[AMBER] QM/MM calculation Amber16/DFTB

From: Amani Eshtiwi <eshtiwia2017.gmail.com>
Date: Fri, 11 Aug 2017 00:38:48 +0000

Dear Amber developers

I am trying to simulate a reaction of an isolated small organic molecule
(15 atoms) using the explicit solvent model. I am using an octahedral water
box of 25 Angstroms. The QM region includes the 15 molecule atoms while
water molecules constitute the MM region. I used PM3 and it could
successfully simulate the reaction. Now, I am cnsidering using DFTB as the
QM theory. I minimised and heated the system. Afterwards, I ran
equilibration and conventional MD production simulation. Before starting
umbrella sampling I am trying to run an equlibration simulation with QM
treatment. I am using these input parameters;
imin=0,irest=1, ntx=7, ntb=2, cut=8, ntr=0, ntc=1, ntf=1, igb=0, ntp=1,
tempi=300, temp0=300, ntt=3, ig=-1, gamma_ln=1, nstlim=100000, dt=0.001,
ntpr,ntwx,ntwr=10, ntxo=1, ioutfm=0, ifqnt=1
diag_routine=0, writepdb=1, qmmask='.1-15', qmcharge=-1, qmshake=0,
printcharges=1, qm_theory='DFTB', qmcut=8, dftb_telec=100,

The equilibration run started, restart and out files were generated.
However, the last step appered in the out file was step 16. It seems that
the calculation halts at step 17 since the out file is no longer updated
even when I left the calculation to run overnight. No error messages
appeared and the command was running without any progress. I also tried a
dftb_telec of 0, 200, and 300 without any success.
Can you please help me with identifying the cause of this problem? Any
advice to help run the calculation successfully?
I am looking forward to hearing from you as soon as possible.

Best regards
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Received on Thu Aug 10 2017 - 18:00:03 PDT
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