Dear Users, I have done clustering of equilibrium ensemble of octa-alanine model system, and when i was trying to find the no. of hydrogen bonds for each cluster, i found different result with different versions.
Is there some bug to version 3.3 in comparison of version 3.14 or am i doing the wrong way. Please guide me. I have used the command g_hbond_mpi -f *.pdb -s *.tpr -num hbnum.xvg -hx hbhelix.xvg -r 0.35 -a 30 n-n n-n+1 n-n+2 n-n+3 n-n+4 n-n+5 n-n>6 0 0 73 180 277 1036 1856 3422 Cut-off r=0.35 a=30 v3.14 0 0 330 243 358 1382 2170 4483 Cut-off r=0.35 a=60 v3.14 1225 2373 404 0 0 0 0 4002 Cut-off r=0.35 a=30 v3.3 PS: In version 3.14 the default is r = 0.35 and a = 60 and in version 3.3 the default is r = 0.35 and a = 30 My worry is that when i did calculation with v 3.3 i got more no of n-n n-n+1 and n-n+2 hydrogen bonds, while on the same system with v 3.14 i found 0(Zero) value for n-n n-n+1 and n-n+2 (Quite Surprising with v3.3!) How come hydrogen bond between n-n is possible, when structures and everything is fine. Thanks in advance, With Regards Anil ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) ----------------------------------------- Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) ------------------------------------------------- Web:http://chemanil.googlepages.com/ -------------------------- "Education is a progressive discovery of our ignorance" - Will Durant ---------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php