<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!<br><br>I have a question about a possible redundancy/conflict in specifying bond-constraints.<br><br>I have in my simulation (among other things) a number of bonds - some of which are harmonic while some are rigid (or constrained).<br><br>I specify the bonds in the .itp (or ultimately in the .top) files as follows:<br><br>[ bonds ]<br>; index1 index2 func deq(nm) k(kJ/mol/nm2)<br> 1 2 1 0.1529000000 224262.4000000000<br> 1
32 1 0.1810000000 185769.6000000000<br> 2 3 1 0.1529000000 224262.4000000000<br> 3 4 1 0.1529000000 224262.4000000000<br>[ constraints ]<br>; index1 index2 funct length(nm)<br> 1 30 1 0.1090000000<br> 1 31
1 0.1090000000<br> 2 28 1 0.1090000000<br> 2 29 1 0.1090000000<br><br>However, it turns out that the .mdp file also requires one to specify constraints in the form of:<br>constraints = all-bonds/h-bonds etc<br><br>Do we have to specify constraints in the .mdp file if we already have specified them in the .itp file?<br><br>Thanks!<br><br>Ashwin<br></div></div><br>
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