Hey Mark Using
[virtual_sitesn] 39 2 34 35 36 37 38 seems to be working to define virtual sites at COM of group of atoms. thanks for the answer... sikandar On Mon, Apr 25, 2011 at 12:15 AM, Mark Abraham <[email protected]>wrote: > On 4/25/2011 2:49 PM, Sikandar Mashayak wrote: > >> Hi >> >> I am not sure , even after reading the manual, about how to specify >> virtual site in topology file which is located at com of 5 atoms. If I were >> to specify it by using [ virutal_sitesn] then how to specify weights, so >> that vsite is at COM? >> > > Table 5.6 says you choose a COM vsite with function type 2. So I expect > that > > [virtual_sitesn] > 39 2 34 35 36 37 38 > > will make atom 39 a vsite formed from the COM of atoms 34-38. > > The manual is a bit deficient in this regard. Let us know how it goes, and > I'll update the manual. > > Mark > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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