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). 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>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>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>
integrator = steep <br>emtol = 10.0 <br>emstep = 0.01 <br>nsteps = 2000 <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>$ 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 (although not immediately). Additionally, it seems that there are no interactions between the waters during equilibration.<br>
<br>I have tried to run the minimisation for a larger number of steps, but it does not help. I have also tried to delete individual water molecules from the structure files, but doing so simply causes the minimisation to "fixate" on another two molecules. I am not sure what values of the energies are reasonable for this system, and how to minimise it further. Please advise.<br>
<br>Thank you.<br><br><br>Nancy<br><br><br><br><div class="gmail_quote">On Thu, Aug 6, 2009 at 8:38 AM, 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><div></div><div class="h5"><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); font-family: times new roman,new york,times,serif;"><span style="border-bottom: 1px dashed rgb(0, 102, 204); background: transparent none repeat scroll 0% 50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"><a href="mailto:nancy5villa@gmail.com" target="_blank">nancy5villa@gmail.com</a></span></span><span style="font-family: times new roman,new york,times,serif;">> wrote:<br>
> </span></font>I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started<br>> with an ethanediol mol2 file from which
topolbuild generated various files. I used editconf<br>> to enlarge to box
of the "ethanediol.gro" file:<br>
> <br>> $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5<br>> <br>> and then I used genbox to solvate it:<br>> <br>> $ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o ethanediol_solv.gro -p ethanediol.top<br>
> <br>>
I ran energy minimisation on it:<br>> <br>> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr<br>> <br>> my minim.mdp file is:<br>> <br>> ==========================<br>> define = -DFLEXIBLE<br>
> integrator = steep<br>>
emtol = 1000.0<br>> emstep = 0.01<br>> nsteps = 5000<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>> nstxout = 1<br>> nstvout = 1<br>> nstenergy = 1<br>> nstlog = 1<br>> ==========================<br>> <br>
> $ mdrun -v -deffnm em<br>> <br>> and the energies converge (although I think that the values are still too large for this system):<br>
> <br>> ==========================<br>> Steepest Descents converged to Fmax < 1000 in 12 steps<br>> Potential Energy = -1.1206108e+04<br>> Maximum force = 9.4016180e+02 on atom 31<br>> Norm of force = 3.4989252e+02<br>
> ==========================<br>
<br></div></div>{remainder snipped}<br><br>The energies do seem large. What happens if you do energy minimization<br>with emtol = 10.0 ?<br><br><br>-- <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 <<a href="mailto:nancy5villa@gmail.com" target="_blank">nancy5villa@gmail.com</a>><br>
<b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, August 5, 2009 10:28:47 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Energy Minimisation and Equilibration Problems</font><br>
</div></div></blockquote></div><br>
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