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

[Zhe Wu]

Yes, you are right! Indeed once I implement the shift scheme in the
table, the problem was solved immediately! Thank you so much for your
help!

Here, I want to include what I did just in case in future, someone has
a similar problem:

1. As David said, run a 1 step MD with -debug 1 to generate shifted
potential tables: ctab.xvg, dtab.xvg, rtab.xvg;
2. Combine these 3 tables together to become table.xvg: ctab.xvg for
electrostatic interaction, dtab.xvg for attraction, rtab.xvg for
replusion. You need to change all the sign for the derivative to be
the right table format.
3. Now if you use this table as your tabulated potential, the total
energy should be conserve in NVE.

Thanks,
Zhe

On Tue, Dec 8, 2009 at 2:32 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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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>>> 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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