Dear Gromacs Users, 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.
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. 2. I changed my topology file accordingly (change the number of DPPC and Water molecules) 3. I move on to energy minimization. During the mdrun i see the following message :- Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is larger than the 1-4 table size 2.800 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I also notice that the max force does not converge to less than 2000 rather its of the order of 2e+06 . 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 Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is larger than the 1-4 table size 2.800 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size 5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc = xyz has been used as default. Same warnings were printed out during energy minimization. 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. 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. 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? Any help will be appreciated thank you Amit
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