From: Md Zobayer Hossain (mdzobaye_at_ualberta.ca)
Date: Sat May 28 2022 - 05:37:17 CDT
Hi Sruthi
You can look into the surfaceTensionTarget settings in the NAMD pressure
control if it helps.
Best
Zobayer
On Sat, 28 May 2022, 03:50 Sruthi Sundaresan, <bo20resch11002_at_iith.ac.in>
wrote:
> I found no difference when I flipped the sign of *langevinPistonTarget* as
> this parameter accepts only positive decimal values (Page:93 -
> http://www.ks.uiuc.edu/Research/namd/cvs/ug.pdf):
>
> LangevinPistonTarget < target pressure (bar) >
> Acceptable Values: *positive decimal*
> Description: Specifies target pressure for Langevin piston method. A
> typical value would be 1.01325 bar, atmospheric pressure at sea level.
>
> On Sat, May 28, 2022 at 12:49 PM Geist, Norman <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> I have answered this before. In a periodic cell there is no such
>> direction. Have you considered flipping the sign of langevinpistontarget?
>>
>> Bests
>> Norman Geist
>>
>>
>> Am Samstag, den 28-05-2022 um 08:38 schrieb Sruthi Sundaresan:
>>
>> Dear Users,
>> I would like to know how to apply pressure on a membrane protein in one
>> direction. I am running the simulations on NAMD3.0 and used the following
>> lines in the input files to apply pressure:
>>
>>
>> *useConstantArea yes;*
>> *useflexiblecell yes;*
>>
>> *SurfaceTensionTarget 0.0;*
>>
>> *langevinPiston on;*
>>
>> *langevinPistonTarget 4000.00;*
>>
>> *langevinPistonPeriod 100.0;*
>>
>> *langevinPistonDecay 50.0;*
>>
>> The above lines help to apply pressure on the z-axis alone while keeping
>> the area of the x-y plane constant.
>> My system seems to get compressed along the z-axis, however, I'd like to
>> know how to apply pressure selectively in one direction alone (either +z or
>> -z).
>>
>> Thanks and regards,
>>
>>
>> <https://urldefense.com/v3/__https://iith.ac.in/__;!!DZ3fjg!8Yq32Y9tumEvFF5hsp1Ux2ge91-dRl8CGnvJ4_K0R35Skzcfmye1M6Q5o1zdnKWsPHnD2V3J95oifkOolanli7QuQG6Bqw$>
>>
>> Sruthi Sundaresan
>>
>> Ph.D. Research Scholar
>>
>> C/o Dr. Thenmalarchelvi Rathinavelan
>>
>> Molecular Biophysics Lab, Department of Biotechnology
>>
>>
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>>
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