<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">Thursday, August 6, 2009 at 11:58:20 AM, </font><font face="Tahoma" size="2"><span style="font-family: times new roman,new york,times,serif;">Nancy <nancy5villa@gmail.com> wrote:</span><br></font><div>> The energies simply do not seem to come down any further within several thousand steps.<br>> <br>> I
start with a .mol2 file which contains the structure of ethylene glycol
(ethanediol).<br>> These are the commands that I use to set up and run the
minimisation:<br>
> <br>> $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6<br>> <br>> the above command outputs the following files:<br>> <br>> ethanediol.gro<br>> ethanediol.log<br>> ethanediolMOL.mol2<br>
> ethanediol.top<br>> ffethanediol.itp<br>> posreethanediol.itp<br><br>Those are the correct files to be generated for the topolbuild command given.<br>Are the parameters blank in any of the lines in ethanediol.top? Are there<br>any lines in ethanediol.log that do not involve nonpolar hydrogens that<br>have asterisks instead of parameter values?<br><br>> I then proceed to enlarge the box and solvate the molecule:<br>> <br>> $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5<br>> <br>> $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p ethanediol.top -shell 1<br><br>Is this a shell of solvent around the molecule rather than a box of solvent containing<br>the molecule of interest? How is that to work with vacuum outside the shell?<br><br>> I then use grompp to configure the minimisation:<br>> <br>> $ grompp -f minim.mdp -c ethanediol_box.gro -p ethanediol.top -o em.tpr<br>>
<br>> This is my .mdp file for minimisation:<br>> <br>> ===============================<br>> define = -DPOSRE<br><br>Why position restraints when doing energy minimization?<br><br>>
integrator = steep <br>> emtol = 10.0 <br>> emstep = 0.01 <br>> nsteps = 2000 <br><br>Why so few steps when the emtol is this small. For this emtol, I would expect<br>to need 10000 to 20000 steps.<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>> nstxout = 1<br>> nstvout = 1<br>> nstenergy = 1<br>> nstlog = 1<br>> nstcomm = 1<br>> Tcoupl = no<br>>
Pcoupl = no<br>> gen_vel = no<br>> ===============================<br><br>I've been told that the last three lines are not needed for energy minimization.<br><br>> $ mdrun -v -deffnm em<br>> <br>> the minimisation runs without error and these are the last few lines of output:<br>> <br>> ===========================================<br>>
Step= 1990, Dmax= 1.1e-05 nm, Epot= -1.76427e+04 Fmax= 1.25524e+04, atom= 304<br>> Step= 1991, Dmax= 1.3e-05 nm, Epot= -1.76433e+04 Fmax= 3.13881e+04, atom= 484<br>> Step= 1992, Dmax= 1.6e-05 nm, Epot= -1.76443e+04 Fmax= 2.11785e+04, atom= 484<br>>
Step= 1993, Dmax= 1.9e-05 nm, Epot= -1.76445e+04 Fmax= 4.22489e+04, atom= 484<br>> Step= 1994, Dmax= 2.3e-05 nm, Epot= -1.76456e+04 Fmax= 3.33021e+04, atom= 484<br>> Step= 1996, Dmax= 1.4e-05 nm, Epot= -1.76468e+04 Fmax= 1.26110e+04, atom= 304<br>>
Step= 1997, Dmax= 1.6e-05 nm, Epot= -1.76474e+04 Fmax= 3.81619e+04, atom= 484<br>> Step= 1998, Dmax= 2.0e-05 nm, Epot= -1.76486e+04 Fmax= 2.68240e+04, atom= 484<br>> Step= 2000, Dmax= 1.2e-05 nm, Epot= -1.76496e+04 Fmax= 1.26501e+04, atom= 304<br>
> <br>> writing lowest energy coordinates.<br>> <br>> Steepest Descents did not converge to Fmax < 10 in 2001 steps.<br>> Potential Energy = -1.7649566e+04<br>> Maximum force = 1.2650057e+04 on atom 30<br>> Norm of force = 1.7544460e+03<br>>
===========================================<br>> <br>> If
I proceed to equilibration after doing the above, the water molecules
simply fly apart<br>> (although not immediately). Additionally, it seems
that there are no interactions between<br>> the waters during equilibration.<br><br>Really no point in proceeding further until the energy minimization issues are solved.<br>
<br>> I have tried to run the minimisation for a larger number of steps,
but it does not help.<br>> I have also tried to delete individual water
molecules from the structure files, but doing<br>> so simply causes the
minimisation to "fixate" on another two molecules. I am not sure<br>> what
values of the energies are reasonable for this system, and how to
minimise it further. <br>> Please advise.<br><br>I've never used the -shell with genbox and don't know what effect that would have on<br>energy minimization.<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<br><br></div><br>
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