[gmx-users] total charge

2013-08-28 Thread Group Gro
Hi Dear Gromacs users, I have a question about the total charge of a system. I executed pdb2gmx command which the result is quited below: "Keeping all generated dihedrals Making cmap torsions...There are 7808 dihedrals,  591 impropers, 5298 angles   7596 pairs, 2922 bonds and 0 vi

[gmx-users] (no subject)

2013-05-05 Thread Group Gro
Dear GROMACS users, I am working on protein-ligand complexes and when I run "mdrun -deffnm nvt.tpr -v" I run into this error: Fatal error: 2 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. I foun

[gmx-users] request

2013-04-16 Thread Group Gro
Dear GROMACS users, Hi. I want to study different protein-drug complexes and I follow the procedure mentioned in the http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/. I copied and pasted the positions of each drug to the end of conf.gro and did other steps. Is thi

[gmx-users] request

2013-02-25 Thread Group Gro
Dear Gromacs Users. I apologize for asking a question that has come up several times by numerous users in the previous e-mails, but I have read the answers and suggestions to those posts and I am not still able to solve the problem based on them. It is completely possible that I am just not