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

[Abhi Acharya]

Thank you.
It seems there is little choice with respect to the non-integer charges, so
I will try and run the simulations. See if it works for my system.

Regards,
Abhishek

On Tue, Oct 7, 2014 at 3:45 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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
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