Hi Case,
I have attached the mdin file, coordinate file and prmtop file. Also, I
have attached extra_pts.f code which I extended to account for the two
extra points in CN- ion.
The sander that I compiled with this code works fine, as I have been able
to reproduce a result from a paper. Also, in the mdin file the ntc=2,ntf=2
works fine, its only when I change it to ntc=ntf=3 it gives me the shake
error.
I have tried using gaussian charges with CN- (using the original sander),
but it gives me same errors.
Thanks for looking into it.
~Surma
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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- text/plain charset=us-ascii attachment: cn.mdin
- text/plain charset=us-ascii attachment: cn.prmtop
- text/plain charset=us-ascii attachment: cn.restrt
Received on Sat Sep 03 2011 - 15:00:03 PDT
