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

[David van der Spoel]

On 2014-10-08 07:00, Abhi Acharya wrote:
> 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.
You will not be able to tell whether "it works" since the concept is 
fundamentally flawed. However, using REST all your replica's but one are 
non-physical anyway, so if the non-zero charge (NOTE: integer charges 
not equal to zero lead to artifacts too) does not occur on the physical 
node you may be ok.

> 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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-- 
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