回复： 回复： [gmx-users] Re Can GROMACs use multiple van der Waals potentials and multiple van der Waals potential cutoffs?

[hong bingbing]

Ohhh! I have not thought of energy groups. Thanks a lot.

 





________________________________
发件人： Roland Schulz <roland at utk.edu>
收件人： Discussion list for GROMACS users <gmx-users at gromacs.org>
发送日期： 2010/3/31 (周三) 6:27:21 下午
主   题： Re: 回复： [gmx-users] Re Can GROMACs use multiple van der Waals potentials and multiple van der Waals potential cutoffs?

Well you must not have looked very careful:

energygrp_table:

When user tables are used for electrostatics and/or VdW, here one can give pairs of energy groups for which seperate user tables should be used. The two energy groups will be appended to the table file name, in order of their definition in energygrps, seperated by underscores. For example, if energygrps = Na Cl Sol and energygrp_table = Na Na Na Cl, mdrun will read table_Na_Na.xvg and table_Na_Cl.xvg in addition to the normal table.xvg which will be used for all other energy group pairs.

On Wed, Mar 31, 2010 at 5:31 PM, hong bingbing <cynthiahong1983 at yahoo.com.cn> wrote:

>
>Thanks. But I've read the manual. It seems not solving it. The two potentials in my system are of totally different function forms. They do not just differ in the parameters. What troubles me is GROMACS seems not to be able to support two function forms simultaneously for van der Waals interactions. 
>>
> 
>
>On 2010-03-31 21.53, hong bingbing wrote:
>>
>> Thanks, David.
>>
>> Let me simplify my system. It includes A and B molecules. The van der
>> Waals interaction between A's is, e.g. U1(r) = -1/r cutted off at r =
>> r_A ; and for B: U2(r) = -1/r^2, cut off at r = r_B.
>>
>>
>> I don't know how to handle with two potentials and
> two cutoffs
>> simultaneously.
>>
>Read manual and online instructions about tabulated potentials in 
>gromacs. You have to specify files for each interaction pair, that is 
>AA, AB, BB, then simulate with cutoff max(r_A,r_B). Make sure the 
>>
>potentials are continuous and smooth to at least the cutoff.
>
>>
>>
>>
>>
>> -----------------------------------
>>
>> Dear all,
>>
>> I'm trying to simulate multiple phases in one system. Each phase has
>>
>> distinct van der Waals potential form and different
>> cutoffs from the rest. Unfortunately, I found only one van der Waals
>> potential and one cutoff can be defined in .mdp file of one run. Did I
>> miss some features of GROMACS? Have you encountered this problem before
>>
>> and could you lend a help?
>>
>> Thank you
>> Cynthia
>>
>>
>>
>
>
>-- 
>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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