[gmx-users] implicit solvent

[Cristina Dezi]

Dear users,

I am performing MD simulations of short peptides (from 7 to 45 units) in
implicit solvent. I found quite bizarre results: all peptides unfold after
few picosends, adopting a rather linear conformation until the end of MD,
irrespective of temperature (I performed simulations at 200K, 400K and 600K
for 50 ns). I am wondering if these results do have any sense, as they are
very different from what I found with similar MD in gas phase, explicit
solvent (water) and also from what is published in literature to the date.

I searched the forum archives and found the different issues related with
implicit solvent but maybe I missed something, I would be very grateful if
some of you with more experience with GROMACS (I have experience expecially
with AMBER and explicit solvents) could take some time to check my input
file to see if I made some mistake. I am using GROMACS version 4.6.

Thank you very much in advance for your help,

Kindest regards

Cristina Dezi, PhD

Chemistry Department,
CINVESTAV
Av. Instituto Politecnico Nacional, 2508
A.P. 14-740 Mexico D.F. 07000
MEXICO

*INPUT FILE*
integrator                 = md
nsteps                     = 2500000
dt                           = 0.002
comm-mode             = ANGULAR
nstxout                    = 5000
nstvout                    = 5000
nstenergy                 = 5000
nstlog                      = 5000
continuation              = no
vdw-type                  = Cut-off
nstlist                       = 0
ns_type                    = simple
pbc                          = no
rlist                          = 0.0
rlistlong                     = 0.0
coulombtype              = cut-off
rcoulomb-switch         = 0
rcoulomb                   = 0.0
rvdw                         = 0.0
rvdw-switch               = 0.0
tcoupl                       = nose-hoover
tc-grps                      = system
tau_t                        = 0.4
ref_t                         = 200
pcoupl                       = no
gen_vel                     = yes
gen_temp                  = 200
gen_seed                   = 290389
implicit_solvent           = GBSA
gb_algorithm              = Still
nstgbradii                   = 1
rgbradii                      = 0
gb_epsilon_solvent       = 80
gb_saltconc                = 0
sa_algorithm               = Ace-approximation
sa_surface_tension       = 2.05016