[gmx-users] genion error sol not continuous

[James Lord]

Hi Justin,
Thanks for your email. I have modified it and the topology looks fine to me
or at least I can't see any problem with it but still genion does not like
it? Would please have a look?
https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing
https://drive.google.com/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing

Thanks
James

On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/14/15 1:25 AM, James Lord wrote:
>
>> Hi all,
>> I am trying to neutralize this system (1HFX.gro) and genion is complaining
>> about solvent not being continuous,then I made the 1HFX_modified.gro in
>> which
>> I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end
>> of
>> the file. I am expecting gromacs to do the reordering for SOL. Am I
>> missing
>> anything?
>>
>
> The topology needs to be modified in a similar manner.  IIRC it is
> topological continuity that genion checks.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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