[gmx-users] genion doubt
Justin A. Lemkul
jalemkul at vt.edu
Sat May 15 17:50:58 CEST 2010
Bharath.K. Chakravarthi wrote:
> HI....
> I'm not sure about this kind of error but as per my knowledge the
> problem might be with the parameter cpp in mdp file.
> In my mdp file it is as follows
>
The problem is unrelated to cpp, since the error complained about the use of
"warnings" in the .mdp file. Further, if we are to assume Gromacs 4.0.x, the
cpp setting is ignored, as Gromacs has its own C pre-processor now.
> title = ecoli_nusG
> cpp = /usr/bin/cpp
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 100000 ; total 100 ps.
> nstcomm = 1
> ..
> ..
>
> and somewhere i read the nsteps should be between 50000-100000 for pr
> dynamics.....
In general, yes, to obtain good equilibration you would certainly want to run
for more than 1.0 ps, but I would say there is no absolute setting that should
be applied.
-Justin
> search gromacs tutorial for better clue...
>
> On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan <manjubfs at gmail.com
> <mailto:manjubfs at gmail.com>> 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.
>
> 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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>
>
>
> --
> Bharath.K.Chakravarthi
> Post Graduate Student
> Kuvempu University
> Shimoga
> Karnataka
> Ph:9535629260
>
--
========================================
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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