Kirill Bessonov wrote:
Hi guys,
I am trying to start simulation on lipid - peptide system, but receive
LINCS warnings of angles rotating more than 30 deg which means that my
system is unstable. I have tried to do mdrun on the DMPC box itself and
had no problems. Once I insert my peptide, the problems starts. I have
run Energy MInimization with LIncs order or 4 and Lincs iterations 8,
but still could not bring system to 200 kJ/mol Fmax. Received the
following message.
Converged to machine precision,
but not to the requested precision Fmax < 100
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up sys_EM_ready.gro to ./#sys_EM_ready.gro.2#
Steepest Descents converged to machine precision in 499 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -1.2830664e+06
Maximum force = 3.4162991e+03 on atom 2
Norm of force = 3.2566280e+01
Now I am trying to just to do EM (energ. minim) on my 14 aa peptide, in
water box just to see if it will work.
My questions:
-How to position peptide into existing lipid box (apart form using
editconf -rotate parameter). I have tried VMD and did it visually, but
new coordingates were not saved?
I wrote a tutorial that gives instructions on how to build membrane protein
systems, you might find it useful:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
-How I can improve on EM, what kinda setting in mdp file can I use to
that system converges even after 10,000 steps?
emstep and emtol are the relevant parameters. Setting nsteps is the maximum
amount of steps allowed; I don't think there is a way (or a reason) to force EM
to run to 10,000 steps.
-How to prevent clashes, maybe there are some settings to try with
genbox -cp -cs command?
You could use genbox, but often what happens is there are substantial voids
between the peptide and lipids. Water seeps in and you have to equilibrate for
a lot longer. See my tutorial above for more rigorous building methods.
-Justin
Thanks
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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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