Re: SMD constant velocity pulling

From: B. Nandy (nandy_at_physics.iisc.ernet.in)
Date: Wed Dec 01 2010 - 23:17:37 CST

Hi Gianluca and Jerome,

Thank you for the reply and the discussion. I have an equilibrated system
consisting of two proteins. I got the equilibrated structure using AMBER
MD . And after then using AMBER forcefield I ran NAMD CPT for 100 ps
before starting SMD. I don't think volume is a problem, because I have
taken a very big water box.

I haven't tried Lowe-Andersen thermostat yet, But before doing that I
want to check what I have done is correct. Following is my script for SMD
please have a look at it and let me know if there is any mistake. And
without using thermostat the rise of temperature depends on the duration
of SMD run as well as the velocity of pulling.

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

# Continuing a job from the restart files
if {1} {
set inputname test_gp-cd_npt
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.xsc
}

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
amber on # Specify this is AMBER force field
parmfile gp120-cd4-v2.top # Input PARM file
#ambercoor md_prod_900_ps.restart # Input coordinate file
ambercoor md_prod_900_ps.restart.img.restart # imaged
outputname test_gp-cd-af_npt-cns-t-smd # Prefix of output files

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
#temperature $temperature

wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333 # =1/1.2, default is 1.0
cutoff 9.
switching off
#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

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
cellBasisVector1 130.4269071 0. 0.
cellBasisVector2 0. 117.7932744 0.
cellBasisVector3 0. 0 149.4518528
PMEGridSizeX 131
PMEGridSizeY 118
PMEGridSizeZ 150
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 1000
xstFreq 500
outputEnergies 100
outputPressure 100

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
#fixedAtomsFile 900_all_vmd.pdb.ref
fixedAtomsFile vmd-test-gp-cd-npt.ref.pdb
fixedAtomsCol B
}

#############################################################
## EXTRA PARAMETERS ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

SMD on
SMDFile vmd-test-gp-cd-npt.ref.pdb
SMDk 5
SMDVel 0.000032 #0 .016A/ps
SMDDir -0.26928 0.17691 0.94667
SMDOutputFreq 20

#############################################################
## EXECUTION SCRIPT ##
#############################################################

run 1000000 ;# 2000 ps

----------------------------------------------------------------------------

Thanking you.
Bidisha
IISc Bangalore
India

> Thanks Jérôme,
>
> I also prefer Langevin to Berendsen. I might give Lowe-Andersen thermostat
> a try in the future. For now, I continue using Langevin thermo+barostat
> (except SMD where I use none). Or, do you think I should immediately
> switch to Lowe-Andersen since it is the best out there?
>
> Gianluca
>
> On Wed, 1 Dec 2010, Jérôme Hénin wrote:
>
>> Hi Gianluca,
>>
>> On 1 December 2010 19:49, Gianluca Interlandi
>> <gianluca_at_u.washington.edu> wrote:
>>> Hi Jérôme,
>>>
>>> Sorry, I have another question. What kind of pressure control is
>>> recommended
>>> to use in conjunction with the Lowe-Andersen thermostat?
>>
>> In general, I don't know of any requirements. In the particular case
>> of NAMD, since there are only two choices of barostat and one of them
>> is Berendsen, to me there is really only one choice. I admit that this
>> is rooted in heavy personal bias - and an irrational taste for proper
>> statistical ensembles. Add to that guilt by association with the
>> Berendsen thermostat, and its sinister retinue of flying ice cubes.
>>
>> Cheers,
>> Jerome
>>
>>> On Wed, 1 Dec 2010, Jérôme Hénin wrote:
>>>
>>>> Hi Bidisha,
>>>>
>>>> This sounds like a very good application for the recently implemented
>>>> Lowe-Andersen thermostat. It should add virtually no drag.
>>>>
>>>> Best,
>>>> Jerome
>>>>
>>>> On 1 December 2010 10:51, B. Nandy <nandy_at_physics.iisc.ernet.in>
>>>> wrote:
>>>>>
>>>>> Dear NAMD user,
>>>>>
>>>>> I have  question regarding SMD simulation using constant velocity
>>>>> pulling.
>>>>> I have noticed  in different examples that one should switch of  the
>>>>> constant temperature control during constant velocity SMD pulling.
>>>>> But
>>>>> following this method the temperature has increased unreasonably in
>>>>> my
>>>>> system.  On the other hand  using langevin on  temperature remains
>>>>> constant but  I am getting a huge amount of dragging force.  So
>>>>> please
>>>>> suggest me how to deal with the dragging force when thermostat is on.
>>>>>
>>>>>
>>>>> Thanking you
>>>>>
>>>>> Bidisha Nandy
>>>>> IISc Bangalore
>>>>> India
>>>>>
>>>>>
>>>>> --
>>>>> This message has been scanned for viruses and
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>>>>>
>>>>>
>>>>
>>>>
>>>
>>> -----------------------------------------------------
>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>>                    +1 (206) 685 4435
>>>                    http://artemide.bioeng.washington.edu/
>>>
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -----------------------------------------------------
>>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>

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