[gmx-users] Peptide denaturation

[David van der Spoel]

On Mon, 22 Jul 2002, ingemar andre wrote:

>3) Visual inspection of the simulation: Band structure of the ions. Ions with the same charge appear in rows as it appears during the whole simulation. Also there is a large space close to the peptide where no ions enter during the simulation (where water
>is present). It is basically only sidechains that rotates, the whole peptide does not rotate to any conciderable extent.
>
>Basically I have simulated the peptide with scripts of the tutorial
>ribonuclease s-peptide with some minor modifications. I have added ions
>and counterions to the peptides with genion (23 Na and 29 Cl) whose
>positions were randomized.
>
It sounds like you are running with position restraints on the peptide.
Also, if you use salt you need to use PME.


Either I have done some elementary mistake here or the simualtion as such is not trustworthy. Does anyone have an idea ? Below  you find my mdp file.
>
>Regards,
>
>Ingemar
>
>title               =  Peptide_1M_salt
>cpp                 =  /lib/cpp
>constraints         =  all-bonds
>integrator          =  md
>dt                  =  0.002    ;
>nsteps              =  5000000   ;
>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
>; Berendsen temperature coupling is on in two groups
>Tcoupl              =  berendsen
>tc-grps             =  Protein  SOL       Cl      Na
>tau_t               =  0.1      0.1            0.1      0.1
>ref_t               =  300      300          300      300
>; Energy monitoring
>energygrps          =  Protein  SOL      Cl      Na
>; Isotropic pressure coupling is now on
>Pcoupl              =  berendsen
>Pcoupltype          = isotropic
>tau_p               =  0.5
>compressibility     =  4.5e-5
>ref_p               =  1.0
>; Generate velocites is off at 300 K.
>gen_vel             =  no
>gen_temp            =  300
>gen_seed            =  173529
>
>
>--
>______________________________________________________________________
>
>Ingemar André
>Department of Biophysical Chemistry
>Lund University
>Box 124 SE - 221 00 Lund Sweden
>http://www.bpc.lu.se/
>tel. +46 46 222 82 38
>fax. +46 46 222 45 43
>Ingemar.Andre at bpc.lu.se
>______________________________________________________________________
>
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++