Sukesh Chandra Gain wrote:
Dear All,
I have done a simulation (in water) of PfPBGD model protein for 500 ps.
But when I compared the secondary structure of my native protein structure
vs structure after simulation. I observed that lot of unfolding is
happening after simulation.
So, my queries are:
1 Is there any way I can improve my model so that model protein become
stable?
2 Is there any problem with my parameters which i have used for energy
minimization, Position restrained dynamics and final simulation?
3 Can I improve my result changing the parameter files?
what are the changes required?
These are the parameters I have used for different run:
snip
pr.mdp:
title = Yo
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002; ps !
nsteps = 1; total 20 ps.
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb= 1.0
rvdw= 1.4
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
Do not couple solvent and ions separately. Use Protein Non-Protein, and refer
here for more information:
http://wiki.gromacs.org/index.php/Thermostats
snip
full.mdp:
title = Yo
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002; ps !
nsteps = 25 ; total 500 ps.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb= 1.0
rvdw= 1.0
Alright, this confuses me. In your pr.mdp, you used rvdw = 1.4, now it's 1.0.
Which force field are you using? The choice of force field will decide what to
set for these parameters, and your results may depend on you getting this right!
You also did not specify your coulombtype in this .mdp file. I don't know what
the default is, but it may not be PME. Check your mdout.mdp file to verify
this, and if it is not PME, stick with it by actually specifying it in your .mdp
file.
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
Again, same as above.
I expect suggestion from expert.
Do not use the word expect when asking for free help, it can be considered
rude.
-Justin
Thanks,
Sukesh
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--
Justin A. Lemkul
Graduate Research Assistant
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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