<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>Thank you for your response. I am still unclear as to how the whole thing works (and the manual is no help). <br><br>If I do specify (in the .mdp file) something like constraints = all-bonds, will that override the harmonic-bond interactions specified in the .itp files? </div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thursday, 14 May, 2009
4:56:04 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Constraints specified in .mdp as well as in .top files<br></font><br>Vishwanath Dalvi wrote:<br>> 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>I believe so. This is also true of restraints (which are a different concept in GROMACS).<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a
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