Thanks for the heads up, Carlos. I have one last question, is it necessary
to restraint the protein when temperature is increased to 400K from 300K
under constant volume using 10 K increment per 10ps?
Andy
On Sun, Oct 31, 2010 at 10:49 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I just have a few suggestions. you should read the protein unfolding
> literature carefully and pay close attention to the methods that were used.
>
> 1. you are using constant P at 400K. this means you should expect your
> water
> to boil, and turn into a gas. this is certainly not going to properly model
> liqud water around your protein. consider using constant volume.
>
> 2. your water box (you said 10A from solute to wall) is probably nowhere
> near large enough to enclose the protein once it starts to unfold. this
> means that once unfolding starts, you probably do not have a good
> simulation.
>
> 2. comparing unfolding rates (kinetics) is not the same as comparing
> thermodynamic stabilities. you are measuring something quite different from
> the experiment. keep this in mind.
>
> On Sun, Oct 31, 2010 at 1:47 AM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Hi Andy,
> >
> > Set iwrap=1 in your &cntrl namelist. What is happening is that normally
> > pmemd (or sander) does not image molecules during a simulation. When you
> > run
> > a long simulation, 30+ ns, especially at the high temperatures that you
> > have, water molecules can diffuse a long way from the central box. This
> > means their coordinates end up large and when they exceed 999.9d0 you end
> > up
> > with *'s in your restart file and thus the restart file can no longer be
> > read. iwrap=1 fixes this by always wrapping molecules back into the
> central
> > box whenever they diffuse out of one side.
> >
> > Note, you will need to go back to your last good restart file to be able
> to
> > resume the simulation. There is no way to repair the final corrupt
> restart
> > file.
> >
> > ps. You should consider applying the most recent bugfix (bugfix.9)
> released
> > 2 days ago. This fixes a number of minor bugs in the GPU code, plus
> > improves
> > performance and provides support for running in parallel across multiple
> > GPUs. - Be sure to recompile after applying he patch.
> >
> > Good luck,
> > Ross
> >
> > > -----Original Message-----
> > > From: andy ng [mailto:andy810915.gmail.com]
> > > Sent: Saturday, October 30, 2010 8:31 PM
> > > To: amber.ambermd.org
> > > Subject: [AMBER] GPU high temperature unfolding simulation
> > >
> > > Hi amber users,
> > >
> > > I am from molecular biology lab and has limited knowledge regarding MD
> > > simulation. I am hoping some of you might have a better idea on how to
> > > pursue this problem.
> > > What we want to do is using AMBER GPU cuda.spdp version to simulate our
> > > protein at high temperature for as long as we can or until the protein
> > > unfold, say 400K, in a system solvated with TIP3PBOX water molecules
> and
> > > 150mM NaCl in a solute to wall distance of 10A water box.
> > >
> > > The reason we want to do this is we have all short of data including
> > protein
> > > stability of different clinical mutants (10 of them), and we can
> classify
> > > the locations of mutations based on their experimental thermal
> stability.
> > So
> > > we would like to simulate these mutants and observe which part of the
> > > structure has the least stability because of the mutation.
> > >
> > > The strategy is:
> > > 1. Simulate the WT at 300K and 400K to serve as control.
> > > 2. Simulate mutants at 400K to observe the effect of mutation.
> > >
> > > The protocol I used for 400K is as follow.
> > > 1. Minimization with protein fixed.
> > > 2. All atom minimization.
> > > 3. Equilibration to 300K with protein fixed.
> > > 4. Equilibration at 300K all atoms
> > > 5. Increase temp to 400K using 20ps time step.
> > > 6. simulation at 400K for as long as I can.
> > > The input file at 400K is as below
> > >
> > > &cntrl
> > > imin=0, ntx=5, ntb=2, taup=2, ntp=1, cut=10, ntr=0, ntc=2, ntf=2,
> > temp1=400,
> > > temp0=400, ntt=3, gamma_ln=1, ntslim=10000000, dt=0.002, ntpr=1000,
> > > ntwx=1000, ntwr=1000, irest=1, ioutfm=1
> > > /
> > > &ewald
> > > dsum_tol=0.000001, nfft1=128,nfft2=128, nfft3=128
> > > /
> > >
> > > I am able to simulate some of the mutants and WT at 400K up to 30ns (my
> > > plan
> > > is to simulate as long as I can, I have access to a cluster of S2050
> > GPUs),
> > > but then I encountered the error "Could not read coords from
> > > directory_name/file_name.rst " when I try to continue the simulation.I
> > will
> > > only see this error when the simulation went over 30ns, for the WT and
> > > mutants simulations.
> > >
> > > Is there anything wrong with my input parameters?
> > >
> > > Any help and comments would be very much appreciated.
> > >
> > > Andy
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Tue Nov 02 2010 - 18:00:02 PDT
