[gmx-users] what's "inconsistent shifts"?
Xu ZhiPing
xzp02 at mails.tsinghua.edu.cn
Sun Jan 11 10:43:01 CET 2004
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
> > -----------------------------------------------
> >
> >
> > _______________________________________________
> > 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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.
More information about the gromacs.org_gmx-users
mailing list