<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><span style="font-family: times new roman,new york,times,serif;">On </span><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2">Wednesday, August 5, 2009 at 6:03:51 PM</font><span style="font-family: times new roman,new york,times,serif;">, </span><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2"><span style="font-family: times new roman,new york,times,serif;">Nancy <</span><span style="border-bottom: 1px dashed rgb(0, 102, 204); cursor: pointer; font-family: times new roman,new york,times,serif;" class="yshortcuts" id="lw_1249510067_0">nancy5villa@gmail.com</span><span style="font-family: times new roman,new york,times,serif;">> wrote:</span><br></font>> I was trying to run equilibration on my solvated ethylene glycol
system. However, the<br>> system seems to be "exploding". I believe this
is due to inadequate energy minimisation,<br>> however, I am unable to
minimise my system any further. I am using the following .mdp<br>> file
"minim.mdp" for minimsation:<br>
> <br>> ==============================<br>> define = -DFLEXIBLE<br>> integrator = steep<br>> emtol = 1000.0<br>> emstep = 0.5<br>> nsteps = 1000<br><br>I use more steps than 1000 (may want 10000) with:<br> emstep = 0.01<br> nstcomm = 1<br> Tcoupl = no<br> Pcoupl = no<br>
gen_vel = no<br><br>> <br>> nstlist = 1<br>> ns_type = grid<br>> rlist = 1.0<br>>
coulombtype = PME<br>> rcoulomb = 1.0<br>> rvdw = 1.3<br>> pbc = xyz<br>> <br>> pme_order = 4<br>> constraints = none<br>> ==============================<br>> <br>> I
process it with grompp, where "ethanediol_solv.gro" is the solvated
system,<br>> and "ethanediol.top" is the topolgy generated with topolbuild:<br>
> <br>> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr<br>> <br>> I then run it:<br>> <br>> $ mdrun -v -deffnm em<br>> <br>> mdrun outputs the following information:<br>> <br>> ==============================<br>> Steepest Descents did not converge to Fmax < 1000 in 1001 steps.<br>>
Potential Energy = -6.7546914e+03<br>> Maximum force = 2.7262363e+04 on atom 34<br>> Norm of force = 2.5032930e+03<br>> ==============================<br>> <br>> I
have viewed the output trajectory of the minimisation and I can see
that the<br>> waters do not move much. I am wondering if there is a way to
let solvent water<br>> molecules move about during minimsation, and/or how
to remove some of them. <br>> I am also unsure what value of emtol is
reasonable for this type of small system.<br>
<div><br>I use the same value of emtol, but that's just based on examples I've seen where<br>others have used that value.<br><br><br></div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist, and Operations Director<br>NMR Center<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<div><br></div><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><div style="font-family: times new roman,new york,times,serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><b><span style="font-weight: bold;">From:</span></b> Nancy <nancy5villa@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, August 5, 2009 6:03:51 PM<br><b><span style="font-weight:
bold;">Subject:</span></b> [gmx-users] Energy Minimisation Values<br></font><br><br>
</div></div></blockquote></div><br>
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