[gmx-users] Peptide denaturation

ingemar andre ingemar.andre at bpc.lu.se
Mon Jul 22 23:47:28 CEST 2002


I am trying to simulate a small (20 residue) peptide in water + 1M salt. I have little experience of md simulations but to me it is clear that the result of the simulation is unreasonable. The starting structure is an alfa-helix and the peptide is
unstructured in solution so there will be a denaturation of the peptide during the simualtion. I have performed a 20 ns simulation and a number of things tell me that there is something fishy going on:

1)  The gyration radius: The gyration radius in the x, y, z direction never coincide. First two components say x and y have similar values with z much higher (this is can be explained by rotation in the xy plane). Then x and z are the same with the y much
higher (the peptide flips) but the total gyration radius goes down.

2) The autocorrelation function of the gyration radius: Starting from a high value the correlation function is negative for 75% of the time. x y and z components never coincide.

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.

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.



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
tel. +46 46 222 82 38
fax. +46 46 222 45 43
Ingemar.Andre at bpc.lu.se

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