Re: fixed atoms / pressure

From: Arturas Ziemys (
Date: Thu Mar 13 2008 - 10:52:41 CDT

Hi, Peter,

My mistake about units - forgot: it is particles per cubic Angstrom.

As far as I am dealing with anisotropic (quartz) system first time, I
want to find/get more information tunning MD parameters. The whole point
in my question was to get more insight is there any caveats using
flexible cell, constant area, and significant number of frozen particles.

I figured out about my pressure and density - it is consequence of my
system structure. However I still not 100% if I should use frozen
particles (minimized; forces ON) with constant_area/flexible_cell. Or,
let's say, is it reasonable to use frozen particles of my quartz slab
with flexible cell and without constant area - I'm not sure how NAMD
would deal with that.


Peter Freddolino wrote:
> Hi Arturas,
> what units are you using for water density here? Also, is the PRESSURE
> value you're reporting averaged over the entire run? Are you sure you
> ran long enough for it to be equilibrated?
> Using constant pressure with a lot of fixed atoms (eg, the whole quartz
> slab) is probably not a good idea in general... if you must, you might
> want to try with fixedAtomForces on, but you're probably better off
> applying constraints to a few atoms.
> Also, how large is your water layer above and below the quartz slab? And
> how are you calculating the density of water in your (heterogeneous)
> system?
> Best,
> Peter
> Arturas Ziemys wrote:
>> Hi,
>> I need some insights and comments.
>> MY SYSTEM: quartz slab (~15 A wide; patched to mimic infinite layer)
>> on XY plane and TIP3P water on both sides of Z. useFexibleCell is ON.
>> useConstantArea is ON.
>> PROBLEMS: 1) I get higher water density (~0.037) than TIP3P "standart"
>> (~0.033-0.034) at NPT/1bar. 2) PRESSURE fluctuates around very low
>> values (~ -1000 bars).
>> However, my quartz is minimized and fixed after. I get higher water
>> density using system with with fixed and not fixed quartz slab.
>> QUESTIONS: How necessary to use useFexibleCell ON and useConstantArea
>> ON in my case ?
>> Best
>> Arturas

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