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

From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Tue Jul 05 2011 - 21:25:04 CDT

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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