[gmx-users] Re: Why potential energy not in negative value?

[shika]

Hi Justin,

Thanks for your explaination..First of all i got the HFIP topology from
this site which prof Alan give it to me

compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files

Due to before this when i create the structure by using packmol and run it
using gromacs the forcefield that i used is gromos not recognize the F
atom.Thats y i use prof alan suggestion..If i use the prodrg server its
just the united atom and what i need is all atom.

I already discuss with my senior she said that i need to increase the emtol
and also the emsteep.From what i understand the lower emtol is the best for
minimization part.I'm still cant minimize it with the value pe that i
satisfied with..

So can i just proceed with the heating part and then try the equilibration
or not?i wont gve the negative impact for my system right?

Thanks


On Wednesday, October 31, 2012, Justin Lemkul [via GROMACS] <
ml-node+s5086n5002489h43 at n6.nabble.com> wrote:
>
>
> On 10/31/12 4:10 AM, Nur Syafiqah Abdul Ghani wrote:
>> Dear All,
>>
>> Currently I'm doing the minimization part for my solvent which is
>> hexafluoroisopropanol with water.
>> I'm packing them with packmol then use the forcefield gromos96.
>> Now  by using the command
>> grompp -f em1.mdp -c minimize_301012.gro -p topol.top -o
minimize_311012.tpr
>> mdrun -deffnm minimize_311012 -v
>>
>> And its give the result as follow :
>>
>> writing lowest energy coordinates.
>>
>> Back Off! I just backed up minimize_311012.gro to
./#minimize_311012.gro.3#
>>
>> Steepest Descents converged to Fmax < 15 in 36 steps
>> Potential Energy  =  1.88042503678994e+05
>> Maximum force     =  1.46843345643871e+01 on atom 30092
>> Norm of force     =  1.94397813942079e+00
>>
>>
>> I already minimize it with the bigger step that use about 10ns.
>> Next I increase the step which take about 15ns and the result show
>> same as above..
>>
> Note that EM is not run in time, so your settings below are misleading.
 The
> only settings that matter are nsteps and emstep; dt is ignored completely
when
> running EM.  Note that your cutoff settings are incorrect for Gromos96,
as you
> say you are using.  How did you generate the HFIP topology?
>
> The positive potential indicates that your system has a net repulsive
energy, so
> the configuration isn't very happy.  The maximum force is very good, but
there
> may be unsatisfied interactions that yield the positive energy.  Perhaps a
> gentle equilibration will resolve the situation.
>
> -Justin
>
>> My mdp file was like this :
>>
>> ;
>> ;       Preprocessing
>> title                    = STEEP
>> cpp                      = /usr/bin/cpp
>> include                  = -I/usr/local/gromacs/share/gromacs/top
>> define                   = -DFLEXIBLE
>> ;
>> ;       Run Control
>> ;
>> integrator               = steep
>> nsteps                   = 75000000 ; 75000000 * 0.2 = 15000 ps = 15 ns
>> dt = 0.0002 ; 0.2 fs
>> ;
>> ; Energy Minimization
>> emstep                   = 0.0001 ; used with steep
>> emtol                    = 15
>> nstcgsteep               = 500 ; do a steep every 10 steps of cg
>> energygrps               = System
>> ;
>> ;       Neighbor Searching
>> nstcomm                  = 1
>> nstlist                  = 10
>> ns_type                  = grid
>> pbc                      = xyz
>> rlist                    = 1.2
>> ;
>> ; Electrostatics
>> coulombtype              = pme
>> rcoulomb                 = 1.2
>> rcoulomb-switch          = 0
>> vdw-type                 = cut-off
>> rvdw                     = 1.2
>> rvdw-switch              = 0
>> fourierspacing = 0.2
>> ;
>> ; Output Control
>> nstenergy = 10
>> optimize_fft = yes
>> ;
>> ;       OPTIONS FOR BONDS
>> ; OPTIONS FOR BONDS
>> constraints              = none
>>
>>
>> Is the potential energy need to be in negative value for my simulation?
>> What happened if it not in negative value?Can I just proceed to the
>> next step for equilibration?
>> I already find and read the paper that relate to my simulation and
>> they did not mention the energy that they got from their
>> experiment.
>>
>> Thanks in advance u guys,
>> --
>> Best Regards,
>>
>> Nur Syafiqah Abdul Ghani,
>> Theoretical and Computational Chemistry Laboratory,
>> Department of Chemistry,
>> Faculty of Science,
>> Universiti Putra Malaysia,
>> 43400 Serdang,
>> Selangor.
>> 013-7188131
>> alternative email : [hidden email]
>>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : syafiqahabdulghani at gmail.com




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