[gmx-users] RE: looped dna

[David van der Spoel]

On Tue, 2005-08-09 at 17:36 +0800, Mu Yuguang (Dr) wrote:
> Dear David,
> Thanks. It seems work.
> So in the next release version, this pbc = full should be the default
> setting?
No, because it slightly less efficient. It is useful for special case
like infinite molecules or crystals.
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
> Sent: Tuesday, August 09, 2005 5:35 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] RE: looped dna
> 
> 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
> > 
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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://xray.bmc.uu.se/~spoel
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