hi thanks for such a brief reply.. i have already downloaded these four files from the Peter Tieleman's website: "dppc128.pdb dppc.itp inflategro.pl lipid.itp"
but it looks like it has been simulated in water box for some time.. am i right? (i am afraid that i will not) then what's next and what will be the *.mdp file for this simulation. anupam >> what parameters should I use for lipid simulations > > That depends on the forcefield that you are using. I will tell you > about what I do but this is a poor substitute for what you should > really be doing, which is: > > 1) find the initial paper that publishes the forcefield that you are > using and figure out how they used it > 2) Find some very recent papers that use this same forcefield and > figure out how they use it and then read the relevant papers that they > reference in their methods section. > > That said, I use the forcefield having a united atom representation of > lipids originally proposed by Egberts et. al. (1994), with the charges > from Chiu et. al. (1995), adjusted by Berger et. al. (1997), and with > the additional scaling of 1-4 coulombics introduced by Lindahl and > Edholm (2000). You can download these topologies from Peter Tieleman's > website: > http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies > > It is common to use a twin range cutoff with LJ calculated every step > up to 1.0nm and up to 1.4nm every 10 steps when the nonbonded list is > updated. Coulombics are in real space below 1.0nm and by PME beyond. > Pressure coupling is a semiisotropic berendsen barostat with tau_p of > 4.0ps. Temperature is coupled to a berendsen thermostat separately for > i)lipids ii)water+ions iii)protein witha tau_t of 0.1ps. I use lincs > to constrain all-bonds. > > Note that I personally reduce the short range interaction cutoff to > 0.9nm from 1.0nm. But you would be better to stick with parameters > that are in more common usage. > > The protein forcefield that I use is opls-aa and I use tip4p water. > When combining these forcefields, I use an unpublished method to scale > 1-4 coulombics differently for protein and lipid: > http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html > There are also a variety of related posts that come after that one but > I can't remember what they are. You are going to need to do some > searching. > >> how to insert the protein in that bilayer. > > You can either use the make_hole version of mdrun available for > download from the user contributions section of the gromacs web site > of a program called inflategtro available from Peter Tieleman's > website: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis > > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ gmx-users mailing list [email protected] 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
