[gmx-users] RE: looped dna
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 9 11:57:09 CEST 2005
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
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
> 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.
> > 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 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