Hi everyone,
I am trying to run a qm/mm simulation using sander and Gaussian. For one
frame, I center a particular molecule, define a cutoff and run sander. Then
I choose a different molecule in the same frame, center that one and rerun
the calculation.
I was having the problem that depending on how the molecule was oriented, my
cutoff radius for Gaussian was sometimes too large for the box.
To get around that, I would like to replicate the box along the periodic
boundaries in all directions (including diagonals) before I run sander and
cutoff the region of interest. That way, I am hoping to include all the
molecules I am interested in while still maintaining the cutoff distance.
My question is: Is there an easy way to replicate the box in all directions
including diagonals and output an inpcrd file as well as a new prmtop file
(I assume I will need a new prmtop file that has the replicated boxes to run
sander)?
If it helps, here is my input to sander:
Testing tutorial on website for QMMM with Gaussian
&cntrl
imin=0,nstlim = 0, !do not run a minimization or MD run
ntb=2, !constant pressure periodic boundary conditions
ntf=2,ntc=2,
cut=15.0, !8 ang classic bond cutoff
ntp=1,
ifqnt=1 !switch on QM/MM
&end
&qmmm
qmmask='.16-30',
qmcharge=0,
qm_theory='EXTERN',
qmcut=15.0,
qm_ewald = 0 !Use a real-space cutoff for QM-QM and QM-MM long range
interactions.
&end
&gau
method = 'B3LYP',
basis = '6-31G* Freq'
&end
Thanks so much!
--
Aseel Bala
PhD Candidate, Chemical Engineering
Michigan State University
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Received on Tue Oct 25 2016 - 12:00:02 PDT
