On Wednesday 05 May 2004 16:49, Martin Mielke wrote:
Hi again,
replying to myself? no :P I just want to add something on this subject: can this software (GROMACS or whatever) be used to calculate/simulate proteine torsion/flexibility?
GROMACS is a very powerful tool, but it does not do everything auomatically: very often in order to compute some parameters you have to use the options flag for each command and/or modify the index files (the files that contain parts of the system defined through atomic poition and topologies). For example, Phi/Psi angles are not computed automatically for each residue, but I have managed to compute them for a single residue setting up the index file correctly and defining planes, dihedral and vectors accordingly So, very often with GROMACS you have to work a lot in a tuning fashion in order to compute quantities you are interested in. Please browse GMX mailing list at the URL http://www.gromacs.org/search/index.php and maybe you will find something about your query: this mailing list is very active, and you wil find almost every answers to your questions. cheers LM