CCL: DLPOLY error mesage

 Sent to CCL by: "Sidney Ramos Santana" [santanasidney.:.yahoo.com.br]
 --- sabri alkis wrote --
 > Data: Tue, 26 Sep 2006 16:49:20 -0400
 > De: "sabri alkis alkis . ufl.edu" <owner-chemistry. ~~
 .ccl.net>
 > Para: "Santana, Sidney Ramos -id4k3-" <santanasidney. ~~
 .yahoo.com.br>
 > Assunto: CCL: DLPOLY error mesage
 >     Sent to CCL by: "sabri  alkis" [alkis*o*ufl.edu]
 > Dear all,
 >
 > I have 6329 atoms(alkanthiol monolayer on gold surface and a silver
 > cluster on top of these molecules) I used UFF(universal force field)
 > parameters to calculate the vdw parameters between the atoms. When I run
 the
 > simulation, I keep getting this error message "1-4 separation exceeds
 > cutoff range". I tried different cutoff values but I got the same
 error
 > message again.. I looked at the source code but I do not know why I got
 > this message. What do u guys think the problem is? Is it wrong vdw
 > parameters? What could I try?
 > Best wishes
 > Sab..
 --
 Dear Sabri Alkis,
   Problably your simulations box is much bigger than it must be.
 Don't worry, this is normal! This usually happens when we
 want to simulate biological or organic system.
 I had a similar problem to simulate Biodiesel system with 11,000
 atoms because the size of simulation box decreases while the simulation
 is runnning. My simulation box started with its box side equal to 90 angstroms
 and finished with 46 angstroms.
 Tips:
 1) Let the volume to change !! So, Use NPT ensemble!
 2) Problably, in your initial input, the CONFIG file, there is
 only the coordinates, and for a NPT simulation you also will need
 velocities and forces of the atoms. So, you must run a very small
 simulation using NVT ensemble, and in the end, you will get these properties.
   I would like to suggest some articles where you can undestand how the SPME
 Ewald
 works and how can we choose some parameter to get trustable and precise
 simulations.
   Please see:
 "How to mesh up Ewald sums. I. A theoretical and numerical comparison
 of various particle mesh routines"
 J. Chem. Phys. 109 (1998) 7678 - 7693
 "How to mesh up Ewald sums. II. An accurate error estimate for the
 particle-particle particle-mesh algorithm"
 J. Chem. Phys. 109 (1998) 7694 - 7701
 3) Copy the last simulation box, in the REVCON file, to the CONFIG file and
 now, start a NPT long time simulations. Im my case I have been used 400,000 fs
 with a time step of 1 fs.
 4) Repeate the Step 3) until the temperature and the pressure attain the room
 temperature and 1 atm, respectively.
 Warnings:
   If I understood well, you want to simulate a "gold surface".
 Well, computer simulations to describe surfaces only "make sense" if
 you employ
 a SLAB geometry in your periodic boundary conditions.
 But, when you do this the Ewald sum can not be used to calculate de
 long range interactions due some Ewald sum convergence problems
 in the reciprocal space that makes the calculation much more
 expensive computationally than its tre-dimensional counterpart.
 To more details, please see:
 Chapter 12.4 "Ewald Summation in a Slab Geometry"
 in "Understanding Molecular Simulation
 > From Algorithms to Applications"
 Daan Frenkel & Berend Smit
 2nd Edition, Academic Press (2002)
   An alternative to this problem raise by the employment of
 a others methods, to calculate long range interactions as
 "Reaction Field". This method is implemented in the DLPOLY.
 Use the "chemometric" fit the dieletric constant for your system
 using, for example, the diffusion coefficient as a probe.
 Best regards,
 Sidney R. Santana
 Theoretical and Computational Chemistry Lab. (LQTC)
 Fundamental Chemistry Depart. (DQF)
 Federal University of Pernambuco (UFPE)
 Recife - PE - Brazil
 e-mail: santanasidney_at_yahoo.com.br