[gmx-users] shell molecular dynamics

[David van der Spoel]

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