[gmx-users] periodic boundary condition

[Cherry Y. Yates]

Dear David, 

I tried to use x2top, but it ended up with the following error:

 0: GROMOS96 43a1 force field 
 1: GROMOS96 43b1 vacuum force field
 2: GROMOS96 43a2 force field (improved alkane dihedrals)
 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 
 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 
 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 7: [DEPRECATED] Gromacs force field (see manual)
 8: [DEPRECATED] Gromacs force field with hydrogens for NMR
 9: Encad all-atom force field, using scaled-down vacuum charges
10: Encad all-atom force field, using full solvent charges    
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.rtp
Generating bonds from distances...
Opening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.atp
There are 49 type to mass translations
atom 438
-------------------------------------------------------
Program x2top, VERSION 3.3
Source code file: futil.c, line: 537

Fatal error:
Library file ffG43a1.n2t not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

Could you tell me what is wrong? Many thanks!!!

Cherry


David van der Spoel <spoel at xray.bmc.uu.se> wrote: Cherry Y. Yates wrote:
> Dear gromacs developers and users,
> 
> I am calculating a nanotube which has periodic boundary condition along 
> one direction. I wonder how to make an itp file for this system. The 
> difficulty lies in describing the bond between two end atoms, e.g., two 
> atoms are bonded in an infinite length system, but are located on the 
> bottom and top of a unit cell.
use x2top
and in your mdp file use pbc=full

> 
> Thanks,
> 
> Cherry
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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