Hi!<br>I have an issue with my protein modelling. I find that some of the helices (not all) have greatly unfolded during a 8ns distance restrained MD run. I am using the parameters below for the MD run. Is there any thing that can treat the system better than PME?<br>
thanks<br>Jayant James<br><br>title               =  Yo<br>cpp                 =  /usr/bin/cpp<br>define              = -DDISRES<br>constraints         =  none<br>;constraint_algorithm =  lincs<br>;lincs_order         =  4<br>
integrator          =  md<br>dt                  =  0.001    ; ps !<br>nsteps              =  1000000  ; total 1.0ns.<br>nstcomm             =  1<br>nstxout             =  5000<br>nstvout             =  5000<br>nstfout             =  5000<br>
nstlog              =  5000<br>nstenergy           =  500<br>nstlist             =  10<br>ns_type             =  grid<br>rlist               =  1.0<br>coulombtype         =  PME<br>rcoulomb            =  1.0<br>vdwtype             =  cut-off<br>
rvdw                =  1.4<br>fourierspacing      = 0.12<br>fourier_nx          = 0<br>fourier_ny          = 0<br>fourier_nz          = 0<br>pme_order           = 4<br>ewald_rtol          = 1e-5<br>optimize_fft        = yes<br>
disre               =  simple<br>disre_weighting     =  equal<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl              =  V-rescale<br>tc-grps             =  tnc Non-Protein tnt NMR tni<br>tau_t               =  0.1 0.1 0.1 0.1 0.1<br>
ref_t               =  300 300 300 300 300<br>; Energy monitoring<br>energygrps          = Protein Non-Protein<br>;tnc Non-Protein tnt NMR tni<br>; Pressure coupling is not on<br>Pcoupl              =  parrinello-rahman<br>
tau_p               =  0.5<br>compressibility     =  4.5e-5<br>ref_p               =  1.0<br>; Generate velocites is on at 300 K.<br>gen_vel             =  yes<br>gen_temp            =  300.0<br>gen_seed            =  173529<br>
<br clear="all"><br>-- <br>Jayasundar Jayant James<br><br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br><br>