Re: [gmx-users] Fw: The results of your email commands
On 1/01/2012 9:38 PM, banafsheh mehrazma wrote: Hi everyone, I am studying a paper about a DNA simulation using Gromacs and I encountered this in ion addition step: Na+ were added by replacing a solvent molecule at ca. 6 Å from the phosphorus in the direction of the bisector of the angle ?O1P-P-O2P (O1P and O2P being the phosphate nonbridging oxygen atoms) I think what it means is that Na+ was added in a distance of 6 Å from the phosphorus. How can we specify this in GROMACS? You'll need to find one manually. Set up some index groups and use them with g_dist to measure distances. Or whatever else floats your boat. Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fw: The results of your email commands
Hi everyone, I am studying a paper about a DNA simulation using Gromacs and I encountered this in ion addition step: Na+ were added by replacing a solvent molecule at ca. 6 Å from the phosphorus in the direction of the bisector of the angle ∠O1P-P-O2P (O1P and O2P being the phosphate nonbridging oxygen atoms) I think what it means is that Na+ was added in a distance of 6 Å from the phosphorus. How can we specify this in GROMACS? there is no such option in genion tool in gromacs package. Thank you B.Mehrazma--- Begin Message --- Hi everyone, I am studying a paper about a DNA simulation using Gromacs and I encountered this in ion addition step: Na+ were added by replacing a solvent molecule at ca. 6 Å from the phosphorus in the direction of the bisector of the angle ∠O1P-P-O2P (O1P and O2P being the phosphate nonbridging oxygen atoms) I think what it means is that Na+ was added in a distance of 6 Å from the phosphorus. How can we specify this in GROMACS? there is no such option in genion tool in gromacs package. Thank you B.Mehrazma--- End Message --- -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists