[gmx-users] shell molecular dynamics

[Mark Abraham]

On 29/12/2011 9:43 PM, michael zhenin wrote:
>
>     Hello,
>     I would like to run a simulation using the shell option.
>     I tried to restraint solvent molecules which were found within the
>     range of 5-10 angstroms from the box center. I couldn't find any
>     way to do so. I didn't find any information about this topic
>     anywhere else i.e. GROMACS manual, online tutorials etc.
>

There are some threads in the mailing list archives. You need to make 
two different moleculetypes, one which is position restrained, and one 
that isn't. Then you need to identify the ones you want to restrain, 
e.g. with an index group made by g_select. Then you'll need to do some 
cut-and-paste to get the block of restrained solvent contiguous.

Mark
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