Reinaldo Molina Ruiz wrote:
Dear Professor David Spoel
My name is Reinaldo Molina, I am trying to start in the
Molecular-Dynamic Simulation of Crystalline Organic Compounds, but I
have affronted serial difficulties with Gromacs Parameters for find out
the suitable condition to run a simulations.
Please, could you provide me some advises or a place where I can find a
tutorial in order to perform starting from X ray’s structure?
Please put further questions on the mailing list.
I suspect your box is too large, since 288 atoms should fit in 1.5 nm^3
or something. You have to use the exact unitcell (may be triclinic).
I will appreciate any advice from you, and I want to know if OPLS is a
suitable forcefield to simulate crystalline compounds.
My main aim is to simulate the vapor pressure of crystalline organic
compounds a different temperature. I built the topology of my compounds
and applied the space-group symmetry operations to my unit cell. I have
a big box with 16 molecules and
I got my .gro file:
Pure UC-244
288
1MNVF C1 1 0.784 1.182 2.759
1MNVF C2 2 0.762 1.056 2.826
1MNVF C3 3 0.868 1.041 2.936
1MNVF C4 4 0.952 1.159 2.935
.
.
.
16MNVF H17 287 2.930 2.652 1.042
16MNVF H18 288 2.856 2.547 0.920
6.00000 6.00000 6.00000
my top file
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include UC-244 pure
#include "uc244.itp"
[ system ]
Pure UC-244
[ molecules ]
;molecule name number
MNVF 16
And my itp file, together with em.mdp and md.mdp
In this file I used PME as coulomtype, pressure coupling
Parribekki-Rahman and also SHAKE calculations, but I become a error
always at 60 ps that said:
Program mdrun_mpi, VERSION 4.0.5
Source code file: ../../../../src/mdlib/ns.c, line: 2295
Fatal error:
One of the box vectors has become shorter than twice the cut-off length
or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
In waiting for you time and kindness,
Sincerely yours,
Reinaldo Molina
------------------------------------------------------------------------
Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
- Universidad 2010, La Habana, del 8 al 12 de febrero de 2010.
http://www.universidad2010.cu
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
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