[gmx-users] Non-integer charges when using scaled-topology files for REST2 simulation.

[David van der Spoel]

On 2014-10-07 11:34, Scott Dean wrote:
> I recently asked a similar question in a different forum and was led to
> this paper: Heyes, D. M. (1981). Electrostatic potentials and fields in
> infinite point charge lattices. *The Journal of Chemical Physics*, *74*(3),
> 1924-1929.
>
> But I'm afraid I didn't finish reading/understanding it. Maybe now I will.
>
> Scott
>
Using a compensating background charge is non-physical and can lead to 
artifacts. I personally would suggest to reject papers using it.
>
>
> On Tue, Oct 7, 2014 at 5:10 AM, Abhi Acharya <abhi117acharya at gmail.com>
> wrote:
>
>> Hello,
>>
>> Thank you for replying.
>>
>> I have also come across a note on this issue in the following link:
>>
>>
>> https://github.com/GiovanniBussi/plumed2/blob/v2.0-hrex/user-doc/tutorials/hrex.txt
>>
>> It says that Gromacs takes care of this by adding a compensating
>> background, though I am not sure how exactly is this compensation achieved.
>> Any ideas?
>>
>> Regards,
>> Abhishek
>>
>>
>> On Tue, Oct 7, 2014 at 1:40 PM, Scott Dean <scottnathandean at gmail.com>
>> wrote:
>>
>>> Hey Abhi,
>>>
>>> I've gotten REST2 simulations working well in gromacs. So far, only the
>>> -maxwarn flag has been needed... Not that ignoring the issue is the best
>>> way of doing things, but the trajectories appear to be correct and
>>> replicating the TrpCage example from the Wang et al., 2011 paper has been
>>> possible.
>>>
>>> Scott
>>>
>>
>>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se