[gmx-users] implicit solvent

[Mark Abraham]

Yes, this is probably caused by a known bug in 4.6 that has been fixed
for a month or two and mentioned in the release notes. Some
work-arounds are suggested here
http://redmine.gromacs.org/issues/1249, but you should probably update
to 4.6.3 :-)

Mark

On Wed, Jul 10, 2013 at 5:43 PM, Cristina Dezi <cristina.dezi at gmail.com> wrote:
> 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
> --
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