[gmx-users] Problem with dynamics using ENDADS and CVS GMX version

Leonardo Sepulveda Durán leonardosepulveda at gmail.com
Fri Dec 16 20:57:07 CET 2005


Thanks Yang.

My CVS version was downloaded as you said, David suggeted that way a
few weeks ago, so maybe the problem is not there.

I made a mistake in the previous mail, the DIN.mdp was for a high
temperature simulation (498K). So i Checked if the Temperature would
be a problem. I runned the same protocol with 300K:

title                             = Simulated annealing
cpp                             = /lib/cpp
constraints             = none
integrator              = md
;       Molecualr Dynamics
dt                                = 0.001       ;
nsteps                  = 1050000       ;
comm_mode                = linear
nstcomm                       = 1
nstxout                 = 1000
nstvout                 = 1000
nstfout                 = 0
nstenergy               = 1000
;       Nonbond
nstlist                           = 5
ns_type                 = grid
rlist                             = 1.0
coulombtype             = encadshift
vdwtype                           = encadshift
rcoulomb                = 0.8
rvdw                              = 0.8
;       Temp coupling
Tcoupl                  = berendsen
tau_t                             = 0.1     0.1
tc-grps                 = Protein SOL
ref_t                             = 300     300
;       Annealing
annealing               = single single
annealing_npoints       = 2      2
annealing_time          = 0 50   0 50
annealing_temp          = 0 300  0 300

Whith this protocol the same happen, the simulation stops abruptly,
but two mensajes appear, one at the end of md1.log:

Large VCM(group rest):  22500.83984, 293711.37500,  14498.22070,
ekin-cm:  2.48457e+15

The second at the end of the output:

Warning: 1-4 interaction between 1031 and 1046 at distance 4.172 which
is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 2263 failed on node n0 (192.168.1.11) due to signal 11.
-----------------------------------------------------------------------------

I checked the dynamics in VMD. The box is not exploding. Nevertheless
some waterbonds span al the box lengh, but a detailed inspection shows
the large bonds appear beetween the hidrogen and an oxigen of diferent
water molecules. It seems to be only a display error. There is also a
display error in the protein, the last residue is missing, but exists
in the .gro file.

This are the atoms, from the input .gro file
63VAL     CA 1031   1.654   2.707   1.911 -0.3666 -0.4253  0.5873
64GLY      H 1046   1.741   2.955   1.957 -0.0365  0.4927  1.0323
 In vmd they are ~2.7 angstrom appart

I ran other simulation at 498K, but without the last residue (GLY) and
this appears

Warning: 1-4 interaction between 1007 and 1030 at distance 1.048 which
is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 1103 failed on node n0 (192.168.1.11) due to signal 11.
-----------------------------------------------------------------------------

And at the end of the md0.log of that run
Large VCM(group rest): -11641.75293, -174976.14062,   -775.30066,
ekin-cm:  8.86408e+14

The atoms involved:
62ARG     CA 1007   1.459   2.602   2.212  0.1020 -0.6429 -0.0779
63VAL      H 1030   1.475   2.755   1.988  1.6822  0.5463  1.4324

So it seem to be a bug...is rare to see the error beetween the same
kind of atoms. What do you think? Someone have seen this error using
Encad?

The other question is about which value have to be used for
"table-extension", the default is 1, but I dont know if rlist also
have to be changued.

But it seems rare that the error says those pairs of atoms are more
than 10 angstrom apart, but in the .gro they are very close. Can it be
a trouble with image conventions?.

Thanks

Leonardo



On 12/15/05, Yang Ye <leafyoung81-group at yahoo.com> wrote:
> It was a bit adventurous to try the HEAD branch. Try 3.3-patch branch.
> This applies to future releases, I think.
>
> cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login
> cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co -r
> release-3-3-patches gmx
>
> Yang Ye
>
> Leonardo Sepulveda Durán wrote:
>
> >Thanks David.
> >
> >I tested the released code first, nevertheless i moved to CVS because
> >GMX3.3 had a bug concerning prolines in pdb2gmx, which was solved in
> >CVS version (Erik told me). May the CVS version have an error not
> >present in the released code?
> >
> >Leonardo
> >
> >
> >
> >>could be, but that's impossible to debug. check the released 3.3 first
> >>please.
> >>
> >>
> >>>Leonardo
> >>>_______________________________________________
> >>>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, Assoc. 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.
> >>
> >>
> >>
> >_______________________________________________
> >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.
> >
> >
> >
>
> --
> /Regards,/
> Yang Ye
> /Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884
> /
>
> _______________________________________________
> 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.
>


--
~~~~~~~~~~~~~~~~~~~~~~~~~
Leonardo Andres Sepúlveda Durán
Biochemist
Universidad de Chile
Codigo postal:  752-0249
~~~~~~~~~~~~~~~~~~~~~~~~~



More information about the gromacs.org_gmx-users mailing list