Re: [gmx-users] radial densities

Can't think of a current program that does this. One option is to: 1. Use g_sdf from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001786.html 1b. With the bug fix from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001791.html BUG: line 216 of 298 should h

Re: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA

Yes, I'm using Cut-off. And the Error is reproducable. I'll post the bug report. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 20

[gmx-users] trjconv for hexa-meric protein

Hi I simulate a hexa-meric protein (443*6=2658 residues with about 9 water) Especially, I'm interested in water behavior around the protein. The 1ns simulation is finished normally, but trjconv produces abnormal structure. For example, the protein go outside my waterbox, water molecules are d

[gmx-users] change number of processors after tpbconv

hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please do

Re: [gmx-users] change number of processors after tpbconv

Carsten Baldauf wrote: hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/list

Re: [gmx-users] OPLS + ffgmx

Hi Mark and Chris, Thanks a lot to both of you for going through my query, for suggesting the positive and negative points of this procedure. I will think and then decide how to go about it. I am really thankful to Chris for the detailed suggestion regarding the procedure. I will come back to

Re: [gmx-users] change number of processors after tpbconv

thank you// David van der Spoel wrote: Carsten Baldauf wrote: hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromac

[gmx-users] about gromacs

Hello, everyone: Would you please tell me that whether Gromacs can be used to do Molecular Dynamics studies for Polymer like PVC or PET? Thanks a lot. dai0601 2006-09-07 ___ gmx-users mailing listgmx-users@gromacs.org http://www.

Re: [gmx-users] Simulation problem with extended membrane system!

Hi ChrisThank you for your suggestions!These days I also tried anisotropic and semiisotropic for my simulation, but I still got the same result, so I wonder maybe there's something wrong with my initial structure, but it will take time to check it out. I'm trying to use the method you suggested, I