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-- Sent from my iPad. On 07/09/2011, at 18:37, Brian Radak <radak004.umn.edu> wrote: > I am running many QM/MM NVT simulations of small organic molecules (QM) in > water (MM) using rhombic dodecahedral PBCs. The starting structures come > from 1 ns NpT MM equilibrations with the volume reset to a rounded value > (these are for TI calculations and I thought it sensible and not > unreasonable to set the volume constant amongst all lambda values, the > change is usually less than 0.5%). Sometimes, but not always, sander bombs > out with the following error, either after many steps of QM/MM MD or > sometimes after no steps at all: > > **************************************************** > ERROR: QM region + cutoff larger than box dimension: > QM-MM Cutoff = 10.0000 > Coord Lower Upper Size Radius of largest sphere inside unit > cell > X -11.486 11.276 22.762 12.092 > Y -12.143 12.058 24.200 12.092 > Z -11.619 11.293 22.911 12.092 > **************************************************** > SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> > QM region + cutoff larger than box > cannot continue, need larger box. > > As a specific example this happens to isopropanol (generously ~6 A wide) in > a 34 A RHDO. I don't think I am wrong in concluding that there is easily 12 > A (qm_cut + skinnb) to the nearest RHDO face. In any event I got no such > error during the MM simulation. > > I looked in the code and I don't fully understand how the table of values is > arrived at. It would seem that the system is shifted by the geometric > center of mass of the QM region (which is why "Lower" is negative and > "Upper" is positive?), but I'm not exactly sure what the reason for this is > (I'm sure it's a very good one, I just don't know what it is). Anyway, > somewhere in that shifting, the molecule seems to get split across a > periodic wall and thus the "size" of the molecule is calculated > erroneously. There is also a comment in the code that something bad (this?) > would happen if the QM region diffuses extensively. > > Can anyone explain what's going on here? Has anyone seen this problem > before? I'm willing to give fixing this a try, but I think I need a little > bit broader vision of the code as this extends across sqm, the image code, > and the ewald code. > > Thanks! > Brian > > P.S. On a related note, 12.092 A seems too small for the largest sphere in > the "familiar" form of a RHDO. Is this a consequence of the triclinic form > used in the simulation? > > -- > ================================ Current Address ======================= > Brian Radak : BioMaPS > Institute for Quantitative Biology > PhD candidate - York Research Group : Rutgers, The State > University of New Jersey > University of Minnesota - Twin Cities : Wright-Rieman Hall 101 > Graduate Program in Chemical Physics : 610 Taylor Road, > Department of Chemistry : Piscataway, NJ > 08854-8066 > radak004.umn.edu : > radakb.biomaps.rutgers.edu > ==================================================================== > Sorry for the multiple e-mail addresses, just use the institute appropriate > address. > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Sep 07 2011 - 17:30:02 PDT