[gmx-users] what's "inconsistent shifts"?
David
spoel at xray.bmc.uu.se
Sun Jan 11 10:51:02 CET 2004
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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