[gmx-users] Unstable model : need suggesstion

[Justin A. Lemkul]

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              =  10000	; 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              =  250000	; 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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-- 
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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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