for the full nstlim range.
On Tue, Jul 25, 2023 at 4:06 PM Yang, Li-Yen via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I am running a heating process under NVT.
>
> I have previously run it with the same parameters (except the cutoff is
> different), and there weren’t any issues.
> But now when I changed the cutoff from 30 to 10, I started to get NaN
> values in TEMP, EKtot, and Etot.
>
> In my output file, it went from 0 to NaN as follows:
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -763233.3804 EKtot = 0.0000 EPtot =
> -763233.3804
> BOND = 177.5013 ANGLE = 900.7922 DIHED =
> 3291.6735
> 1-4 NB = 1075.8873 1-4 EEL = 15422.6675 VDWAALS =
> 153707.8033
> EELEC = -937809.7054 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = NaN PRESS =
> 0.0
> Etot = NaN EKtot = NaN EPtot =
> -521630.7470
> BOND = 203.3871 ANGLE = 974.0687 DIHED =
> 3309.1011
> 1-4 NB = 1091.6651 1-4 EEL = 15411.0298 VDWAALS =
> 91794.1575
> EELEC = -634414.1564 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
>
> Below is the parameter settings I have:
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> ntpr=1000,
> ntwx=1000,
>
> !MD settings
> nstlim=200000,
> dt=0.002,
>
> !Temperature Regulation
> ntt=3
> gamma_ln=5.0,
> ig=-1,
>
> !SHAKE bond length constraints.
> ntc=2,
> ntf=2,
> cut=10,
>
> !Potential function parameters
> ntb=1,
> iwrap=1,
> ioutfm=1,
> nmropt=1,
> /
> &wt
> TYPE='TEMP0',
> ISTEP1=0,
> ISTEP2=150000,
> VALUE1=10.0,
> VALUE2=300.0,
> /
> &wt TYPE='END' /
>
>
>
> Could anyone please point out to me what could be wrong with the
> simulation?
>
> Thank you very much!
>
> Best,
> Zoey
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 25 2023 - 14:30:02 PDT
