<div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> This is continuation to my previous mail. I am trying to simulate a<br>molecule using mdrun but i am getting errors.
<br><br>After 2 steps i got<br><br> " Warning: 1-4 interaction between 245 and 251 at distance 1.922 which<br>is larger than the 1-4 table size 1.000 nm<br>These are ignored for the rest of the simulation. This usually means your
<br>system is exploding, if not, you should increase table-extension in your<br>mdp file. "<br><br>and then finally the program is quitting giving the message.<br><br> "Number of grid cells is zero. Probably the system and box collapsed"
<br><br>i am unable to sort out the real problem of this.I have tried increasing<br>the grid size and also table-extension,but still i am getting the same<br>message.<br><br>Can someone suggest me where i am going wrong and what is to be done???Is
<br>this problem because of the compiler???<br><br></blockquote></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Ramya,</blockquote>
<br>
I have observed similar problem with another protein. It seems not an
issue with the program, but with the protein. U can try running again
after a short geometry optimization of the protein (eg: minimization
with Argus lab tool). This usually happens for proteins with bad
Ramachandran plots. See that also.<br>
<br>
Good luck.<br clear="all"><br>-- <br>M.N. MANOJ<br>PROJECT LEADER - BIOINFORMATICS<br>VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION<br>BANGALORE<br>INDIA