[gmx-users] .XYZ file format to .gro format

Hi I have structure of a molecule in .xyz format, is there an option similar to pdb2gmx in gromacs to convert .xyz file to .gro files? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Error in NPT simulation

-nan, max 0.003869 (between atoms 33 and 76) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Segmentation fault (core dumped) Not sure, what could be the reason for error. Any thoughts ? With Regards Nagasree Garapati Research Assistant

[gmx-users] zig-zag stacking

to create zig zag stacking? Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] zig-zag stacking

genconf which can do zigzag stacking for such a big super cell. Lakshman I am not sure if I followed your suggestion, how can we translate only one molecule in a box using editconf? With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West

[gmx-users] Energy minimization of solvated MOFs.

tial Energy = -3.38556029741624e+13 Maximum force = 2.45386477264935e+25 on atom 306 Norm of force = 1.49337454338593e+24" Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26

[gmx-users] Fw: Geometry Optimization for Metal organic Frame works

(final.gro) file in OBGMX, nothing is created I have empty files for both .top and .itp files. I believe there is something wrong with the topology files, but I am not able to figure out where is the mistake. Any suggestions ? Thank You With Regards Nagasree Garapati Research Assistant Professor

[gmx-users] Geometry Optimization for Metal organic Frame works

cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028<tel:304%20293-5028>(O) 304 276-3674(M) --

[gmx-users] Dihedral restraint for entire super structure

to specify dihedral restraints so as to maintain MOF rigid. How can I restrain all the dihedrals of MOF in dihedral restrain, for a single unit cell I have about 1000 dihedrals. Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering