Moutusi Manna wrote:
Dear Justin,
i am trying to insert a peptide in trans-bialyer
orientation into a pre-equilibrated POPC bilayer using *inflategro*
<http://moose.bio.ucalgary.ca/files/inflategro> script. After 13 steps
of compression, the area per lipid is 2.61956768363491 nm^2, whereas the
desired area per lipid is 0.658 nm^2. But when i try to energy minimize
the compressed structure after 13th steps of compression, the energy did
not converged and give the following errors. During em i use strong
position restraints on peptide heavy atom using force constants of 100000.
------------------------------
perl inflategro em_13.gro 0.95 POPC 0 com_13.gro 5 area_lip.dat
grompp -f enermin.mdp -c com_13.gro -p system.top -o em_14.tpr
mdrun -s em_14.tpr -nice 4 -o em_14 -c em_14 -e em_14 -g em_14&
Reading file em_14.tpr, VERSION 3.3.1 (single precision)
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
<snip>
From the LINCS warnings, you have a nice listing of where problems are
occurring in terms of atom numbers. Have a look at the structure and see what's
causing the clash; that may help in diagnosing what's going wrong.
Steepest Descents converged to machine precision in 43 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -1.2865473e+05
Maximum force = 4.7082656e+04 on atom 547
Norm of force = 6.7057188e+04
<snip>
---------------
should i continue further compression with this energy minimized
structure (em_14.gro)??
Try it and see. The forces don't look astronomical (they're high, but perhaps
further EM can resolve them). Furthermore, the LINCS warnings didn't indicate
major changes in the constraint lengths.
-Justin
if not how can i slove this problem.
waiting for ur suggestion.
Moutusi Manna
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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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