Dear David, Thanks for the reply, guess i will do some literature survey and see if i can find some validated urea parameters.<br><br>karan<br><br><div class="gmail_quote">On Mon, Sep 21, 2009 at 8:51 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">karan syal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin,<br>
<br>
Thanks for the reply!<br>
<br>
I will surely try minimize the protein in Vacuum and then try adding Urea again.<br>
<br>
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.<br>
<br>
</blockquote></div>
Don't use the Urea topology that is in the gromacs distribution. It is not based on any force field known to man.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thanks again,<br>
<br>
cherrz<br>
karan<div><div></div><div class="h5"><br>
<br>
On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
karan syal wrote:<br>
<br>
Dear Gromacs users,<br>
<br>
I am trying to run a urea+protein simulation and encountering a<br>
few problems at various stages.<br>
<br>
I have taken an equilibrated 10M urea box of size<br>
2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea +<br>
398 SOL, ran NPT @ 1 bar and 300K)<br>
<br>
I am using this equilibrated box to add to a globular protein of<br>
about 250 residues using following commands :<br>
<br>
<br>
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<br>
volume, for 10M urea the number of urea above box should add is<br>
2448.)<br>
<br>
genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro (*This adds 2064 Urea only, shouldnt it be adding 2448 urea<br>
molecules, corresponding to 10M urea box i have solvated with??)*<br>
<br>
<br>
No, it shouldn't. The protein occupies space within that volume, as<br>
well.<br>
<br>
<br>
<br>
When i try to minimize this using the following em.mdp<br>
<br>
<br>
cpp = /usr/bin/cpp<br>
constraints = none<br>
integrator = steep<br>
nsteps = 5000<br>
coulombtype = PME<br>
pme_order = 4<br>
nstlist = 5<br>
ns_type = grid<br>
rlist = 1.0<br>
rcoulomb = 1.0<br>
rvdw = 1.0<br>
Tcoupl = no<br>
Pcoupl = no<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; Energy minimizing stuff<br>
;<br>
emtol = 100<br>
emstep = 0.01<br>
<br>
<br>
*It gives me the following output*<br>
<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+02<br>
Number of steps = 5000<br>
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727<br>
which is larger than the 1-4 table size 2.000 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
<br>
t = 0.015 ps: Water molecule starting at atom 34477 can not be<br>
settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 100<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy, or turn<br>
off constraints alltogether (set constraints = none in mdp file)<br>
<br>
writing lowest energy coordinates.<br>
<br>
Steepest Descents converged to machine precision in 34 steps,<br>
but did not reach the requested Fmax < 100.<br>
Potential Energy = -1.3092671e+22<br>
Maximum force = inf on atom 12598<br>
Norm of force = inf<br>
<br>
gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)<br>
<br>
<br>
<br>
/When i look at the file in VMD, the protein is completely out<br>
of the box + There are unusual bonds between a lot of UREA and<br>
SOL molecules/. ( The unusual bonds are artifcats after<br>
minimization which are not there when i initially look at my<br>
P48_10Mrea.gro, that is the gro generated after genbox wth -cs<br>
as 10M urea)<br>
<br>
<br>
"Out of the box" doesn't exist for a periodic system. The "bonds"<br>
you see are also *not* generated by Gromacs, but are also just an<br>
artefact of visualization. Bonds are not created or broken in<br>
molecular mechanics.<br>
<br>
<br>
I tried constraining hbonds as well in em.mdp bit to no effect.<br>
<br>
<br>
I used the above em.gro to run a production run, with following<br>
pr.mdp<br>
<br>
<br>
Don't, it's a waste of time. Never just plow ahead when something<br>
isn't working. There is something unreasonable about the starting<br>
structure. Try minimizing the protein in vacuo first, then add your<br>
urea and try EM again.<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font><div>
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