Re: [gmx-users] boundwaters

2013-01-28 Thread Justin Lemkul
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

Re: [gmx-users] boundwaters

2013-01-28 Thread shahid nayeem
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 jalem...@vt.edu wrote: On 1/28/13 10:02 AM,

Re: [gmx-users] boundwaters

2013-01-28 Thread Justin Lemkul
On 1/28/13 10:53 AM, shahid nayeem wrote: 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. Presumably. Probably faster to try it and see rather