[AMBER] Bond energy discrepancy between amber simulated results and cpptraj

From: Ruihan Zhou via AMBER <amber.ambermd.org>
Date: Mon, 29 Aug 2022 05:27:56 -0700

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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Aug 29 2022 - 05:30:04 PDT
Custom Search