Re: Re: namd simulation input file setting from NPT to NVT

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Sep 10 2018 - 11:25:54 CDT

As Joshua explained, the default ensemble is constant-volume, and it would
only change to constant-pressure if you define the corresponding keywords.

The volume will remain constant at the value that you set at the initial
conditions. Try running it, and you can monitor the unit cell's volume
from the standard output, or the unit cell parameters in the XST trajectory.

Giacomo

On Mon, Sep 10, 2018 at 12:20 PM Yi Lun Lee <ylee45_at_students.tntech.edu>
wrote:

> Hi Joshua,
>
>
> When I convert NPT to NVT system, I increase the volume two times bigger
> than the original volume.
>
> In the system has some liquid vapor.
>
>
> In this situation how do i setting the input file for this part
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure ;# needed for rigidBonds
> useFlexibleCell
> useConstantArea
> langevinPiston
> langevinPistonTarget
> langevinPistonPeriod
> langevinPistonDecay
> langevinPistonTemp $temperature
>
> Thank you for your comments in advance
>
> Lee
>
> ------------------------------
> *From:* Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> *Sent:* Thursday, September 6, 2018 5:04:20 PM
> *To:* namd-l_at_ks.uiuc.edu; Yi Lun Lee
> *Subject:* RE: namd simulation input file setting from NPT to NVT
>
> Hi Lee,
>
> Those input options can be deleted your configuration file. If you specify
> a periodic cell, the default for NAMD is NVT. Only if you specify the
> pressure control options to change it to NPT do you need to specify those
> settings.
>
> -Josh
>
>
>
> On 2018-09-06 14:50:47-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Dear NAMD user,
>
>
> I am trying to run a system under NVT after a long NPT equilibration
> process.
> The NVT system was started with the pressure control off and using the
> restart.coor, restart.vel, and restart.xsc files from the NPT equilibration
> process.
> How do I setting the input file for this part
> # Constant Pressure Control (variable volume)
> useGroupPressure ;# needed for rigidBonds
> useFlexibleCell
> useConstantArea
> langevinPiston
> langevinPistonTarget
> langevinPistonPeriod
> langevinPistonDecay
> langevinPistonTemp $temperature
> Thank you for your comments in advance
> Lee
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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