[gmx-users] Re: Asking for help into crystalline organic Compound Simulations

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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