[gmx-users] potential tables not working

[avinash kumar]

Hello all,

I am trying to learn to use tabulated potential in GROAMCS for
defining my own potential. For learning purposes I have created a pdb
of silicon atoms of 28 atoms. I want to create two groups each of
which will interact in a different way . The gro file is

GRowing Old MAkes el Chrono Sweat
   28
    1SI      SI    1   0.229   0.250   0.500
    2SI      SI    2   0.589   0.250   0.500
    3SI      SI    3   0.948   0.250   0.500
    4SI      SI    4   1.297   0.250   0.500
    5SI      SI    5   1.666   0.250   0.500
    6SI      SI    6   2.025   0.250   0.500
    7SI      SI    7   2.385   0.250   0.500
    8SI      SI    8   2.744   0.250   0.500
    9SI      SI    9   3.103   0.250   0.500
   10SI      SI   10   0.050   0.561   0.500
   11SI      SI   11   0.409   0.561   0.500
   12SI      SI   12   0.768   0.561   0.500
   13SI      SI   13   1.127   0.561   0.500
   14SI      SI   14   1.487   0.561   0.500
   15SI      SI   15   1.846   0.561   0.500
   16SI      SI   16   2.205   0.561   0.500
   17SI      SI   17   2.574   0.561   0.500
   18SI      SI   18   3.283   0.561   0.720
   19SI      SI   19   0.229   0.872   0.720
   20SI      SI   20   0.589   0.872   0.720
   21SI      SI   21   0.948   0.872   0.720
   22SI      SI   22   1.297   0.872   0.720
   23SI      SI   23   1.666   0.872   0.720
   24SI      SI   24   2.025   0.872   0.720
   25SI      SI   25   2.385   0.872   0.720
   26SI      SI   26   2.744   0.872   0.720
   27SI      SI   27   3.103   0.872   0.720
   28SI      SI   28   0.050   1.183   0.720
   3.23280   2.93330   2.21980


Now I make a index file which is as shown
[ s1 ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14

[ s2 ]
  15   16   17   18   19   20   21   22   23   24   25   26   27   28


The mdp file is as shown
title                    = md
cpp                      = cpp
include                  = -I../top
define                   =
integrator               = md
dt                       = 0.002
nsteps                   = 10000
nstcomm                  = 1
nstxout                  = 10
nstvout                  = 10
nstfout                  = 10
nstxtcout                = 0
nstcheckpoint            = 20
table-extension          = 0
vdwtype                  = user
xtc_grps                 = s1 s2
energygrps               = s1 s2
energygrp_table          = s1 s1 s2 s2 s1 s2
nstlist                  = 10
ns_type                  = simple
rlist                    = 0.5
coulombtype              = user
rcoulomb                 = 0.5
rvdw                     = 0.5
tcoupl                   = Berendsen
tc-grps                  = s1 s2
tau_t                    = 0.1   0.1
ref_t                    = 300  300
acc-grps                 = s1
accelerate               = 0.004108  0.00  0.00
gen-vel                  = yes
nstenergy                = 10
constraints              = none

Then i proceed on to the making the tpr file and making the run.

I give the following command for run:

mdrun -nice 0 -v -s cgi.tpr -o cgi1.trr -c chi1.gro -e cgi1.edr -g
cgi1.log -table table.xvg -tablep table_s1_s1.xvg -tablep
table_s1_s2.xvg -tablep table_s2_s2.xvg

The simulation runs okay but the log file is full of infinite numbers.
It says
Large VCM(group rest): 13422573811400704.00000, 97768580317184.00000,
-12705115630731264.00000, ekin-cm:  1.34288e+35

 Step           Time         Lambda
            100        0.02000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
    0.00000e+00    0.00000e+00    0.00000e+00            nan            nan
    Temperature Pressure (bar)
            nan            nan

           Step           Time         Lambda
            200        0.04000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
    0.00000e+00    0.00000e+00    0.00000e+00            nan            nan
    Temperature Pressure (bar)
            nan            nan


Can somebody tell me why the mdrun is not taking the tables as
expected. I have separate tables for table.xvg , table_s1_s1.xvg ,
table_s1_s2.xvg , table_s2_s2.xvg in the folder where my other files
are and "s1" and "s2" are name of the groups.


Thanks in advance,
Avinash Kumar