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 > >
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