thanks for your advice Mr. Manoj<br>
I tried the same simulation by taking a structure which was already
minimized by another software Amber. Using that structure as the
starting structure also, i got the same error i mention earlier.<br>
please suggest me something <br>
thanks <br>
<br><div><span class="gmail_quote">On 6/29/07, <b class="gmail_sendername">M.N. Manoj</b> <<a href="mailto:mnmanoj@gmail.com">mnmanoj@gmail.com</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;">
It could be an error in protein structure ( because 1 - 9 interaction
), and we usually overcome similar issues by a pre -energy minimization
before submitting to gromacs.<span class="q"><br><br>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><br></span><div><span class="e" id="q_11376709f8e62e16_2">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><br></span></div><span class="q">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><br></span>thanks<br><br><br>Gurpreet<br>IIT MADRAS<br clear="all"><span class="sg"><br>-- <br>M.N. MANOJ<br>PROJECT LEADER - BIOINFORMATICS<br>VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION<br>BANGALORE<br>INDIA
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