Hard to say if this is correct since we don't know what "resname A" is. Also, we don't know how you manually merged the DNA.
Still, you are coming back to the list too early. View your final structure in VMD and see if the ions are in the positions that you desire. Also, make a topology and a .tpr file and run an energy minimization and then a short MD simulation. Does it crash? Chris. -- original message -- Hello Tsjerk, I followed below steps to create a box with DNA and water molecules that are close to it at some distance: 1. g_select -s Test.gro -select '"Close to A" resname SOL and within 0.5 of resname A' -on (since I need around DNA molecule, I randomly chose residue A, such that water molecules are around A) 2. trjconv -n index.ndx -f Test.gro -s Test.gro -o Testoutput.gro (Testoutput.gro - has all the water molecules that are close to the A residue at a distance of 0.5 nm) 3. I then merged manually the original file that has DNA molecule dna.gro with the Testoutput.gro. Need some advice if I proceeded in the right direction to have a box that has DNA + water molecules that are close to it. With Regards, Satya. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
