[gmx-users] shell molecular dynamics

[David van der Spoel]

Shuangxing Dai wrote:
> Thank you for help. The harmonic potential between core and shell is 
> attractive. The charges they have are opposite, this means that there 
> will only be attractive force between them. My result also show that 
> they nearly overlap. Is this reasonable and shell model correctly used? 
> If not, where is the problem.
This is fine. The shell interacts with other molecules. In the SW paper 
we have computed the distribution of dipole moments in the liquid phase, 
and the average dipole is 2.7 D, compared to 1.85 in the gas phase. 
Hence the shell particle moves sufficiently far away from the core to 
get effective polarization.

> Shuangxing Dai
> ----- Original Message ----- From: "David van der Spoel" 
> <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: 13 April, 2009 11:15 AM
> Subject: Re: [gmx-users] shell molecular dynamics
> 
> 
>> Shuangxing Dai wrote:
>>> Hi, all,
>>>   I am doing shell molecular dynamics and I have read the sw.itp. Now 
>>> my question is:
>>> 1. For the shell "atom", what element should be used in .pdb file, 
>>> since the 77-78th digits of pdb file is element symbol ?
>>
>> Anything you like. Gromacs does not use this information anyway.
>>
>>> 2. What does the 1 in [ polarization ] part mean in sw.itp?
>> Function type, see manual ch. 5.
>>
>>> 3. Is it reasonable to set initial position of shell arbitrally and 
>>> let energy minimization to find the optimum position for shell?
>> At first step the shell will be put in the place of the virtual site 
>> and will be minimized from there.
>>
>>> I also do not understand [ exclusion ] part:
>>> ; iatom excluded from interaction with i
>>> 1 2 3 4 5
>>> 2 1 3 4 5
>>> 3 1 2 4 5
>>> 4 1 2 3 5
>>> 5 1 2 3 4
>>> For the first line, does that mean that the interaction of 2, 3, 4 
>>> and 5 with 1 is excluded? If so, this table will exclude all the 
>>> interactions. Is it right?
>> Yes. You need at least two molecules to do anything useful.
>>
>>> Thank you in advance.
>>> Shuangxing Dai
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
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>>
>>
>> -- 
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se