Hey :) Why would you want to keep it constant? It's asking for trouble. The fluctuations in a small part of the system like a fullerene molecule can be pretty large. If you try to correct the VCM of that bit only, you make it constantly bump into your solvent molecules. Especially if you have nstcomm = 10 or so, the shift may be considerable, and you may cause overlaps and crash your system. And that while it's so easy to center on the fullerene afterwards!
Cheers, Tsjerk On Thu, Mar 15, 2012 at 11:16 AM, R.Perez Garcia <r.perez.gar...@student.rug.nl> wrote: > Dear all, > I am running a simulation in of a fullerene in different solvents. I would > like to keep the fullerene somehow centred in the box, so I changed co > comm_grps = System to mm_grps = FUL. > If I do this the following error pop up: > > There are: 395 Other residues > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > > NOTE 1 [file short1.mdp]: > 4728 atoms are not part of any of the VCM groups > > WARNING 1 [file short1.mdp]: > Some atoms are not part of any center of mass motion removal group. > This may lead to artifacts. > In most cases one should use one group for the whole system. > > I am not sure if it is possible to tackle this.... > Any suggestion would be welcomed. > Best regards: R > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
