how exactly are you getting the amber energies? note that the energies in
the mdout files do not correspond to structures in the trajectory file. if
you want Amber energies, it might be best to read the snapshots into sander
using imin=5.
On Mon, Aug 29, 2022 at 8:28 AM Ruihan Zhou via AMBER <amber.ambermd.org>
wrote:
> Dear Amber Users,
>
> I'm working on converting amber force fields to another MD engine LAMMPS.
> During the conversion I've noticed a bond energy discrepancy between the
> results from amber simulations and cpptraj results when using GAFF and I
> want to know why this happens.
>
> Take dialanine as an example, we've run amber simulations without periodic
> boundary conditions under NVE with a cutoff effectively covering the whole
> molecule using FF14SB, FF19SB and GAFF. With cpptraj on the same molecule,
> we take in the initial configuration and output the energy.
>
> With FF14SB, FF19SB, all molecular energies have matched, but for GAFF the
> bond energy was different. This observation holds true for some other
> molecules we've tested like n-methylacetamide and trialanine. (As a side
> note, the bond energies from cpptraj matched all the LAMMPS test we've
> ran.)
>
> The bond energy comparisons for ala2 are listed here:
> ff14sb 0.7569 cpptraj 0.7569
> ff19sb 0.7846 cpptraj 0.7846
> gaff 2.2579 cpptraj 2.8260
>
> For ala3:
> ff14sb 0.7572 cpptraj 0.7572
> ff19sb 0.7723 cpptraj 0.7723
> gaff 3.2580 cpptraj 3.8895
>
> The NVE.in script I've used is like this:
> Production NVE
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> nstlim=1,
> dt=0.001,
> ntf=2,
> ntc=2,
> ntpr=10,
> ntwx=10,
> cut=999.0,
> ntb=0,
> ntp=0,
> ntt=0,
> ig=-1,
> tol = 0.0000001,
> nscm=0,
> /
>
> Here's the cpptraj log:
> # Args: -p ala2_gaff.prmtop -c ala2_gaff.rst7
> # Loaded topologies:
> # ala2_gaff.prmtop
> energy system out sys.agr
> run
> quit
>
> In the attachment I have the prmtop and rst7 files for ala2 of all the
> force fields tested. All info files are from amber simulation and all agr
> files are energy outputs from cpptraj.
>
> I would appreciate any help on this issue! Thanks in advance!
>
>
> Best,
> Ruihan
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Received on Mon Aug 29 2022 - 06:30:03 PDT
