sunny mishra wrote:
Hi Justin,
I have set up the whole system correctly but now at the final step
when I do mdrun it gives me the fatal error by saying that Number of
grid cells is zero. Probably the system and box collapsed.
Then "correctly" is debatable :)
Do you have any idea about this?
Something is unstable in your system. See here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Beyond that, you'll have to describe what you've done as far as energy
minimization and equilibration, and the level of success of each of those steps.
-Justin
Sunny
On Sun, Oct 11, 2009 at 4:45 PM, sunny mishra <mishra.su...@gmail.com> wrote:
Hi Justin,
Thanks for the quick reply. I am also following the martini tutorial
in order to do the CG simulations. Here are the following steps which
I am doing. Please have a look at them.
1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb
2) converted 1SU4_clean.pdb to its CG structure using awk script and
named it to 1SU4_cleancg.pdb
3) Then created the sequence of 1SU4_clean.pdb file and also the .ssd files.
4) Then using the seq2itp script created the protein.itp file for 1SU4.
5) Now I don't understand after this point what should I do because I
also have to include DSPC molecules. Where should I include them I
mean at which step?
When I make my .top file for the protein do I include DSPC molecules
there or anywhere else? Please let me know
Sunny
On Sun, Oct 11, 2009 at 4:30 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
sunny mishra wrote:
Hi All,
I am working on the CG simulations of the proteins and lipid bilayers.
I am confused of how to set up the whole system for simulations. I got
the DSPC lipid bilayer from martini website and I have 1SU4.pdb file
with me. I cleaned the .pdb file and now I want to include the 14 DSPC
molecules in my .pdb file. I don't know if I am going in the right
direction or not. Please let me know how to set up the simulation for
the same if you have some idea. I will appreciate your help.
I wrote a tutorial for atomistic membrane protein systems:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
It may provide some useful information, since the premise for constructing
the system is the same. Our web server is currently down due to a power
outage at our University, but I should have everything up and running by
tomorrow.
-Justin
Thanks,
Suny
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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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--
========================================
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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