[gmx-users] Secondary structure loss in implicit solvent simulations

[K. Singhal]

Hi

I have a question regarding the implicit solvent implementation in GROMACS 4.5.1 (with GPU acceleration). I have been trying to simulate molecules with varying size (PYP with 125 AAs, BBA5 with ~20 AAs, and and Trigger Factor with 432 AAs), but can't seem to be able to maintain the secondary structure in any of them. Can any one suggest a particular set of parameters than need to be taken care of or used with certain fixed values for better results?

While I have used a varied range of values for almost all parameters, here is the list of parameters recently and unsuccessfully used:
   integrator           = sd
   nsteps               = 10000000
   init_step            = 0
   ns_type              = Grid
   nstlist              = 10
   ndelta               = 2
   nstcomm              = 10
   comm_mode            = Linear
   delta_t              = 0.002
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xyz
   bPeriodicMols        = FALSE
   bContinuation        = FALSE
   bShakeSOR            = FALSE
   etc                  = No
   nsttcouple           = -1
   epc                  = No
   epctype              = Isotropic
   nstpcouple           = -1
   tau_p                = 1
   andersen_seed        = 815131
   rlist                = 1.1
   rlistlong            = 2.5
   rtpi                 = 0.05
   coulombtype          = Cut-off
   rcoulomb_switch      = 0
   rcoulomb             = 2.5
   vdwtype              = Cut-off
   rvdw_switch          = 0
   rvdw                 = 2.5
   epsilon_r            = 1
   epsilon_rf           = 1
   implicit_solvent     = GBSA
   gb_algorithm         = OBC
   gb_epsilon_solvent   = 80
   nstgbradii           = 1
   rgbradii             = 1.1
   gb_saltconc          = 0.02
   gb_obc_alpha         = 1
   gb_obc_beta          = 0.8
   gb_obc_gamma         = 4.85
   gb_dielectric_offset = 0.009
   sa_algorithm         = Still
   sa_surface_tension   = 2.092
   shake_tol            = 7.5e-06
   bd_fric              = 0.5
   ld_seed              = 2010

Thanks and Regards
Kush

  

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Kushagra Singhal
Promovendus, Computational Chemistry
Universiteit van Amsterdam