Re: Z-direction shrinking

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Thu Jul 29 2010 - 09:43:23 CDT

Hi, ABF has very little to do with thermostats or barostats. You should
look to some other reason why Z is shrinking.

Giacomo

---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

2010/7/29 crazylyf <crazylyf_at_163.com>

> Hi,
>
> I'm running a ABF simulation using NPT system, I find that the system
> shrinked in the Z direction. At the meantime, the XY plane is enlarged. Here
> is part of the configration file:
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell yes ;# no for water box, yes for membrane
> #useConstantRatio yes
> useConstantArea yes ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
> To solve the problem, I want to try add oneSiteSystemForce, Does it useful
> and how this parameter can be used?
> Best regards
>
>
> ------------------------------
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