AMBER Archive (2007)

Subject: RE: AMBER: QMMM with printcharges

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 17 2007 - 16:37:27 CDT

Dear Kijeong,
 
Further investigation of this problem has uncovered that this is actually a
bug in the sander QM/MM code. Essentially the mulliken charges that are
printed are 1 step out of sequence with the energies that are printed. So
when nstep=10 the energies are printed for step 10 but the mullikent charges
that are printed immediately afterwards are actually for nstep=11.
 
I attach a bugfix that should address this problem. Can you please try it
out. Take a clean copy of amber9 and apply bugfix.all from the amber website
(http://amber.scripps.edu/bugfixes/9.0/bugfix.all). Then copy the attached
bugfix.35 to $AMBERHOME and run "patch -p0 <bugfix.35. This should patch
without errors. Then build yourself a fresh copy of amber and run the test
cases to make sure they are okay and then try it on your system and see if
it works. If this all works okay then I'll post it on the Amber website as a
formal bugfix.
 
All the best
Ross
 

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

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  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Kijeong Kwac
Sent: Friday, April 13, 2007 17:38
To: amber_at_scripps.edu
Subject: AMBER: QMMM with printcharges

Hello,

I would like to ask you how to get the Mulliken charge values for the atoms
in the QM region of QMMM run.

When I run QMMM run with sander, I set printcharges=1 to get the Mulliken
charge information as follows:

 

 &cntrl
  imin = 0, irest = 1, ntx = 5,
  nstlim = 200000, nsnb = 10, dt = 0.0005,
  temp0 = 300.0,
  ntt = 1, ntb = 1, ntp = 0,
  ntf = 2, ntc = 2, cut = 9.0, scee = 1.2,
  ntwx = 10, ntpr = 10, iwrap = 1,
  ifqnt = 1,
 /
 &qmmm
  qmmask = ':1-3',
  qmcut = 9.0,
  qmtheory = 2,
  peptide_corr = 1,
  qmcharge = 0,
  printcharges = 1,
  qmshake = 0,

 

In the output file, the charge values was written every 10 steps. but at the
last step (200000th step), no charge information is written. How can I get
the Mulliken charges for the atoms in the QM region for the final step?

Thank you in advance.

        
        
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  • application/octet-stream attachment: bugfix.35

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