Hi Mark, Yes i checked the procedure on the original structure. It woks fine. As for genconf i used the following
genconf -f dppc128.pdb -o out.gro -nbox 2 2 1 As Justin pointed out, I did not correct the periodicity of original structure before using genconf . Thank you, Amit On Fri, Oct 9, 2009 at 5:44 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > Amit Choubey wrote: > >> 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. >> > > What command line did you use? > > 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 :- >> > > Test your protocol on the original coordinate file. It needs to work for > your procedure to be sound. > > 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. >> > > You don't have periodic molecules. Changing mdp options haphazardly is a > recipe for problems. Read 7.3 about them in the first instance, and then > look up in the table of contents for more background. > > 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. >> > > Yup, bad idea. Fix the underlying problem, not the symptoms. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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