karan syal wrote:
Dear Justin,
Thanks for the reply!
I will surely try minimize the protein in Vacuum and then try adding
Urea again.
Just that i was wondering how will that effect my artifact bonds which
are between Urea and Water, and not at all between any Protein atom and
Urea/Sol?? As i mentioned earlier, these bonds are formed only after
minimization, they are not present before adding 10M urea+water box (No
such bonds in its individual 10M urea+water .gro either ) to protein,
they are neither there in the before minimized protein+10M urea+water
system.
Don't use the Urea topology that is in the gromacs distribution. It is
not based on any force field known to man.
Thanks again,
cherrz
karan
On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
karan syal wrote:
Dear Gromacs users,
I am trying to run a urea+protein simulation and encountering a
few problems at various stages.
I have taken an equilibrated 10M urea box of size
2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea +
398 SOL, ran NPT @ 1 bar and 300K)
I am using this equilibrated box to add to a globular protein of
about 250 residues using following commands :
editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron
(Giving me a dodecahedron with Vol = 407.98nm^3, so for this
volume, for 10M urea the number of urea above box should add is
2448.)
genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro
(*This adds 2064 Urea only, shouldnt it be adding 2448 urea
molecules, corresponding to 10M urea box i have solvated with??)*
No, it shouldn't. The protein occupies space within that volume, as
well.
When i try to minimize this using the following em.mdp
cpp = /usr/bin/cpp
constraints = none
integrator = steep
nsteps = 5000
coulombtype = PME
pme_order = 4
nstlist = 5
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; Energy minimizing stuff
;
emtol = 100
emstep = 0.01
*It gives me the following output*
Steepest Descents:
Tolerance (Fmax) = 1.00000e+02
Number of steps = 5000
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727
which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
t = 0.015 ps: Water molecule starting at atom 34477 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Stepsize too small, or no change in energy.
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.
Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -1.3092671e+22
Maximum force = inf on atom 12598
Norm of force = inf
gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)
/When i look at the file in VMD, the protein is completely out
of the box + There are unusual bonds between a lot of UREA and
SOL molecules/. ( The unusual bonds are artifcats after
minimization which are not there when i initially look at my
P48_10Mrea.gro, that is the gro generated after genbox wth -cs
as 10M urea)
"Out of the box" doesn't exist for a periodic system. The "bonds"
you see are also *not* generated by Gromacs, but are also just an
artefact of visualization. Bonds are not created or broken in
molecular mechanics.
I tried constraining hbonds as well in em.mdp bit to no effect.
I used the above em.gro to run a production run, with following
pr.mdp
Don't, it's a waste of time. Never just plow ahead when something
isn't working. There is something unreasonable about the starting
structure. Try minimizing the protein in vacuo first, then add your
urea and try EM again.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
