[gmx-users] RE: looped dna

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 9 11:34:39 CEST 2005


On Tue, 2005-08-09 at 17:16 +0800, Mu Yuguang (Dr) wrote:
> Dear Gromacs users
> When I try to simulate a looped DNA system, also called periodic dna
> (the two ends of dna is bonded). 
> But there is some errors:
> 
> Removing pbc first time
> There were 4 inconsistent shifts. Check your topology
> Done rmpbc
try
pbc = full
you can not use shake or lince in 3.2.1 (you can use lincs in the CVS
version)
> 
> When I remove the bond which link the two ends, everything is OK.
> 
> Regards
> Yuguang
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++





More information about the gromacs.org_gmx-users mailing list