Hi,
You may want to try the protocol/script here:
https://github.com/drroe/AmberMdPrep
-Dan
On Tue, Jun 10, 2025 at 9:29 AM Sudipti Priyadarsinee via AMBER
<amber.ambermd.org> wrote:
>
> Hi experts,
> I have given production runs in CUDA for an enzyme-inhibitor system in the
> OPC water model. However, I obtained the following error after a few steps
> due to a sudden increase in temperature or some other reason:
>
>
>
>
>
>
> *NSTEP = 7900000 TIME(PS) = 8800.000 TEMP(K) =********* PRESS =
> 0.0 Etot = ************** EKtot = ************** EPtot =
> ************** BOND = 45640928.0483 ANGLE = 401600.0594 DIHED
> = 2120.2028 UB = 0.0000 IMP = 0.0000 CMAP
> = 241.5422 1-4 NB = 0.0000 1-4 EEL = 0.0001
> VDWAALS = ************** EELEC = -83478.2065 EHBOND =
> 0.0000 RESTRAINT = 0.0000*
>
> A similar error is also observed in the TIP4P-ew water model for the same
> system.
> Enzyme-inhibitor system is ribonuclease A with a dinucleotide
> I have used ff19SB forcefield for protein and gaff2 for inhibitor.
> Below is my input file for your reference:
>
> Production
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> nstlim=10000000,
> dt=0.001
> temp0=300.00,
> ntpr=5000,
> ntwx=5000,
> cut=10.0,
> ntb=1,
> ntp=0,
> ntt=3,
> gamma_ln=2.0,
> ig=-1,
> iwrap=1
> /
>
> Please give me your suggestions on this.
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Received on Thu Jun 12 2025 - 08:30:02 PDT
