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On 29/12/2011 9:43 PM, michael zhenin wrote:
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<div dir="ltr" align="left">Hello,</div>
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<div dir="ltr" align="left">I would like to run a simulation
using the shell option. </div>
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<div dir="ltr" align="left">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.</div>
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<br>
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.<br>
<br>
Mark<br>
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