[gmx-users] genion doubt

manjula kasinathan manjubfs at gmail.com
Sat May 15 15:03:33 CEST 2010


hi snip

        Thank u. as per ur suggestion i added sodium ions to my protein.
then i carried out mdrun for energy minimization nsteps 3000 but i runs only
for 1108 steps. then i went to position restrain steps the command i gave

        grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr

i got a fatal error
            Too many warnings (1), grompp terminated.
            If you are sure all warnings are harmless, use the -maxwarn
option

WARNING 1 [file pr.mdp, line unknown]:
  Unknown or double left-hand 'warnings' in parameter file

y i'm getting this error.how can i correct this could any one help plz.

my pr.mdp file

title               = FWS
warnings            = 10
cpp                 = /usr/local/gromacs/share/gromacs/cpp
define              = -DPOSRES
constraints         = all-bonds
integrator          = md
dt                  = 0.002 ; ps !
nsteps              = 500 ; total 1.0 ps.
nstcomm             = 1
nstxout             = 250     ; collect data every 0.5 ps
nstvout             = 1000
nstfout             = 0
nstlog              = 10
nstenergy           = 10
nstlist             = 10
ns_type             = grid
rlist               = 1.0
coulombtype         = PME
rcoulomb            = 1.0
vdwtype             = cut-off
rvdw                = 1.4
fourierspacing      = 0.12
fourier_nx          = 0
fourier_ny          = 0
fourier_nz          = 0
pme_order           = 4
ewald_rtol          = 1e-5
optimize_fft        = yes
; Berendsen temperature coupling is on
Tcoupl              = v-rescale
tau_t               = 0.1     0.1
tc-grps             = protein non-protein
ref_t               = 300     300
; Pressure coupling is on
Pcoupl              = parrinello-rahman
Pcoupltype          = isotropic
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529

with this warnings i proceeded with mdrun but i get the following LINCS
warnnings

starting mdrun 'Protein in water'
500 steps,      1.0 ps.
step 300, will finish Sat May 15 08:57:23 2010
Step 394, time 0.788 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000103, max 0.001028 (between atoms 4478 and 4480)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4478   4480   33.4    0.1081   0.1091      0.1090
Step 423, time 0.846 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.442275, max 40.666431 (between atoms 8211 and 8212)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8473   8476   88.6    0.1527   0.2741      0.1522
   8473   8475   89.9    0.1094   3.6185      0.1090
   8473   8474   89.5    0.1094   0.2778      0.1090
   8471   8473   87.2    0.1455   0.2548      0.1449
   8471   8472   33.2    0.1013   0.1241      0.1010
   8215   8217   32.8    0.1090   0.1240      0.1090
   8215   8216   39.2    0.1091   0.1282      0.1090
   8211   8215   45.8    0.1536   0.1603      0.1529
   8211   8213   44.0    0.1425   0.1645      0.1410
   8211   8212   90.2    0.4225   4.5416      0.1090
   8209   8211   45.6    0.1511   0.1348      0.1529
   8209   8210   32.4    0.1098   0.1199      0.1090
   8207   8209   33.3    0.1482   0.1823      0.1449
   7224   7225   30.4    0.1013   0.1010      0.1010
   5296   5297   30.5    0.1093   0.1092      0.1090
Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which is
larger than the 1-4 table size 2.400 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
or with user tables increase the table size

Step 424, time 0.848 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 171806.092017, max 19412182.000000 (between atoms 8235 and 8236)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8507   8508   90.0    0.1011   0.2179      0.1010
   8497   8499   39.8    0.1460   0.2065      0.1449
   8497   8498   59.8    0.1009   0.1923      0.1010
   8495   8497   44.0    0.1354 729.7847      0.1335
   8495   8496   94.4    0.1235 729.7617      0.1229
   8491   8493   89.7    0.1091   0.2077      0.1090
   8487   8489   89.8    0.1091   0.5344      0.1090
   8485   8491   32.7    0.1531   0.1890      0.1529
   8485   8486   47.4    0.1091   0.1421      0.1090
   8482   8485   50.7    0.1536 215.0330      0.1529
   8482   8484   71.0    0.1094 214.9777      0.1090
   8482   8483   92.6    0.1091 215.0566      0.1090
   8480   8495   77.1    0.1633 417.3555      0.1522
   8480   8482   84.2    0.1556 871.1644      0.1529
   8480   8481   80.7    0.1078 911.5953      0.1090
   8478   8480   43.4    0.1559 3067.7700      0.1449
   8478   8479   92.3    0.1070 3786.8391      0.1010

t = 0.848 ps: Water molecule starting at atom 80338 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

could any one help me to overcome this problem. thanks in advance

hi justin as per ur suggestion i viewed my structure but there is no clash
in it.
y i'm getting this error?????

Cheers,
Manju





-- 
With Regards,

Manjulakasinathan
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