[gmx-users] Simulation parameter problem about protein unfolding

Chen amethyst0 at 126.com
Mon Oct 18 14:12:31 CEST 2010

>At 2010-10-18 16:38:30,"David van der Spoel" <spoel at xray.bmc.uu.se> wrote:

>>On 2010-10-18 06.56, chris.neale at utoronto.ca wrote:
>> Generally, forcefields are not parameterized for temperatures other than
>> 298K, so simulations are not expected to reproduce the expected
>> properties (like boiling water and the correct temperature denaturation
>> of proteins).
>> There's almost certainly other issues here (including the fact that I'm
>> entirely sure that you can get a lot more than 24 ns of simulation on a
>> 54 aa protein; and 26 atom of pressure seems pretty arbitrary) but it
>> will come down to this eventually.
>> Just because you found a paper in which they get a denatured state does
>> not imply that they got the correct denatured state.
>There is no correct denatured state. There are infinitely many. Check 
>out recent work on NMR of "unfolded" proteins.

I thought about the unfolding state space is huge. I just wonder
whether the relative low radius of gyration value space sampled by us is caused
by some error setting in MD parameters. If no one here finds there's problem in
my MD parameters, then I can keep going. Thanks!

At 2010-10-18 16:19:02,"Gerrit Groenhof" <ggroenh at gwdg.de> wrote:Hi,

You write it yourself: In paper you mention, they have used a 0.8 nm cutoff range for both electrostatics and cutoff. You are doing something different by using PME for the electrostatics. Also you are using a much longer cutoff for the VDW interactions. 
If you want to reproduce their results, you need to stick to to the parameters mentioned in that paper and use cut-offs as well.

BTW I do not believe this to be a good idea though.


I didn't want to simply reproduce their results I've mentioned. I
guess even if I set the same cutoff, the result wouldn't change too much or
would be different for some other reason (e.g. the force field or the MD
software :) ). Anyway I would try it! 

I chose PME for the electrostatics and set longer cutoff for the VDW
in order to get more precise interaction calculation. I've noticed the force
field bias at high temperature and even the couple algorithm would flaw the
protein unfolding. However, that's what I could do by now. I would take these
parameters if no one here finds there's problem. Thanks!

integrator               = md
dt                       = 0.002
nsteps                   = 3000000
nstxout                  = 500
nstvout                  = 500
nstlog                   = 500
nstenergy                = 500
nstxtcout                = 1000

energygrps               = protein non-protein

nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0

coulombtype              = PME
rcoulomb                 = 1.0
vdwtype                  = cut-off
rvdw                     = 1.4
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4
ewald_rtol               = 1e-5
optimize_fft             = yes

tcoupl                   = v-rescale
tc_grps                  = protein non-protein
tau_t                    = 0.1  0.1
ref_t                    = 498  498
Pcoupl                   = Parrinello-Rahman
pcoupltype               = isotropic
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 26.0

gen_vel                  = yes
gen_temp                 = 498
gen_seed                 = 173529

constraints              = hbonds
lincs_order              = 10
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