Re: abrupt deviation in rmsd values

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Thu May 03 2007 - 11:34:22 CDT

Hi Monika,
this may be a useful example:
starting from T=10 and heating the system up to 480K
with an increase of 10 degrees K bewteen the different runs (50000 steps
each).

In your config file:
...
set temperature 10
....
... langevin thermostat parameters and other simulation parameters
...
run 50000
for {set i 20} {$i <= 480} {incr i 10} {
langevinTemp $i
run 50000
}

Giovanni

> Hii!!
> Thanks all for the suggestions. But one think I want to ask is that
> how can we change the Langevin dynamics (for temp) in between the run
> commands. Actually I wanted my system to gradually heat up and the
> rmsd changes that occur. And I want to use Langevin dynamics as per
> heating up. But inbetween the run commands Langevin dynamics cannot be
> changed, since the simulation aborts saying "Langevin Parameters
> cannot set off or on". I also tried introducing the LangevinTemp $Temp
> into the loop. I dont know how to fix that prob. The langevin dynamics
> have to be set in the beginning; and cannot be hold inbetween on and
> off as per my experience. (Do correct me if I am wrong or if there is
> any other way??) So the reassigning parameters also doesnt work as I
> want.. :-( Regards,
> Monika
>
> Peter Freddolino wrote:
>
>> Hi Monika,
>> three things:
>> First, it's unclear how you're actually planning on heating the system.
>> There's nothing in your temperature increment loop that is actually
>> changing the system temperature (such as, say temperature $temp).
>> Second, you've set the langevin temperature to your desired temperature
>> from the beginning -- this will mean that your system is always coupled
>> to a 480 K bath, which probably is not what you want. I'd recommend
>> holding off on the langevin dynamics until after your heating is done
>> (you've turned off the Langevin barostat, but not the thermostat).
>> Finally, you may want to turn langevinHydrogen off, since you're using
>> rigidBonds.
>>
>> You should have a look at Temperature rescaling (or reassignment) in the
>> NAMD manual for the type of heating you're looking to do; see
>> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node30.html.
>>
>> Best, Peter
>>
>> Monika Sharma wrote:
>>
>>
>>> Dear All,
>>> I am new to this MD thing and newer to NAMD. I am trying to unfolding
>>> simulation of a small protein. And the protocol I am using is like:
>>>
>>> 1. Energy minimization with fixed atoms, then with no fixed atoms
>>> 2. Heating the system form 0 to 480 k using Langevin Dynamics
>>> 3. Position restratined MD, fixing backbone atoms, and then
>>> 4. free MD equilibration.
>>>
>>> The run ends ok, but when i plot the rmsd over time. the plot shows
>>> the deviation of about 4.0 in the initial phase of 10 ps or so... :-(
>>> When I look at the log file created, its seen that the temperature
>>> rises abruptly from 0 to 167K in a first go; whereas I have given it
>>> the incr of 48K with each run. Dont know where the problem arises.
>>> May be the sudden increase of the temp is destabilizing the protien to
>>> such an extent. Can there be other possible way for getting the
>>> temperature increased gradually?? I am attaching the .conf file and
>>> the rmsd data file for the reference. If anybody can help me out.
>>>
>>> ----------------------------------------------------------------------------------------------------------------------
>>>
>>>
>>> the execution code is like..
>>> #Minimization
>>>
>>> #run to get into scripting mode
>>> minimize 0
>>>
>>> # turn off pressure control
>>> langevinPiston off
>>> #minimize non-backbone atoms
>>> minimize 2500
>>>
>>> #minimize all atoms
>>> fixedAtoms off
>>> minimize 2500
>>>
>>> #Heat with Ps restrained
>>> for {set temp 0} {$temp <= 480} {incr temp 48} {
>>> run 10000
>>> }
>>> #equilibrate volume with Ps restrained
>>> langevinPiston on
>>> run 100000
>>> #equilibrate volume without restraints
>>> constraintScaling 0
>>> run 500000
>>> ------------------------------------------------------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>>
>>> #molecules
>>> set import ionized
>>> set minim runmod_incr
>>> set export run_270407 structure ${import}.psf
>>> coordinates ${import}.pdb
>>> bincoordinates ${minim}.coor
>>> extendedSystem ${minim}.xsc
>>>
>>> #forcefield parameters
>>> paratypecharmm on
>>> parameters /home/guest/projects/c32b1/toppar/par_all22_prot.inp
>>> exclude scaled1-4
>>> 1-4scaling 1.0
>>>
>>> #integrator parameters timestep 1.0
>>> fullElectFrequency 4
>>>
>>> outputenergies 100
>>> outputTiming 100
>>> outputPressure 100
>>> #initial config
>>> set init_temp 0
>>> set desired_temp 480
>>> temperature $init_temp
>>>
>>> #outputfiles and restart options
>>> outputname ${export}
>>> binaryoutput no
>>> restartname run_270407_res
>>> restartfreq 1000
>>> binaryrestart yes
>>> dcdfreq 1000
>>> xstfreq 1000
>>>
>>> #others
>>> nonbondedFreq 1
>>> rigidBonds all
>>> rigidTolerance 1.00E-7
>>> stepspercycle 20
>>>
>>>
>>> #simulation spacing partitioning
>>> switching on
>>> switchDist 10
>>> cutoff 12
>>> pairlistdist 16
>>> margin 1
>>>
>>>
>>> #Periodic Boundary Conditions
>>> cellBasisVector1 38 0 0
>>> cellBasisVector2 0 41 0
>>> cellBasisVector3 0 0 45
>>> cellOrigin 4 -4 -16
>>>
>>> wrapWater on
>>> wrapAll on
>>> wrapNearest on
>>>
>>> #PME params
>>> PME yes
>>> PMEGridSpacing 1.0
>>> PMEGridSizeX 45
>>> PMEGridSizeY 45
>>> PMEGridSizeZ 45
>>>
>>> #Fixed atoms for initial heating up steps
>>> fixedAtoms on
>>> fixedAtomsForces on
>>> fixedAtomsFile zwv_fix_backbone.pdb
>>> fixedAtomsCol B
>>>
>>> #Restrained atoms for initial heating-up
>>> constraints on
>>> consRef zwv_constraint_ca.pdb
>>> consKFile zwv_constraint_ca.pdb
>>> consKCol B
>>>
>>> #langevin dynamics params
>>>
>>> #langevin temp control
>>> Langevin on
>>> LangevinDamping 4
>>> LangevinHydrogen on
>>> LangevinTemp $desired_temp
>>> #langevin pressure control
>>> LangevinPiston on
>>> LangevinPistonTarget 1.01325
>>> LangevinPistonPeriod 200
>>> LangevinPistonDecay 100
>>> LangevinPistonTemp $desired_temp
>>> useGroupPressure yes
>>>
>>> #Minimization
>>>
>>> #run 1 step to get into scripting mode
>>> minimize 0
>>>
>>> #turn off pressure control until later
>>> langevinPiston off
>>> #minimize non-backbone atoms
>>> minimize 2500
>>> #minimize all atoms
>>> fixedAtoms off
>>> minimize 2500
>>> #Heat with Ps restrained for {set temp 0} {$temp<=480} {incr temp 48} {
>>> run 10000
>>> }
>>>
>>> #equilibrate volume with Ps restrained
>>> langevinPiston on
>>> run 100000
>>> #equilibrate volume without restraints
>>> constraintScaling 0
>>> run 500000
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>

-- 
------------------------------------------
Giovanni Bellesia
Department of Chemistry and Biochemistry
University of California, Santa Barbara
Santa Barbara, California 93106-9510, USA.
Email: gbellesia_at_chem.ucsb.edu
Phone: 805 893 2767
------------------------------------------

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