[gmx-users] Re: protein unfolding

[Xavier Periole]

>constraints         =  all-bonds
>integrator          =  md
>dt                  =  0.002	; ps !
>nsteps              =  5000000	
>nstcomm             =  1
>nstxout             =  5000
>nstvout             =  0
>nstfout             =  0
>nstlist             =  10
>ns_type             =  grid
>rlist               =  1.0
>rcoulomb            =  1.0
>rvdw                =  1.0
>  
>
rlist = 0.8
rcoulomb = 1.4
rvdw = 1.4
This si the way Gromos force field have been parametrized.
may be nstlist = 5

>; Berendsen temperature coupling is on in two groups
>Tcoupl              =  berendsen
>tau_t               =  0.1	     0.1
>tc-grps		    =  protein	     sol
>ref_t               =  300	     300
>; Generate velocites is on at 300 K.
>gen_vel             =  yes
>gen_temp            =  300.0
>gen_seed            =  173529
>
>  
>
No pressure coupling ??

>shoud i use PME for coulomb interactions?
>  
>
No !! I would first try to find out why your protein is falling apart.
After that this is a matter of choice, your's actually.

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
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