[gmx-users] RE: looped dna

[Mu Yuguang (Dr)]

Dear David,
Thanks. It seems work.
So in the next release version, this pbc = full should be the default
setting?


-----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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