Re: fixed atom/Constraint failure in RATTLE algorithm/

From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Tue Jun 04 2013 - 10:26:47 CDT

Dear Norman,

Problem solved :). Using "Berendsen pressure bath coupling" did not work
since it does rescaling like "Langevin piston pressure control". However,
smoother time scale works perfectly.
this is what I am using now :
LangevinPistonPeriod 300
LangevinPistonDecay 150*

*
thank you for your great idea,

All the best,

Mehran

On Tue, Jun 4, 2013 at 3:01 AM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:

> Mehran,****
>
> ** **
>
> you are right, constant pressure simulations with fixed atoms run into
> problem often, but usually if these atoms are near the box boundaries, as
> the box can’t shrink then and will come with a message like “Periodic cell
> has become too small for original patch grid”. The problem you face may
> happen due the coordinate rescaling which comes with changing the box size.
> Here the fixed atoms can’t be rescaled and so atoms will get moved into
> each other what causes high repulsion forces which unload as huge
> velocities and blow apart your molecular system. It’s a good idea to
> equilibrate your box density/pressure first, before starting the pulling
> stuff. Maybe modifying the barostats “period” and “decay” times to a
> smoother timescale could also work, so that the cell fluctuation amplitude
> is lower and a higher decay time would let the system relax to the new
> pressure conditions. ****
>
> ** **
>
> Good luck****
>
> Norman Geist.****
>
> ** **
>
> *Von:* mb.mehran_at_gmail.com [mailto:mb.mehran_at_gmail.com] *Im Auftrag von *MEHRAN
> MB
> *Gesendet:* Montag, 3. Juni 2013 21:55
> *An:* Norman Geist
> *Betreff:* Re: namd-l: fixed atom/Constraint failure in RATTLE algorithm/*
> ***
>
> ** **
>
> ** **
>
> Hi Norman, ****
>
> First of all let me thank you for the reply, I really appreciate your
> help. I totally agree with you, it must be a bad initial structure and it
> must have some thing to do with pressure. when I turn off my " Constant
> Pressure Control " it works perfectly. I increased number of minimization
> steps, as you suggest, to 5000 and the pressure went from -6250 bar to
> -3475 bar. I think problem is happen at the beginning of dynamic when
> langevinPiston starts to increase the pressure (pressure set to be 1 bar),
> those atoms bonded directly or by the others to the fixed atom cannot obey
> langevinPiston. Although boundary is at least 30A away from fix residue,
> still it does not work. In NAMD tutorial for pulling protein, they do not
> control pressure at all. So I believe that it is not easy to fix residue
> near boundary and also fix pressure. ****
>
>
> Now, I am trying to do Equilibration without controlling pressure for few
> thousands step then if the pressure is dropped enough, use its output for
> new MD simulation. if it does not work I will try other pressure control
> method "Berendsen pressure bath coupling". I will keep this post updated
> if my solutions works. ****
>
> please let me know if you any suggestion or comment, ****
>
> ** **
>
> Best,****
>
> Mehran****
>
> ** **
>

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