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. -- View this message in context: http://gromacs.5086.n6.nabble.com/DNA-simulations-tp4998988p4999134.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
