[gmx-users] RE: looped dna
Mu Yuguang (Dr)
YGMu at ntu.edu.sg
Tue Aug 9 11:36:57 CEST 2005
Thanks. It seems work.
So in the next release version, this pbc = full should be the default
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
pbc = full
you can not use shake or lince in 3.2.1 (you can use lincs in the CVS
> When I remove the bond which link the two ends, everything is OK.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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