Hello,
I'm simulating a QM/MM ligand rearrangement using the PNEB method in Amber
and am following the tutorial for this (
http://ambermd.org/tutorials/advanced/tutorial5_amber11/index.htm)closely.
My reaction system (~40 atoms) is treated with QM and my solvent is treated
with MM. I am getting a vlimit exceeded for step X almost every step
during the 2EQUIL stage. My gut feeling is something is wrong, but I'm not
sure what. I just wanted to check to see if perhaps this is fine. Here's
an example of the error:
-----------------------------------------------------------------------------------------------------------
*vlimit exceeded for step 233; vmax = 63.4667*
NSTEP = 234 TIME(PS) = 0.234 TEMP(K) = 298.43 PRESS =
0.0
Etot = -18325.1819 EKtot = 6314.9018 EPtot =
-24640.0837
BOND = 3682.7728 ANGLE = 651.9584 DIHED =
0.0000
1-4 NB = -17.5382 1-4 EEL = -7836.6209 VDWAALS =
2422.9934
EELEC = -23715.0863 EHBOND = 0.0000 RESTRAINT =
0.0000
PM6ESCF= 171.4372
NEB replicate breakdown:
Energy for replicate 1 = -31593.4728
Energy for replicate 2 = -24525.5529
Energy for replicate 3 = -24640.0837
Energy for replicate 4 = -24544.4482
Energy for replicate 5 = -24825.3203
Energy for replicate 6 = -24817.7617
Energy for replicate 7 = -24587.4927
Energy for replicate 8 = -24582.3421
Energy for replicate 9 = -24753.0370
Energy for replicate 10 = -24611.4301
Energy for replicate 11 = -24592.6793
Energy for replicate 12 = -24665.0988
Energy for replicate 13 = -24585.0417
Energy for replicate 14 = -24562.9814
Energy for replicate 15 = -24539.6053
Energy for replicate 16 = -24617.7770
Energy for replicate 17 = -24654.5143
Energy for replicate 18 = -24599.0472
Energy for replicate 19 = -24581.8019
Energy for replicate 20 = -24723.1166
Energy for replicate 21 = -24554.8562
Energy for replicate 22 = -24498.3815
Energy for replicate 23 = -24602.4552
Energy for replicate 24 = -31671.1194
Total Energy of replicates = -604929.4173
Ewald error estimate: 0.1569E-01
----------------------------------------------------------------
And here is my input for this step:
NEB initial with small K
&cntrl
ig = -1,
imin = 0,
ntb = 1,
cut = 10.0,
ntc = 1, ntf=1,
tol=1.0E-6,
temp0 = 300.0,
ntt = 3,
gamma_ln = 100.0,
ntp = 0,
ntr =0,
restraint_wt = 1,
restraintmask = ':1',
nstlim = 100000, dt = 0.001,
irest = 0, ntx = 5,
iwrap=1,
ntpr = 1, ntwx = 1, ntwr = 5000,
tgtfitmask=':1',
tgtrmsmask='.34-36',
ineb = 1,skmin = 25,skmax = 25,
nmropt = 0,
ifqnt = 1,
/
&qmmm
qmmask=':1',
qm_ewald = 1,
qm_pme = 1,
qm_theory = 'PM6-D',
qmcharge = 0,
qmshake = 0,
/
&wt type='END'
/
----------------------------------------------
A few notes:
- I used a smaller gamma_ln since I am using explicit solvent. This
should be fine as per the main Amber paper on this method.
- I am using an skmin and skmax of 25 kcal/mol, this is smaller than in
the tutorial (50 kcal/mol) but I would like to be gentler here. I also
tried this with skmin/max = 50 kcal/mol and was also getting a vlimit
exceeded error.
- I am fitting based off of all 40ish atoms in my QM region, but am only
using the RMSD from the ligand atoms (34-36). Could this be causing the
issue? I think this is preferred rather than calculating the RMSD for all
QM atoms.
- The previous heating step worked fine.
- I visualized the trajectory from one of these equilibrations in VMD
and nothing looked obviously wrong.
- The vmax is consistently around 50-60, making me think maybe this is
something with the added forces from NEB?
Any thoughts?
Thanks,
Anthony Bogetti
Graduate Student: University of Pittsburgh
Dr. Lillian Chong's Lab
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Received on Wed Sep 11 2019 - 08:30:03 PDT
