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

[David van der Spoel]

Zhe Wu wrote:
> 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?
>
>   
Yes you can make a shifted vdw table as well. A simple way to do this is 
to select vdwtype = shift with the cutoffs of your choice and then run 1 
step of MD with the -debug 1 option. Then the tables will be printed 
into xvg files.
> 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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>>>>>           
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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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>>     


-- 
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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