ram bio wrote:
Dear Gromacs Users,
I have inserted the protein in lipid bilayer and performed Inflategro
I am able to reach the required area per lipid after certain
iterations but was unable to get the standard Epot and Fmax values
that is negative and to the power of 5 or 6 and Fmax less than 1000
You won't get that magnitude of Epot without water. If you can't reach Fmax
< 1000, you shouldn't just plow ahead. Analyze where the problem is,
because it is unlikely to go away by magic!
during the last minimization , later i solvated the protein using a
vanderwaal radii for carbon as 0.375, i found some water molecules not
in the core of the lipid layer but to the sides, as they were not in
the centre i ionated the complex with 13 chloride ions as the charge
Did you get rid of these waters? You can always try tweaking the entry in
vdwradii.dat for C. As far as those on the sides are concerned, it sounds
like the box you've created is too large for the lipids. I wouldn't use
this system, because you'll waste a huge amount of time hoping it
equilibrates right.
shown was non-zero total intergral charge 1.30000e+01, then i minized
the ionized complex with the minim.mdp file in as per justin tutorial,
i am following all the mdp files as per the tutorial till now, and was
able to obtain Potential Energy = -1.8947278e+05
Maximum force = 9.1642163e+02 on atom 7647
Norm of force = 5.0845932e+01
That looks fine, but I still think there is an underlying problem in your
InflateGRO construction step.
and then i created the index file ane while running the nvt
equilllibrqtion i am getting
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007117, max 0.443345 (between atoms 6311 and 6312)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
The classic case of "blowing up." See either my Advanced Troubleshooting
page in the tutorial, or
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you want
more specific advice, you'll have to provide information at least about what
type of lipid you're using, and what you have in your .mdp file.
Can any body suggest me how to rectify the defect and is it the
problem with compliation as i am using gromacs 4.0.3 or the memory
space or my running the job.
Well, first off I'd recommend always using the most current version of the
software, not that it's likely to impact your system, but just in general.
This is a problem reported to this list almost daily, so please also check
the archives. There are literally thousands of posts regarding LINCS
warnings and unstable systems.
-Justin
Thanks
Ram
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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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