Hey :) There's a suggested trjconv workflow at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Cheers, T. On Thu, Mar 15, 2012 at 11:41 AM, R.Perez Garcia <[email protected]> wrote: > Dear Tsjerk, > Thank you for your answer! > I dont like trouble, so, Ii will leave comm_grps = System... > But, could you spare some comments how to center it afterwards? I dont know > why but the fullerene like to spend a lot of time in the boundary (i.e. > divided in two, where it is difficult to see). > Best regards: R > > > On 15-03-12, Tsjerk Wassenaar <[email protected]> wrote: > > 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 > <[email protected]> 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 [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 > > > > -- > 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 [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 > > > -- > 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 -- 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 [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
