[gmx-users] PME on a non-neutral system

[Albert Solernou]

Hi all,
thanks for your prompt replies. Given the fact that artifacts could 
appear, I double checked my results using
   coulombtype = Cut-Off
instead of PME. After adjusting the cut-off distances for the 
electrostatics and van der Waals terms, I obtained really close results. 
Great stuff, given the speed-up that you get when using PME.

Cheers,
Albert


On 10/21/2015 07:36 PM, Smith, Micholas D. wrote:
> Thank you for correcting me Justin. I hadn't seen the old comment about the background plasma. And I should emphize, that I said it may not "nescessarily" result in problems, Justin is absolutely correct that if the system has even mild inhomogenties, artifacts will be produced.
>
> -Micholas
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: Wednesday, October 21, 2015 1:08 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] PME on a non-neutral system
>
> On 10/21/15 12:14 PM, Smith, Micholas D. wrote:
>> Albert,
>>
>> Gromacs won't automatically neutralize the system (as far as I know). If I recall being non-neutral doesn't necessarily result in problems, but may instead slow your run-time. I am sure someone will correct me if I am wrong.
>>
> Old posts suggest that GROMACS does in fact apply a neutralizing background plasma:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-April/020821.html
>
> I suspect this is still the case.
>
> Non-neutral systems can be problematic if they are inhomogeneous, e.g. a bilayer
> or something similar.  You can get big artifacts in those cases.
>
> -Justin
>
>> -Micholas
>>
>> ===================
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Albert Solernou <a.solernou at leeds.ac.uk>
>> Sent: Wednesday, October 21, 2015 11:14 AM
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: [gmx-users] PME on a non-neutral system
>>
>> Hi all,
>> I accidentally rerun a trajectory that is not neutral, but that has a
>> net charge of +2e. However, the system did not explode and the forces
>> were not infinite, although I used PME. Is Gromacs neutralising the
>> system automatically?
>>
>> Thanks,
>> Albert
>>
>>
>> --
>> ---------------------------------
>>      Dr Albert Solernou
>>      EPSRC Research Fellow,
>>      Department of Physics and Astronomy,
>>      University of Leeds
>>      Tel: +44 (0)1133 431451
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>

-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451