Justin A. Lemkul wrote:
Edvin Erdtman wrote:
Hi again
I don't know if you were aware of it, but I have commented some
Justin's questions further down in the e-mail (my last e-mail wasn't
only a thank-email). Since it took so long, and other similar
discussions are still running I thought you have missed my comments
(see below).
Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl
inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5
em2/area.dat), and position restraints on the protein, I have also
merged Cl and SOL in the same temp group, but it does not seem to work
anyway. We still get the LINCS warnings.
Why are you using a cutoff during the compression phase? You will
continue to delete lipids! I have never had a problem if I scale up by
a factor of 4, with a 1.4-nm cutoff, then compress by a factor of 0.95
(with no cutoff).
Maybe that will make a difference?
-Justin
Thankful for all help!
/Edvin
Edvin Erdtman wrote:
Hi again an Thank you for comments!
Justin A. Lemkul wrote:
Edvin Erdtman wrote:
Hi
We have a problem of equilibrate the system with a protein within
DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have
been using their perl script inflategro.pl to insert our protein.
We used position restraints for the protein as mentioned in Methods
41 (2007) 475-488.
We have tried with a scaling factor of 0,95 and 0,97, and a cut-off
value of 14 to expand the box and 0 to reduce the box (is that ok???).
perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5
em2/area.dat
with scaling factor 0.95 23 steps were needed, and with 0,97 39
steps were followed.
This seems reasonable.
When we have not used position restraints for the protein, and used
a cutoff value of 4 Å, the simulation were performed well even
without annealing.
4 A cutoff? For what? That is far too short for a lipid bilayer
simulation. Or am I misunderstanding where you are applying this 4
A? Is it part of InflateGRO?
Yes that is a cut-off for the InflateGRO. cutoff of distance between
alpha-carbon of protein and phosphorus atoms in DPPC (0 in the upper
example of running the perl script). If the distance are within this
value, then that DPPC will be removed. I thought that this parameter
was used only in the diverging step with Inflategro, not when
compressing the system. Therefore we tried to run calculations with
that parameter set to 0 instead (above).
We have tried to energy minimize the system with steepest descent
method in each step of decreasing the box.
Do each of these minimizations complete satisfactorily?
Most of them converged to Fmax < 1000.
After water soaking, we have tried with both cg and steep energy
minimizations.
The problems we are facing:
- All the energy minimizations are not reaching Fmax < 1000
How close to Fmax are you getting? If it's still on the order of
10^3 you may be OK; if it's a lot larger then you have other
problems to deal with.
The highest force we got (using scaling factor = 0.97) at step 33:
"Maximum force = 2.6218958e+03 on atom 4591"
<snip>
tcoupl = Nose-hoover
tc-grps = DPPC Cl SOL Protein
tau_t = 0.1 0.1 0.1 0.1
ref_t = 100 100 100 100
Here is a potential problem. Never couple solvent and ions
separately. Make an index group of these two merged species. See
here:
http://wiki.gromacs.org/index.php/thermostats
Thank you for that advice, I will do that. But really I don't think
that is our main problem. We tried also without chlorine (system
total charge of +2), but we got the same error.
Another bit of general advice. I had a very mysterious problem once
where during equilibration of a DPPC bilayer my lipids were blowing
apart for no apparent reason. Upon very close inspection of the
trajectory (setting nstxout = 1) I identified the initial location
of the explosion. A Cl- ion was immediately next to a phosphate
oxygen (very hard to see!), and it was causing a huge force that was
ripping my lipid apart.
Just an idea, if the InflateGRO minimizations are working OK, but
the solvated system with ions is not working.
-Justin
Thankful for all help we can get!
/Edvin and Sujith
/Edvin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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