[gmx-users] Martini force field: elastic network

2011-10-14 Thread Li, Hualin
Dear all, I am using martini force field to generate elastic network for my protein. I generate a list of distance between all beads within a certain distance by: genrestr -f ***.gro -n index.ndx -constr -o constraints getting the constraints.itp file and will continue

Re: [gmx-users] Martini force field: elastic network

2011-10-14 Thread XAvier Periole
The website has been updated to fit a CG tutorial starting monday in Lausanne. The manner of the construction you describe in your email is not the proper way to do it! The new script is doing it properly. If you want the old script to only generate the elastic network (as it seems

RE: [gmx-users] Martini force field: elastic network

2011-10-14 Thread Li, Hualin
Of XAvier Periole [x.peri...@rug.nl] Sent: Friday, October 14, 2011 11:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Martini force field: elastic network The website has been updated to fit a CG tutorial starting monday in Lausanne. The manner of the construction you

Re: RE: [gmx-users] Martini force field: elastic network

2011-10-14 Thread Tsjerk Wassenaar
Subject: Re: [gmx-users] Martini force field: elastic network The website has been updated to fit a CG tutorial starting monday in Lausanne. The manner of the c... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

RE: RE: [gmx-users] Martini force field: elastic network

2011-10-14 Thread Li, Hualin
for GROMACS users Subject: Re: RE: [gmx-users] Martini force field: elastic network Hi Hualin, The elastic network should work; the help should be updated... Note that only the 'elnedyn' method has really been tested. Cheers, Tsjerk On Oct 14, 2011 7:11 PM, Li, Hualin hualin