Re: protein collapsing problem!

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Sun Jun 28 2009 - 03:10:43 CDT

Hi Yandong,

For starters, please keep discussions on the list instead of replying
to a single individual. It helps everyone in the long run.

 From your config file, it is unclear to me what parameter set you are
using, and I'm not sure what 'v22 b4' actually refers to. From your
config file it also appears as if you are flash heating your system
(minimizing and then jumping to 310 K) which can be problematic. A
more standard procedure would involve slowly heating your system to
the desired temperature, possibly while restraining your protein and
then gradually removing the restraints. If you search the mailing list
archive, I and others have posted information about this. I'm actually
surprised that your system doesn't blow up immediately, instead of 5
ns into the simulation, as you described in an earlier email.

Also, it might help if you actually define what you mean by the system
is unstable/falls apart. You said that you lose secondary structure,
but does that mean that the helices actually completely lose their
structure? Also what does the RMSD of your protein look like? For
individual sub-domains that you think should be stable? Have you
checked to make sure that your water box looks ok, that ions haven't
bound in strange ways? How did you set up the system (solvation and
ion placement)? There are some ligands in the PDB file for your
protein (at least I'm guessing from the file names); have these been
appropriately parameterized, and are they near where your protein
starts to fall apart initially. These are all things you should check.
If you can pinpoint where things start to go bad in your simulation,
you may have an easier time trying to figure out what went wrong.

Josh

On Jun 27, 2009, at 8:02 PM, ydhuang2727 wrote:

> Hi, Josh,
>
> Yes, my parameter is : Charmm parameter set for proteins v22 b4.
>
> My .conf file is as follows:
> Hopefully you can find something improper.
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
> # Minimization and Equilibration of
> # Ubiquitin in a Water Box
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> structure ../../common/1v4s_wb.psf
> coordinates ../../common/wb_md.pdb
>
> set outputname 1v4s_wb_eq
>
> firsttimestep 0
> set T 310
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> #paraTypeCharmm on
> parameters ../../common/parallh22xpro
> #parameters ./../common/water.param
> parameters ../../common/ion.param
> #parameters ../../common/mrk.param
> temperature 100
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 14.5
>
> # Integrator Parameters
> timestep 1.0 ;# 2fs/step
> #rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $T
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> # Periodic Boundary Conditions
> cellBasisVector1 89.2 0. 0.
> cellBasisVector2 0. 98.5 0.
> cellBasisVector3 0. 0. 91.0
> cellOrigin 29.689 1.377 69.685
> #wrapWater on
> wrapAll on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 90
> PMEGridSizeY 100
> PMEGridSizeZ 96
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $T
>
> # Output
> outputName $outputname
> binaryoutput no
> restartfreq 10000 ;# 500steps = every 1ps
> dcdfreq 10000
> xstFreq 10000
> outputEnergies 5000
> outputPressure 5000
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> #############################################################
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> # Minimization
> minimize 50000
>
> run 5000000 ;# 10ns
>
>
>
> Thanks for your consideration and look forward!
>
> Good day!
>
> Yandong,
>
>
>
>
>
>> Hi,
>>
>> I'm running a somewhat big monomer protein with about 448 residues
>> and about 7000 atoms, the total number after adding periodic water
>> box is 80383. It gets 11 beta-sheet and 13 alpha-helices.At the
>> beginning 5 ns, everything goes well. While after 5 ns, its total
>> secondary structure number, let's ignore what happens to tertiary
>> structure firstly, start decreases, especially those alpha-helices
>> who contact with water moleculars. Till 15ns, there are only 6
>> alpha-helices left and 10 beta-sheets. As to the tertiary
>> structure, the whole struture seems to unstable after 15ns.
>> The protein's intrinsic allosteric trait require a long-time running.
>> Whit such a problem, i'm not be able to go on with my simulation.
>> What should i do ?
>> Can anybody help me out?
>>
>> Thanks so much for your kind consideration and look forward to your
>> reply!
>>
>>
>> Good day!
>>
>>
>> Yandong
>
>
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