Hello, I am wondering about a response I got a while ago about indexing atoms. I am not very familiar with awk, but it seems like a fairly simple way to search through a .gro file and find the solvent molecules with a particular z-coordinate range, as I need for my simulation. My question however, concerns implementing this into an md run. I would like to add an acceleration to solvent molecules that are within a certain distance from a lipid bilayer. However, if the solvent molecules diffuse too far away during the md run, I no longer want them to have an acceleration. Therefore, it appears that at every time step I need to perform a check to see which solvent molecules are close enough to warrant an acceleration. So, is there a way that I can incorporate the awk file such that it runs and creates a particular index group at every time step? If not, is there some other way that I can check at each time step (or every several time steps) which solvent molecules have a particular z-coordinate and give them an acceleration?
Thank you, Mike Tomasini On 31 Oct 2006, Erik Marklund wrote: > You can sort the atoms according to position using grompp, but I don't > think that's the easiest solution. I would use awk or something along > those lines, to find all atoms within z=3D[4 5] nm and remove everything > except the indexes. Put a bracketed name on top of it all and viol=C3=A0,= > you > have turned them into an index group. > > /Erik > > On Tue, 2006-10-31 at 00:37 -0600, toma0052 wrote: > > Hello, > > I have a question regarding indexing atoms for use with > > non-equilibrium MD. The manual says that I can select atoms by number = > or > > type; I was wondering if there is a way in Gromacs to index atoms by > > position with the simulation box. I am looking to add an acceleration = > to > > the solvent, but not the entire solvent. Is there a way that I can spe= > cify > > solvent molecules within a certain coordinate ie. a z-position from 4nm= > to > > 5nm with the simulation box being 6nm in height? I am looking to > > accelerate solvent molecules near a lipid bilayer, but if a particular > > solvent molecule diffuses too far from the bilayer, I no longer want it= > to > > keep its fixed acceleration. Is there any way that indexing by coordin= > ates > > is possible? > >=20 > > Thank you, > > Mike Tomasini > >=20 > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the=20 > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > --=20 > Erik Marklund, PhD Student, Molecular Biopcysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > [EMAIL PROTECTED] > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the=20 > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php