[gmx-users] implicit solvent
Mark Abraham
mark.j.abraham at gmail.com
Thu Jul 11 00:56:17 CEST 2013
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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