Dear Gromacs Users,<div><br></div><div>I have been trying to generate a larger lipid system but am running into troubles due to improper initial co-ordinates set up. Following are the steps i am trying to follow.</div><div>
<br></div><div>1. I start with a 128 dppc membrane and use genconf to create a larger system. I got the dppc128.pdb from Dr. Peter Tieleman's website.</div><div><br></div><div>2. I changed my topology file accordingly (change the number of DPPC and Water molecules)</div>
<div><br></div><div>3. I move on to energy minimization. During the mdrun i see the following message :-</div><div><br></div><div><div>Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is larger than the 1-4 table size 2.800 nm</div>
<div>These are ignored for the rest of the simulation</div><div>This usually means your system is exploding,</div><div>if not, you should increase table-extension in your mdp file</div><div>or with user tables increase the table size</div>
<div><br></div><div>I also notice that the max force does not converge to less than 2000 rather its of the order of 2e+06 .</div><div><br></div><div>4. I tried to do energy minimization again on the above system but the steepest descent could not change the potential energy substantially and terminated after less that 20 steps. I again noticed the following warning </div>
<div><div><br></div><div>Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is larger than the 1-4 table size 2.800 nm</div><div>These are ignored for the rest of the simulation</div><div>This usually means your system is exploding,</div>
<div>if not, you should increase table-extension in your mdp file</div><div>or with user tables increase the table size</div></div><div><br></div><div>5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc = xyz has been used as default.</div>
<div><br></div><div>Same warnings were printed out during energy minimization.</div><div><br></div><div>6. I also tried to use the table-extension option and increased its value to 10 nm but later the LINCS printed out too many warnings and MD could not be done. I know that its not at all a good idea to increase the 1-4 cut off.</div>
<div><br></div><div>By the way to be specific the system size was 12 x 12 x 6 in nm3. I had 256 lipids and about 7300 water molecules.</div><div> </div><div><br></div><div>I believe that this might not be the best way to create a larger bilayer system. Could somebody suggest me other ways of doing this?</div>
<div><br></div><div>Any help will be appreciated thank you</div><div><br></div><div>Amit</div><div><br></div><div><br></div></div>