[gmx-users] (no subject)

[Justin A. Lemkul]

On 7/11/12 6:19 AM, amir abbasi wrote:
> 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.
>

 From my understanding, this remains an unresolved issue.

-Justin

>
> 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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>

-- 
========================================

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

========================================