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

[David]

On Sat, 2004-01-10 at 10:41, Xu ZhiPing wrote:
> Dear David:
>     I forgot to say that I have do "export $GMXFULLPBC=1", and here I
> post the energies after em:
>  
For bash you want
export GMXFULLPBC=1
(wihout dollar), or was that a type? Anwyay, the energies look
reasonable...

If you have full pbc turned on and your simulation is well behaved you
can ignore the message I think. In 3.2 you will not get such a message
with pbc = full.

> ------------------------------------------------------------------------
> ---------------------------------------
>   Energies (kJ/mol)
>            Bond                    Angle               Proper Dih.
> LJ-14             Coulomb-14
>     7.93172e+02    2.97784e+01    1.21617e+01      9.80219e+03
> 0.00000e+00
>         LJ (SR)                    LJ (LR)      Coulomb (SR)
> Potential          Kinetic En.
>    -6.54870e+03   -1.53338e+02    0.00000e+00    3.93526e+03
> 0.00000e+00
>       Total Energy    Temperature     Pressure (bar)
>     0.00000e+00    0.00000e+00    0.00000e+00
>  
> ------------------------------------------------------------------------
> ---------------------------------------
>     And the em.mdp file looks like 
>  
> ------------------------------------------------------------------------
> ---------------------------------------
> title               =  DWNT
> cpp                 =  /lib/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  10000
> nstlist             =  10
> ns_type             =  grid
> ; cutoff parameters
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.7
> 
> pbc                 =  xyz
> ;
> ;  mdp option: Energy minimizing stuff
> ;
> emtol               =  10.0
> emstep              =  0.01
> nstcgsteep          =  100 
>  
> ------------------------------------------------------------------------
> ---------------------------------------  
> 
>     Any problem here?
> 
> 
> ZP
> -----------------------------------------------
> Xu ZhiPing
> Ph.D Candidate
> Room: 3405, Phone: 86-10-627-83814
> Department of Mechanics,
> Qinghua University, Beijing, CHINA
> -----------------------------------------------
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> On Behalf Of David
> Sent: Sunday, January 11, 2004 4:31 PM
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] what's "inconsistent shifts"?
> 
> 
> 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
> > > -----------------------------------------------
> > > 
> > > 
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-- 
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
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