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
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