Re: Re: Protein moving out of box during npt simulation

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jul 07 2011 - 10:02:09 CDT

I don't know but one final shot you can try..

try to move the protein center to origin of coordinate system.
Check right now what is the center coordiate in your system, and also check
the center coordinate after moving to origin of coordinate system. Try it.

On Tue, Jul 5, 2011 at 9:25 PM, bharat gupta <bharat.85.monu_at_gmail.com>wrote:

> Hi,
>
> I repeated the nvt equilibration again with margin 2.5 , but still the
> protein comes out of box from the very start of the simulation. What shall I
> do now ??..
>
>
> On Wed, Jul 6, 2011 at 8:20 AM, bharat gupta <bharat.85.monu_at_gmail.com>wrote:
>
>> Hi,
>> I did the minimization for 30000 steps and everything was fine during
>> minimization. During nvt equilibration , the protein moves out of the box.
>> Here is the configuration file that I am using for nvt equilibration :-
>>
>>
>> ## JOB DESCRIPTION ##
>> #############################################################
>> # Minimization and Equilibration of
>> #GFP in a Water Box
>> #############################################################
>> ## ADJUSTABLE PARAMETERS ##
>> #############################################################
>> structure ./ionized.psf
>> coordinates ./ionized.pdb
>> set temperature 310
>> set outputname complex_eq
>> firsttimestep 0
>> #############################################################
>> ## SIMULATION PARAMETERS ##
>> #############################################################
>> # Input
>> binCoordinates ./complex_min.restart.coor
>> binaryrestart yes
>> extendedSystem ./complex_min.xsc
>> paraTypeCharmm on
>> parameters ../common/par_all27_prot_na.prm
>> temperature $temperature
>> # Force-Field Parameters
>> exclude scaled1-4
>> 1-4scaling 1.0
>> cutoff 12.
>> switching on
>> switchdist 10.
>> pairlistdist 13.5
>> # Integrator Parameters
>> timestep 2.0 ;# 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 $temperature
>> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>> # Periodic Boundary Conditions
>> cellBasisVector1 65. 0. 0.
>> cellBasisVector2 0. 53. 0.
>> cellBasisVector3 0. 0 49.
>> cellOrigin 8.35 69.64 -10.16
>> wrapAll on
>> # PME (for full-system periodic electrostatics)
>> PME yes
>> PMEGridSizeX 60
>> PMEGridSizeY 60
>> PMEGridSizeZ 60
>> useGroupPressure yes ;# needed for rigidBonds
>> useFlexibleCell no
>> useConstantArea no
>> #Note the lack of langevinpiston, which is the pressure control
>> # Output
>> outputName $outputname
>> restartfreq 500 ;# 500steps = every 1ps
>> dcdfreq 250
>> xstFreq 250
>> outputEnergies 100
>> outputPressure 100
>> #############################################################
>> ## EXTRA PARAMETERS ##
>> #############################################################
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>>
>> numsteps 30000
>>
>>
>> I did not understand ur last statement "protein ahs to be equilibrated
>> well" . So does it mean that I should for 2ns nvt and 2ns npt equilibration
>> , finally the free dynamics.. please comment ...
>>
>>
>>
>> On Wed, Jul 6, 2011 at 12:00 AM, snoze pa <snoze.pa_at_gmail.com> wrote:
>>
>>> Increase the margin and minimize for atleast 20000 steps. Also Make sure
>>> that protein is well equilibrated(do it atleast 2ns).
>>>
>>>
>>> On Tue, Jul 5, 2011 at 4:22 AM, Bjoern Olausson <namdlist_at_googlemail.com
>>> > wrote:
>>>
>>>> On Tuesday 05 July 2011 10:40:59 bharat gupta wrote:
>>>> > I repeated the nvt equilibration again with cell origin (the actual
>>>> one),
>>>> > but still I am getting the protein going out of the box. But the
>>>> energy and
>>>> > temperature is stable. What shall I do in this case, shall I continue
>>>> with
>>>> > npt simulation without keeping the protein in the center of the box
>>>> as I
>>>> > have taken PBC into consideratioon ???
>>>> >
>>>>
>>>> When you are using PBC you don't have to worry about that.
>>>> You can recenter the trajectory on the protein and eliminate the protein
>>>> drift
>>>> this way once your simulation is complete.
>>>>
>>>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>>>> Search for "pbc wrap"
>>>>
>>>> Cheers,
>>>> Bjoern
>>>>
>>>> --
>>>> Bjoern Olausson
>>>> Martin-Luther-Universitšt Halle-Wittenberg
>>>> Fachbereich Biochemie/Biotechnologie
>>>> Kurt-Mothes-Str. 3
>>>> 06120 Halle/Saale
>>>>
>>>> Phone: +49-345-55-24942
>>>>
>>>
>>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010_at_yahoo.com
>>
>>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010_at_yahoo.com
>
>

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