[gmx-users] genion doubt
Justin A. Lemkul
jalemkul at vt.edu
Sat May 15 17:48:49 CEST 2010
manjula kasinathan wrote:
>
> 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.
>
http://www.gromacs.org/Documentation/Errors#Unknown_left-hand_XXXX_in_parameter_file
Read the manual - there is no such setting as "warnings."
> 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?????
>
See the diagnostic tips here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
You could also try an NVT equilibration prior to NPT, in case any bad clashes
generated during the dynamics are causing pressure spikes that are unmanageable
by the barostat.
-Justin
> Cheers,
> Manju
>
>
>
>
>
> --
> With Regards,
>
> Manjulakasinathan
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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