[gmx-users] Energy Minimisation Values

[Mark Abraham]

Bruce D. Ray wrote:
> On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy <nancy5villa at gmail.com> wrote:
>> I was trying to run equilibration on my solvated ethylene glycol
> system.  However, the
>> system seems to be "exploding".  I believe this
> is due to inadequate energy minimisation,
>> however, I am unable to
> minimise my system any further.  I am using the following .mdp
>> file
> "minim.mdp" for minimsation:
>> ==============================
>> define        = -DFLEXIBLE
>> integrator    = steep
>> emtol        = 1000.0
>> emstep          = 0.5
>> nsteps        = 1000
> 
> I use more steps than 1000 (may want 10000) with:
>      emstep               =  0.01
>      nstcomm            =  1
>      Tcoupl               =  no
>      Pcoupl               =  no
>      gen_vel             =  no

These last three are not relevant for energy minimization. There are no 
velocities, so they can't be generated, and thus there's no temperature 
or pressure. nstcomm is probably moot or ignored.

Mark

>> nstlist        = 1
>> ns_type        = grid
>> rlist        = 1.0
>>
> coulombtype    = PME
>> rcoulomb    = 1.0
>> rvdw        = 1.3
>> pbc        = xyz
>>
>> pme_order    = 4
>> constraints     = none
>> ==============================
>>
>> I
> process it with grompp, where "ethanediol_solv.gro" is the solvated
> system,
>> and "ethanediol.top" is the topolgy generated with topolbuild:
>>
>> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
>>
>> I then run it:
>>
>> $ mdrun -v -deffnm em
>>
>> mdrun outputs the following information:
>>
>> ==============================
>> Steepest Descents did not converge to Fmax < 1000 in 1001 steps.
>>
> Potential Energy  = -6.7546914e+03
>> Maximum force     =  2.7262363e+04 on atom 34
>> Norm of force     =  2.5032930e+03
>> ==============================
>>
>> I
> have viewed the output trajectory of the minimisation and I can see
> that the
>> waters do not move much.  I am wondering if there is a way to
> let solvent water
>> molecules move about during minimsation, and/or how
> to remove some of them. 
>> I am also unsure what value of emtol is
> reasonable for this type of small system.
> 
> 
> I use the same value of emtol, but that's just based on examples I've seen where
> others have used that value.
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php