Hallo, I have several (12) simulations running in which I simulate a protein in a water box (cubic 9x9x9). For all simulations I can see the following: After a few simulations (total time of 7.6ns) the protein moves out of the water box - for all the twelve simulations. Since the following simulation is started with the output .gro file of the prior simulation the protein moves further and further out of the box. I have no idea if this is a problem because of periodic boundaries or if this is a problem with my vmd installation. Can anyone give me a hint what I could to to fix this and not have to restart all the runs?
I am using a script I used before and I am doing everything like last time but last time I did not see this behavior of the protein. I am using vmd to look at the protein and its trajectory (commands see below) FYI the commands I use to setup the simulations (just an example of two): grompp -f md2.mdp -c Protein-struct_md1.gro -p Protein.top -o Protein_md2.tpr mdrun -nt 3 -s Protein_md2.tpr -o Protein_md2.trr -x Protein_md2.xtc -c Protein-struct_md2.gro -g Protein_md2.log grompp -f md3.mdp -c Protein-struct_md2.gro -p Protein.top -o Protein_md3.tpr mdrun -nt 3 -s Protein_md3.tpr -o Protein_md3.trr -x Protein_md3.xtc -c Protein-struct_md3.gro -g Protein_md3.log and so on and so forth. GROMACS version is 4.5.5 VMD version is 1.9.1. Thanks in advance Marc Hoemberger -- 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
