[gmx-users] charges

[David van der Spoel]

On 2012-04-02 20:40, R.Perez Garcia wrote:
> Dear prof. van der Spoel,
> I know.. Dr. Alex de Vries is supervising me for my colloquium.
> Unfortunately (for me), they are very busy and (mainly) I am doing four
> months stage at Perugia universityv (It) which means I can not
> personally ask...so I prefer to ask the list.
> Thank you for your answer, even if the literature concerning virtual
> charges is not a lot, I will keep looking.
> Best regards: R
>
It's in the manual.
[ virtual_sites2 ]
; k i j type constant
3  1 2 1  0.5

will give you a virtual site 3 half-way atoms 1 & 2.


> On 02-04-12, *David van der Spoel * <spoel at xray.bmc.uu.se> wrote:
>> On 2012-04-02 20:29, R.Perez Garcia wrote:
>> >Dear GROMACS users,
>> >I would like to place the charge more localized in the "bonds region"
>> >and not exactly in the atoms.
>> >Please let me know if you know there is a way to do this in GROMACS.
>> >Thank you in advance, R
>> >
>> >
>> Yes, using virtual sites.
>> There's an expert group of gromacs users at the department of
>> biophysical chemistry at your university, Marrink. You may want to
>> talk to then.
>>
>> --
>> 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