Thanks Niel and Insuk !!! I will try again. Thanks again!!
Victor
On Fri, Aug 26, 2011 at 11:31 AM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
> Hi Victor,
>
> Keep looking through the mailing list archive for more things to try.
> I've had success with some of the following:
>
> - Reduce the timestep (dt)
> - Try using noshakemask on the entire solute.
> - If applicable, make sure ig is set to the same number for v0 and
> v1 (see amber11 bugfix 13)
>
> --Niel
>
> ________________________________________
> From: Victor Ma [victordsmagift.gmail.com]
> Sent: Friday, August 26, 2011 10:19 AM
> To: AMBER Mailing List
> Subject: [AMBER] problem with TI calculation, help!!
>
> 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 - 10:00:05 PDT
