Hi, all:<br>I got the initial structure of a DPPC bilayer from Dr. Karttunen's website, use the parameters (hopefully) from their paper: Patra, Karttunen, Hyvönen, Falck, Lindqvist, Vattulainen,
Biophys. J. <b>84</b>, 3636-3645 (2003) to run for 100ns then replace some DPPC molecules with cholesterols, do the energy minimization, run for 20ns and the cholesterols are distorted as shown in the attached file.<br>
<br>Here are parameters for the pure DPPC run which I deem important:<br><br>nstcomm = 1<br>comm_grps = DPPC SOL<br>nstlist = 10 <br>ns_type = grid<br>pbc = xyz<br>
rlist = 1.0 <br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = Cutoff<br>rvdw = 1.0<br>ewald_rtol = 1e-5<br>
optimize_fft = yes<br>tcoupl = Berendsen<br>tau_t = 0.1 0.1<br>tc_grps = DPPC SOL<br>ref_t = 323 323<br>pcoupl = Berendsen<br>
pcoupltype = semiisotropic<br>tau_p = 1 1 <br>compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0 <br>gen_vel = yes<br>gen_temp = 325<br>
gen_seed = 173529<br>constraints = all-bonds<br>constraint_algorithm = LINCS<br>lincs_order = 4<br><br>For the DPPC-CHOL combined system I only changed corresponding sections to:<br>
<br>comm_grps = DPPC CHOL SOL<br>tau_t = 0.1 0.1 0.1<br>
tc_grps = DPPC CHOL SOL<br>
ref_t = 323 323 323<br><br>Any suggestion is appreciated. Thank you.<br><br>Jian<br>