Hi, Are you sure this is not a periodic visualization artefact? Did you check the distane with e.g. mindist?
Erik 25 maj 2012 kl. 16.01 skrev Matthias Ernst: > Hi, > > I have a question regarding simulation of a protein-DNA-complex where the > protein encloses the DNA double helix. I did not find a tutorial for a system > of three rather big molecules like these, that's why I ask. If there is such, > I would appreciate a hint. > > I want to start with a crystal structure from PDB. When I do the steps in J. > Lemkuls tutorial "Lysozyme in water", first thing would be an energy > minimization in vacuo. Unfortunately, doing this I end up with the two > strands of the DNA double helix being far away from the protein and seperated > from each other. Can this result from clashes and therefore high energy in > the system that allows the DNA strands to move "through" the protein or how > else can this happen? And how can I prevent this? > > I mean, usually the protocol is: > - minimize system in vacuo > - add solvent and ions > - minimize again > - add thermostat and barostat > - simulate > Obviously, I cannot follow this if the first step already does not work. When > I tried to skip in-vacuo-minimization and to minimize the system in solvent, > it ended up bei either reaching machine precision without the maximum force > being small enough or in the simulation, the atom were moving to fast. Would > it be a good idea to use position restraints for the minimizations? If yes, > for which part, in which order and in which steps? > > Thank you for your help, > Matthias > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > 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/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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/Support/Mailing_Lists
