[gmx-users] parameters of em.mdp
ahmedo047 at gmail.com
Fri Mar 23 19:42:39 CET 2012
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
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 ;
>> 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:
> 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
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