Hello, I have searched thoroughly the manual and the gmx list, yet with no avail. I'm trying to understand how I will be able to implement to gromacs my system which is complicated as far as the non bonded interactions are concerned.
My system comprises three different types of atoms. The LJ interactions (non bonded) among them are divided in two different categories : local and non local. The local ones are the interactions of atoms 3 and 4 bonds away and the non local for every combination of atoms more than 4 bonds away. 1st question: nrescl is equal to 4? 2nd question: in my itp file for the intramolecular 1-4 interactions I have created the [ pairs ] tab in which I give the 1-4(3bonds apart) and 1-5(4bonds apart) atoms with their corresponding c6=4*σ^6 and c12=4*σ^12 as follows: [ pairs ] ; ai aj funct c6 c12 atom1 atom4 1 atom1 atom5 1 Am I correct? 3rd question: Which is the difference between the S(hort)R(ange) LJ and LJ 1-4? For me the short range interactions are the 1-4LJ, yet it seems that this is not the case. 4th question: I want after 1,45*σ till 2,33*σ to use the cubic spline in such a way that the LJ potential will go smoothly to zero at 2,33σ. If I use the biggest σ I have, then in the mdp file rvdw-switch=5.56 and rvdw=8.9. Between these two values does the cubic spline work as a switch function using vdw-type = Switch ? 5th question: Given the above if I use vdw-type =Cut-off and rvdw=8.9 then gromacs will use cubic spline till the LJ will reach zero for a value greater than 8.9, yet to me uknown? If this is not the case how LJ goes to zero with this option? 6th question: If I want to use a quintic spline between 1,45*σ till 2,33*σ(cut-off value) for the different combination of atoms(they have different ε and σ), then should I use a tabulated potential? And if I do that which will be the meaning of cutoffs in the mdp file as I would like them to be different for each of the different types of atoms I have? Can I use different cut-offs for the different types of atoms I have? Forgive me for the long list of questions, yet with what I have to my disposal (mailing list, manual) it was impossible for me to find a solution. Yours Sincerely, Nikos Jetzt Mails schnell in einem Vorschaufenster überfliegen. Dies und viel mehr bietet das neue Yahoo! Mail - www.yahoo.de/mail _______________________________________________ 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