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

[Xu ZhiPing]

Dear David:
    I forgot to say that I have do "export $GMXFULLPBC=1", and here I
post the energies after em:
 
------------------------------------------------------------------------
---------------------------------------
  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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> 
> 
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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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