Hi Justin If I use the boundwaters.ndx to write another .ndx file using 1 & 2 & 3 & 4 and so on over all snapshots then also I should get the common water molecules in these snapshots. Am I right. Shahid
On Mon, Jan 28, 2013 at 9:03 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/28/13 10:02 AM, shahid nayeem wrote: >> >> Dear Users >> I am interested in knowing only the water molecules which remains >> bounded to the protein during MD. Using g_select I can make a >> boundwater.ndx file which gives water molecules within a specified >> distance from the protein but it gives different water molecule from >> each snapshot. Now I want onle those water which is common in all >> frames. How to proceed from here and is there any other way to do >> this. Please help. > > > You should be able to write a simple script that runs through each group, > stores the atom numbers, and then checks which ones are common to all > frames. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
