Amit Choubey wrote:
Hi Justin,
Yes you are right. I didnt fix the periodicity to start with. Could you
tell me how to do that, which command to work with?
Thanks.
Periodicity is corrected using trjconv. This involves creating a .tpr file of
to represent the system and using trjconv -pbc mol -ur compact, or some such
equivalent.
My tutorial gives some information on doing this. Please see:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
-Justin
amit
On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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.
Did you correct for periodicity before you extended the system? The
files distributed by Tieleman are compact representations.
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
Looks to me like two bonded atoms are across the box from each
other, which seems to answer my question above :)
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.
Bad idea. This option is for "infinite" molecules, like nanotubes
or graphene sheets that are supposed to extend across the simulation
box.
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.
The standard advice is to fix the problem with the system, not
change the table-extension.
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?
Fix periodicity, then use genconf.
-Justin
Any help will be appreciated thank you
Amit
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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