Sorry <br>
I will take care of this in the future.<br>
Thanks for your advice . <br><br><div><span class="gmail_quote">On 6/29/07, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> i m carryin a protein explicit solvent simulation using gromacs 3.3<br>> for intially minimizing the hydrogen i did some small mini and equi in the<br>> vaccum by maintaing the restraints<br>> then i added ions and water but in the very first minimization i m getting
<br>> the following error<br><br>Please use normal capitalization and punctuation and do not invent your<br>own abbreviations and shorthands. You're trying to communicate with busy<br>people whose advice you want for free. To improve your chances of getting
<br>useful help, you should make things easy for them, not easy for yourself.<br><br>If you were still using restraints in this second minimization, try taking<br>them off for a second vacuum geometry optimization phase.<br>
<br>> 1-4 interaction between 1 and 9 at distance 8.454 which is larger than the<br>> 1-4 table size 1.000 nm<br>> These are ignored for the rest of the simulation<br>> This usually means your system is exploding,
<br>><br>><br>> in the log file im geting :<br>><br>> 4 inconsistant shifts check ur topology<br>><br>> following is my input file :<br>><br>> title = 1min in water<br>> define = -DPOSRES
<br>> integrator = steep<br>> dt = 0.001<br>> constraints = none<br>> nsteps = 500<br>> nstlist = 10<br>> rcoulomb = 1<br>> rlist = 1
<br>> rvdw = 1.4<br>> ns_type = grid<br>> coulombtype = PME<br>> pbc = xyz<br>> gen_vel = no<br>> fourierspacing = 0.12<br>> pme_order = 6
<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes<br>> comm_mode = angular<br>> emtol = 100.0<br>> emstep = 0.01<br><br>This seems fine.<br><br>> after adding the ions i have modified the topology file,
<br>> plz tel me what is the exact reason for this error or what are the other<br>> things i should check in relation to the error<br><br>Mark<br><br>_______________________________________________<br>gmx-users mailing list
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