[AMBER] problem with TI calculation, help!!

From: Victor Ma <victordsmagift.gmail.com>
Date: Fri, 26 Aug 2011 11:19:15 -0500

hi all

I'm working on the thermodynamic integration calculation. I'm trying to
change a CH3 group to CF3 group. I initially did this directly and the
simulation did not converge very well. So I thought changing three heavy
atoms at the same time might be too much. I decided to do it one by one.
First I'd like to change CH3 to CH2F. However I'm seeing errors like this:
vlimit exceeded for step 62685; vmax = 37.6809

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 2 63 67

These are the distances between C and H/F in the CH2F group. I did some
research and tried a few things, like optimizing the initial structure,
longer minimization, slowly raising temperature,etc. So far, none of them
worked. I'm also seeing similar problem when I'm changing phenyl to phenol
(H to OH). So I'm wondering if this is because the relative big
reorganization of charge distribution between the reference compound and new
compound and the bond distance and angles between the C-H and C-F are too
different.(?)

This error occurs typically at the middle step, when changing H to F using
soft core potential. In addition, in the amber tutorial, the minimization
for this step uses SHAKE (ntf=2, ntc=2). However it never went through in my
calculation. THe program complains that you can only do steepest decent and
"softcore potentials require ntf=1 because SHAKE constraints on some bonds
might be removed". So i'm using "ntmin=2, ntf=1,ntc=1" instead. I'm not sure
if this is causing problem.

Any idea? I really appreciate it. Thanks a lot.


Victor.
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Received on Fri Aug 26 2011 - 09:30:02 PDT
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