Hi, If you have time, I have some questions about the neighbor list and cut-off values.
I am running NVT simulations with coulombtype = PME and vdwtype = cut-off. I have specified equal neighbor search, vdw, and Coulomb cut-offs: rlist = 1.5 nm, rvdw = 1.5 nm, rcoulomb = 1.5 nm. Is it a good idea to use rlist = rvdw = rcoulomb? (I typically use the default value of nstlist: nstlist = 10.) According to the manual (http://manual.gromacs.org/current/online/mdp_opt.html#vdw), using vdwtype = cut-off means that neighbor searching will be performed using a twin-range approach. rvdw must be greater than or equal to rlist, rvdw >= rlist; in my case, I am using rvdw = rlist. Is this a good idea? Section 4.6.3 of the manual describes. Of course, in the neighbor list, "all interaction pairs within rlist are stored." But "interactions between pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw) are computed during neighbor searching." Does this statement imply that I should use rvdw > rlist, rather than rvdw = rlist? However, there is no "grace distance" in Gromacs (http://lists.gromacs.org/pipermail/gmx-users/2004-January/008831.html). According to Berk Hess: "There is no 'grace distance' in Gromacs. A pair of atoms is put in the neighborlist if the centers of geometry of the charge groups they belong to are inside the cut-off distance. Thus some atom pairs might not interact while they are inside the cut-off distance, while other atom pairs might interact while they are outside the cut-off distance. These charge groups are important for simulations with cut-off electrostatics as they reduce the cut-off noise significantly. With shiftted electrostatics or PME charge groups are only important for performance reasons." The above paragraph seems to imply that I should use rvdw = rlist. The above paragraph seems to say that since, unlike other MD codes that do not use charge groups, in Gromacs there is really no need for a "grace distance" -- because the use of charge groups, rather than atoms, in a sense has a "bult-in" grace distance. The charge groups are unlikely to move much between neighbor list updates every nstlist steps. So, my question is, am I at risk for artifacts if I use rvdw = rlist? Should I instead use rvdw >= rlist? (I am using nstlist = 10 with a liquid that I anneal from 700 K down to 350 K.) Thank you kindly! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
