[gmx-users] center the system on specific atoms type
r.perez.garcia at student.rug.nl
Thu Mar 15 11:41:09 CET 2012
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 <tsjerkw at gmail.com> 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!
> On Thu, Mar 15, 2012 at 11:16 AM, R.Perez Garcia
> <r.perez.garcia at 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
> > --
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> 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
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