Hi, Thank you for the response. Being that Fortran is much more my language of choice than C, I was wondering if someone could point me in the right direction as far as modifying the C code to do what I want. It is my understanding that an mdrun begins by making a neighbor list, computing the forces, globally summing the forces, and then updating the positions and velocities. So I am assuming that, just after globally summing the forces, I can run an if statement over all of the solvent molecules testing whether their z-coordinate is within certain bounds, and if so, simply add Fsum = Fsum + Fext. My question is, where do I do this? Do I have to do it in multiple files? Where are those files stored in Gromacs? Is it the mdrun.h and force.h files that I need to modify? Sorry if this should be obvious, but again, my C skills are not the best.
Thank you, Mike On 29 Nov 2006, Mark Abraham wrote: > toma0052 wrote: > > 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? > > I presume you've read the relevant manual sections. If there's nothing > useful there, the only way to do something like this would be to get > inside the C code, loop over all solvent molecules after do_force to > check for their position, and then adjust the force on them accordingly. > > Mark > _______________________________________________ > 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 > _______________________________________________ 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