[gmx-users] what's "inconsistent shifts"?

[David]

On Sat, 2004-01-10 at 10:19, Xu ZhiPing wrote:
> On Fri, 2003-01-10 at 04:32, Xu ZhiPing wrote:
> > Dear all:
> > 	I am now using GMX 3.1.4 to simulate a periodic system of CNT,
> and I 
> > following the em-md procodure, but I the log file, I found warning
> like " There were 60 inconsistent shifts. Check your topology. ", I do
> not know what's the meaning of "inconsistent shifts", so I search all
> the posts before, some similar posts were found, but I still do not know
> how to solve this, I have relaxed my simulation box.
> > 	Can anyone help me and tell me what's the meaning of  "shifs",
> and 
> > will and how this "shifts" affect the simulation results? or just a 
> > fussy warning?
> > 
> What kind of system is this? What is CNT?
> Carbon Nanotube.

I suspected something like that. Your most rigorous solution is to
upgrade to gromacs 3.2.0beta and use pbc = full in the mdp file.

You can also set an environment variable:
setenv GMXFULLPBC 1
that should work in older gromacs versions. Without either of these you
will see very large bond and angle energies. It is explained a bit in
the manual (appendix).

> By the way, your computer's date is a year behind.
> Thanks:-)
> 
> > 	Thanks a lot.
> > 
> > ZP
> > 
> > -----------------------------------------------
> > Xu ZhiPing
> > Ph.D Candidate
> > Room: 3405, Phone: 86-10-627-83814
> > Department of Mechanics,
> > Qinghua University, Beijing, CHINA
> > -----------------------------------------------
> > 
> > 
> > _______________________________________________
> > 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.
> 
> 
> 
> _______________________________________________
> 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, Assist. 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++