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

[Michael Shirts]

A few questions:

1) What force field are you using?
2) do you get the same answers with and without GPU acceleration?
3) How long does it take for secondary structure to disappear?  100's
of ps?  10's of ns?


On Mon, Jan 17, 2011 at 8:45 AM, K. Singhal <k.singhal at uva.nl> wrote:
> 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
>
>
>
> --
> Kushagra Singhal
> Promovendus, Computational Chemistry
> Universiteit van Amsterdam
>
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