Re: [AMBER] SHAKE error help

From: <tsurma.umich.edu>
Date: Sat, 03 Sep 2011 12:22:39 -0400

Hi dac,

Thanks for helping. Atoms 5 and 6 are the second C and N (of the second
cyanide ion). I have tried ntc=ntf=2, it works perfect. But I need to
freeze the CN bond as I am calculating the force of the solvent on the
frozen solute configuration, so I need ntc=ntf=3. I have minimized the
system and equilibrated with ntc=ntf=2 for a long time and have checked the
energies as well. But, then I changed it to ntc=ntf=3 and at step=0, it
gave me the error. I checked the restrt and mdcrd files using vmd, they
look fine.

I tried to increase the number of water molecules to ~999 and it still
failed.

Also, shake works fine (ntc=ntf=3) with just one K+CN-.

Could you suggest a remedy ?

--
~Surma Talapatra
Graduate Student
Geva Group
University of Michigan
On Sat, 3 Sep 2011 08:50:13 -0400, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Sep 02, 2011, tsurma.umich.edu wrote:
>> 
>> I am running a simple MD equilibration with CN- and K+ ions in ~500 H2O.
>> When I have 1 CN-K+ in the system, it works perfectly. But, the moment I
>> have 2K+CN- in H2O the SHAKE (ntc=3, ntf=3) is giving me this error:
>> 
>> 
>>  Coordinate resetting (SHAKE) cannot be accomplished,
>>      deviation is too large
>>      NITER, NIT, LL, I and J are :    0    0 2966    5    6
> 
> This means that atoms 5 and 6 are the ones where shake fails.  Finding
out
> what those are (C and N?) might help.  Make sure you have done some
> minimization on the system; visualize where the K+ and CN- ions are; try
> a short run with ntc=ntf=2.  (Do you have any real need for ntc=3?)
> 
> ...dac
> 
> 
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Received on Sat Sep 03 2011 - 09:30:03 PDT