[gmx-users] Two Types of van de Waals interactions in one system

[Zhe Wu]

Dear David,

Thank you so much for your reply! I did try to use nstlist = -1 and I
still cannot solve the energy drifting problem. And you can see my
problem in more detail from the following link:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047299.html

And you mentioned I should use shifted VDW. But in the way I use
tabulated potential, the option in vdwtype should be User so that I
can indicate I am using a lookup table for the tabulated potential.
(In my test case, I used the table provide by GMX 4.0.5
/share/gromacs/top/table6-12.xvg directly, and just changed its name
to be table.xvg.) So it seems to me there is no explicit way I can use
shift function. Or should I shift the function by changing the
potential in the table?

Thanks again for your help.

Zhe


On Tue, Dec 8, 2009 at 1:38 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> Zhe Wu wrote:
>>
>> I agree with that. But I don't know why, when using tabulated
>> potential, I cannot even get a box of LJ particles to have energy
>> conservation in NVE. Anyone has some idea?
>>
>
> do you use shifted VdW and nstlist = 1 or nstlist = -1?
>>
>> Zhe
>>
>> On Tue, Dec 8, 2009 at 3:52 AM, XAvier Periole <x.periole at rug.nl> wrote:
>>
>>>
>>> One solution would be to use tabulated potential for which the
>>> analytical form does not matter.
>>>
>>> On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote:
>>>
>>>
>>>>
>>>> hong bingbing wrote:
>>>>
>>>>>
>>>>> Dear all,
>>>>> Has anyone tried to use 2 van de Waals interaction types in one system?
>>>>> For example, the system includes two components A and B. The van de
>>>>> Waas
>>>>> interaction for A is LJ type, while for B Buckingham form is used. Can
>>>>> GROMACS support two forms simultaneously?
>>>>>
>>>>
>>>> No. How would you describe the vdW interaction between an atom from A
>>>> and
>>>> one from B?
>>>>
>>>> If the reason for this question is based on a desire to mix two force
>>>> fields - don't.
>>>>
>>>> Mark
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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