On 28/01/2011 3:51 PM, shahid nayeem wrote:
Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.
You've set up a system that isn't stable, but we don't have enough
information to have any idea why. "I tried with new box size" doesn't go
close to describing your method in enough detail for anyone to know
where you went wrong.
See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for
generic tips
Mark
Please help.
shahid Nayeem
On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul<jalem...@vt.edu> wrote:
shahid nayeem wrote:
Dear All
I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.
Original messge:
I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a box
size of 6x6x6. Energy minimization, simulated annealing (Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly. But finally I get a box where all water
molecules get accumulated in two three small region within the box and
all chaps molecules gets accumulated in another small regions.I wanted
near random uniform distribution of chaps in water. Any help from
user, where I am wrong and what should I do.
Reply to query.
I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
–ci 7 chaps.gro).Then I solvated the output box with genbox using
-maxsol 500 and spc216.gro. On visualization, at this stage itself
uniform solvation did not occur (I got water in one region and chaps
molecule in other region) but I observed a similar situation while
If your box was not completely solvated, then don't use -maxsol. A box of
6x6x6 nm should require more than 500 molecules of water to fill. If you're
trying to achieve some specific mole fraction or concentration, then
re-figure your box size.
-Justin
preparing 10M urea salvation box. This was followed by 1ns simulated
annealing from temp 300K to 0K and pressure 100 bar, then 1ns
simulated annealing from temp. 0k to 300k and then ins equilibriation
at this temperature. In case of urea finally I got uniformly solvated
urea_water_box but in chaps I couldn’t get it.
Shahid Nayeem
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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