[gmx-users] parameters of em.mdp

[ahmet yıldırım]

Dear Justin,

Thanks for your reply. You said "....You should avoid ad hoc changes."
You used different parameters for energy minimization at tutorial called
"Tutorial 5: Protein-Ligand Complex".
*a part of your em.mdp*
nstlist = 1
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
*a part of your md.mdp*
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4

Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for
energy minimization?

Thanks in advance

23 Mart 2012 19:31 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I am using the Reaction-Field method for electrostatics interactions. I
>> used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp,
>> npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set
>> nstlist=rlist=rcoulomb=rvdw=1.**0 for energy minimization, would not it
>> be better? What is your suggestions?
>>
>>
> Why do you think making such changes to the cutoffs would be better?
>  These settings, for the most part, are a fixed part of the force field
> you're using. Unless you have proof (either by your own demonstration or
> one that is published) that making such changes result in better results,
> you should avoid ad hoc changes.
>
>  ; Neighbor Searching Parameters
>> nstlist                 = 5 ns-type                 = Grid       pbc
>>            = xyz           rlist                   = 0.9     ;
>> Electrostatics
>> coulombtype             = Reaction-Field rcoulomb                = 1.4
>>       epsilon_rf              = 54           ; VdW
>> vdw-type                = Cut-off         rvdw                    = 1.4
>>         *
>> Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp,
>> npt.mdp and md.mdp) the reference temperature for coupling. I analysed the
>> temperature after production run. I get "Temperature=312.646" (g_energy -f
>> md.edr -o temperature.xvg). that is, The temperature has increased
>> (approximately 12 K) during the simulation. What could be the reason for
>> the increase in temperature? I had setted to 200 K the reference
>> temperature for coupling in pr.mdp. it can cause?
>>
>>
> This outcome is precisely what you would expect, simply because you're
> using the reaction field method and it introduces cutoff artifacts.
>  Interestingly, this same outcome (an increase of exactly 12K) has been
> reported before:
>
> http://lists.gromacs.org/**pipermail/gmx-users/2009-**January/039113.html<http://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
Ahmet Yıldırım
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