Hi,
I realised that it was the way I was calculating the forces of the extra
points that gave me the error. I am working on fixing it, but am not yet
successful. Thanks for all the help!!
Surma Talapatra
On Sat, 3 Sep 2011 14:05:41 -0400, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Sep 03, 2011, tsurma.umich.edu wrote:
>>
>> 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-.
>
> Can you post the prmtop, coordinate and mdin files that fail? I don't
> think
> we can debug this any further without being able to reproduce the error
> here.
>
> ...thanks...dave
>
>
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Received on Mon Sep 05 2011 - 14:00:11 PDT
