I have attempted to perform energy minimisation from scratch again, and these are the commands that I am using to do so:<br><br>$ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6<br>
<br>which generates the files:<br><br>ethanediol.gro<br>ethanediol.log<br>ethanediolMOL.mol2<br>ethanediol.top<br>ffethanediol.itp<br>posreethanediol.itp<br><br>in the "ethanediol.log" file I noticed the following lines with asterisks:<br>
<br>========================================<br> Angles Force Field Results<br>Angle Atoms force angle method measured<br> 1 H12- C1- H11 ****** ****** ****** 109.403<br> 2 C2- C1- H11 ****** ****** ****** 109.456<br>
3 O1- C1- H11 ****** ****** ****** 109.438<br> 4 C2- C1- H12 ****** ****** ****** 109.537<br> 5 O1- C1- H12 ****** ****** ****** 109.468<br> 6 O1- C1- C2 320.0 109.50 1 109.526<br>
7 C1- C2- O2 320.0 109.50 1 109.526<br> 8 C1- C2- H22 ****** ****** ****** 109.453<br> 9 C1- C2- H21 ****** ****** ****** 109.537<br> 10 H22- C2- O2 ****** ****** ****** 109.439<br>
11 H21- C2- O2 ****** ****** ****** 109.468<br> 12 C2- O2- HO2 450.0 109.50 1 106.864<br> 13 H21- C2- H22 ****** ****** ****** 109.404<br> 14 C1- O1- HO1 450.0 109.50 1 106.864<br>
========================================<br><br>I then enlarge the box and solvate the molecule:<br><br>$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 3 3 3 -c<br><br>$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top -box 3 3 3<br>
<br>There are 2679 atoms (891 waters and 1 ethanediol). I then configure the minimisation with grompp:<br><br>$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr<br><br>using the following .mdp file:<br>
<br>========================================<br>define = -DFLEXIBLE<br>integrator = steep<br>emtol = 10.0<br>emstep = 0.1<br>nsteps = 15000<br><br>nstlist = 1<br>ns_type = grid<br>
rlist = 1.0<br>coulombtype = PME<br>rcoulomb_switch = 1.0<br>rvdw_switch = 1.3<br>pbc = xyz<br><br>pme_order = 4<br>constraints = none<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 then run the simulation for 15,000 steps:<br><br>$ mdrun -v -deffnm em<br>
<br>the last few lines of output are as follows:<br><br>========================================<br>Step=14991, Dmax= 5.3e-06 nm, Epot= -6.24538e+04 Fmax= 2.50258e+04, atom= 2397<br>Step=14992, Dmax= 6.4e-06 nm, Epot= -6.24539e+04 Fmax= 3.52982e+04, atom= 1171<br>
Step=14993, Dmax= 7.6e-06 nm, Epot= -6.24540e+04 Fmax= 3.71731e+04, atom= 2397<br>Step=14994, Dmax= 9.2e-06 nm, Epot= -6.24540e+04 Fmax= 4.93409e+04, atom= 1171<br>Step=14995, Dmax= 1.1e-05 nm, Epot= -6.24541e+04 Fmax= 5.53109e+04, atom= 2397<br>
Step=14997, Dmax= 6.6e-06 nm, Epot= -6.24546e+04 Fmax= 8.50832e+03, atom= 1171<br>Step=14998, Dmax= 7.9e-06 nm, Epot= -6.24547e+04 Fmax= 6.37691e+04, atom= 2397<br>Step=14999, Dmax= 9.5e-06 nm, Epot= -6.24553e+04 Fmax= 2.67488e+04, atom= 1171<br>
Step=15000, Dmax= 1.1e-05 nm, Epot= -6.24548e+04 Fmax= 8.09451e+04, atom= 2397<br>writing lowest energy coordinates.<br><br>Steepest Descents did not converge to Fmax < 10 in 15001 steps.<br>Potential Energy = -6.2455254e+04<br>
Maximum force = 2.6748828e+04 on atom 1171<br>Norm of force = 9.5851715e+02<br>========================================<br><br>After viewing the trajectory with ngmx, I noticed that most of the motion of the water molecules occurs within the first 50 picoseconds.<br>
<br>Please advise on how to further minimise this system.<br><br>Thank you.<br><br>Nancy<br><br><br><br><br><div class="gmail_quote">On Thu, Aug 6, 2009 at 2:23 PM, Bruce D. Ray <span dir="ltr"><<a href="mailto:brucedray@yahoo.com">brucedray@yahoo.com</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><div style="font-family: times new roman,new york,times,serif; font-size: 10pt;"><div class="im">
<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 <<a href="mailto:nancy5villa@gmail.com" target="_blank">nancy5villa@gmail.com</a>> wrote:</span><br>
</font></div><div><div class="im">> 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></div>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?<div class="im"><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></div>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?<div class="im">
<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></div>Why position restraints when doing energy minimization?<div class="im"><br><br>
>
integrator = steep <br>> emtol = 10.0 <br>> emstep = 0.01 <br>> nsteps = 2000 <br><br></div>Why so few steps when the emtol is this small. For this emtol, I would expect<br>to need 10000 to 20000 steps.<div class="im">
<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></div>I've been told that the last three lines are not needed for energy minimization.<div class="im"><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></div>Really no point in proceeding further until the energy minimization issues are solved.<div class="im"><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></div>I've never used the -shell with genbox and don't know what effect that would have on<br>energy minimization.<br><br>
</div><div class="im">-- <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></div><br>
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