<div>HI....<br></div><div>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.</div><div>In my mdp file it is as follows</div><div><br></div><div>title = ecoli_nusG <br>
<span style="background-color: #ffccff;">cpp = /usr/bin/cpp</span> <br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>dt = 0.001 ps !<br>
nsteps = 100000 total 100 ps.<br>nstcomm = 1<br>..<br></div><div>..</div><div><br></div><div>and somewhere i read the nsteps should be between 50000-100000 for pr dynamics.....</div><div>search gromacs tutorial for better clue... <img src="cid:330@goomoji.gmail" style="margin:0 0.2ex;vertical-align:middle" goomoji="330"></div>
<br><div class="gmail_quote">On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan <span dir="ltr"><<a href="mailto:manjubfs@gmail.com">manjubfs@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br clear="all">hi snip<br><br> 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<br>
<br> grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr<br><br>i got a fatal error<br> Too many warnings (1), grompp terminated.<br> If you are sure all warnings are harmless, use the -maxwarn option<br>
<br>WARNING 1 [file pr.mdp, line unknown]:<br> Unknown or double left-hand 'warnings' in parameter file<br><br>y i'm getting this error.how can i correct this could any one help plz.<br><br>my pr.mdp file <br>
<br>title = FWS<br>warnings = 10<br>cpp = /usr/local/gromacs/share/gromacs/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>
dt = 0.002 ; ps !<br>
nsteps = 500 ; total 1.0 ps.<br>nstcomm = 1<br>nstxout = 250 ; collect data every 0.5 ps<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 10<br>
nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>fourierspacing = 0.12<br>
fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on<br>Tcoupl = v-rescale<br>
tau_t = 0.1 0.1<br>tc-grps = protein non-protein<br>ref_t = 300 300<br>; Pressure coupling is on<br>Pcoupl = parrinello-rahman<br>Pcoupltype = isotropic<br>
tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br>
<br>with this warnings i proceeded with mdrun but i get the following LINCS warnnings <br><br>starting mdrun 'Protein in water'<br>500 steps, 1.0 ps.<br>step 300, will finish Sat May 15 08:57:23 2010<br>Step 394, time 0.788 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms 0.000103, max 0.001028 (between atoms 4478 and 4480)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 4478 4480 33.4 0.1081 0.1091 0.1090<br>
Step 423, time 0.846 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.442275, max 40.666431 (between atoms 8211 and 8212)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
8473 8476 88.6 0.1527 0.2741 0.1522<br> 8473 8475 89.9 0.1094 3.6185 0.1090<br> 8473 8474 89.5 0.1094 0.2778 0.1090<br> 8471 8473 87.2 0.1455 0.2548 0.1449<br>
8471 8472 33.2 0.1013 0.1241 0.1010<br> 8215 8217 32.8 0.1090 0.1240 0.1090<br> 8215 8216 39.2 0.1091 0.1282 0.1090<br> 8211 8215 45.8 0.1536 0.1603 0.1529<br>
8211 8213 44.0 0.1425 0.1645 0.1410<br> 8211 8212 90.2 0.4225 4.5416 0.1090<br> 8209 8211 45.6 0.1511 0.1348 0.1529<br> 8209 8210 32.4 0.1098 0.1199 0.1090<br>
8207 8209 33.3 0.1482 0.1823 0.1449<br> 7224 7225 30.4 0.1013 0.1010 0.1010<br> 5296 5297 30.5 0.1093 0.1092 0.1090<br>Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which is larger than the 1-4 table size 2.400 nm<br>
These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>Step 424, time 0.848 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms 171806.092017, max 19412182.000000 (between atoms 8235 and 8236)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
8507 8508 90.0 0.1011 0.2179 0.1010<br> 8497 8499 39.8 0.1460 0.2065 0.1449<br> 8497 8498 59.8 0.1009 0.1923 0.1010<br> 8495 8497 44.0 0.1354 729.7847 0.1335<br>
8495 8496 94.4 0.1235 729.7617 0.1229<br> 8491 8493 89.7 0.1091 0.2077 0.1090<br> 8487 8489 89.8 0.1091 0.5344 0.1090<br> 8485 8491 32.7 0.1531 0.1890 0.1529<br>
8485 8486 47.4 0.1091 0.1421 0.1090<br> 8482 8485 50.7 0.1536 215.0330 0.1529<br> 8482 8484 71.0 0.1094 214.9777 0.1090<br> 8482 8483 92.6 0.1091 215.0566 0.1090<br>
8480 8495 77.1 0.1633 417.3555 0.1522<br> 8480 8482 84.2 0.1556 871.1644 0.1529<br> 8480 8481 80.7 0.1078 911.5953 0.1090<br> 8478 8480 43.4 0.1559 3067.7700 0.1449<br>
8478 8479 92.3 0.1070 3786.8391 0.1010<br> <br>t = 0.848 ps: Water molecule starting at atom 80338 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>
<br>could any one help me to overcome this problem. thanks in advance<br><br>hi justin as per ur suggestion i viewed my structure but there is no clash in it.<br>y i'm getting this error?????<br><br>Cheers,<br>Manju <br>
<font color="#888888">
<br> <br><br><br><br>-- <br>With Regards,<br><br>Manjulakasinathan<br>
</font><br>--<br>
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