Thanks PB, You are right to ensure invisibility also force-field parameters must be 0.0. I think that I can do it replacing the type of those atoms that I want to make invisible for a dummy one (e.g. IW type for Gromacs force-field is defined as a dummy particle with all the parameters in 0.0). The idea behind this is to get rid of LINCS warnings that are so common when you are trying to perform a docking experiment with Gromacs. If you have to setup your ligand near the active site that you are exploring using some molecular modelling tool, it's very common to get LINCS warnings for residues clashing with your ligand. Some experts in the field have suggested that one alternative is grow the ligand near the active site. It means, start with an small portion of the ligand, run energy minimization followed by position restraint, and then add some another part to your ligand and repeat those steps until you have all the ligand builded near the active site. After that, you will be able to run your MD step without LINCS problems. One method to do this is to build those fragments and after each cycle (EM+PR) replace the old fragment of your ligand by the new one. But this is a very time consuming task and still requires manual work. So, one alternative that I'm trying to test with this "invisibility" feature, is start with the whole ligand but making visible just few more atoms after each (EM+PR) cycle. The advantage of this, is that it could be easily automated, because you just need to touch topology text files. So,let's see if I can reach to some interesting result.
Any suggestion, will be appreciated :) Regards, César.- > I was wondering whether one can have atom types with zero charge, zero > vdw (C6=0, C12=0; Or sigma=0; epsilon=0), but with mass. Won't they be > invisible in the energy/force calculations (if they are not connected > by any bonded interaction)? > pb. On Jun 21, 2006, at 9:57 AM, Cesar Araujo wrote: > Cesar Araujo wrote: >> Hi, >> >> Could anybody tell me how to modify an ITP file to ignore certain >> atoms (as > if >> they were not there) during simulations? I've changed charge and >> masses to > 0.0 >> but I've got a lot of warnings during grompp preprocessing telling me >> that >> those atoms has zero mass and the program stops after certain numbers >> of >> warnings. > >>> Well you've still got bonded and LJ interactions acting to create >>> forces >>> on particles with zero mass so it is no great surprise that things >>> are >>> breaking. Probably what you want to do is go back to square one and >>> make >>> topologies that don't have these atoms, but you haven't described >>> your >>> chemistry, so we can't help you there. > > Mark > > > Well, my idea is to "delete" atoms and then "undelete" them without > touching > coordinates file. I guess that it could be done just touching topology > files. > Is it correct??? The results I'm looking for is to turn invisible some > atoms. > > Any suggestion??? > > Thanks in advance, > > César.- _______________________________________________ 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
