<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi,</div><div> I am trying to use trjorder command to generate a sorted trajectory where all the water molecules are certain distance away. I can use the trjorder command to generate the sorted trajectory where all waters are sorted based on distance but I am looking for method for creating a index file which will have only those water molecules which are ,say 0.4 nm away from protein. So far, I could not find any way in trjorder which can give me an index file containing the water molecules certain distance away. -nshell option in trjorder only gives the number of water molecules within a distance but does not specify their indices.</div><div><br></div><div> Also, since the water molecules are always fluctuating, the number of water within a certain distance and
their indexing will change all the time.</div><div>So, I was wondering whether you can suggest a way where I can create an index file from the sorted trajectory so as to have only those waters which are certain distance away. I mean : is there any way in make_ndx tool , where one can do it using certain keywords. </div><div><br></div><div>Any help will be really appreciated.</div><div>Sanku</div><div style="position:fixed"></div>
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