[gmx-users] (no subject)

[amir abbasi]

Thanks Justin,
But I want to neutralize my system in implicit solvent.
In Amber I had use Debye screening but in gromacs I don't know what should I do.


On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/11/12 6:00 AM, amir abbasi wrote:
>>
>> Hi All!
>> I want to use Implicit solvent to simulate a nucleic acid sequence.
>> How can I do it?
>> I use this command:
>> genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname
>> CL -neutral -conc 0.1
>>
>> ions.tpr file is same as umbrella sampling tutorial.
>>
>> I got this error message:
>> Fatal error:
>> Your solvent group size (2898) is not a multiple of 31
>> what should I do?
>>
>
> One does not typically add explicit ions in an implicit solvent system.
> genion fails because it appears you are trying to replace parts of your
> nucleic acid with ions.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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