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Water box change volume
#33932 05/16/14 01:00 AM
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Hi,all.
The dynamics command of mine as:
.....
scalar mass stat
calc pmass = int ( ?stot / 50.0 )
calc tmass = @pmass * 10
......
dyna leap cpt restart - !NVT ensemble
timestep 0.001 nstep 500000 nprint 5000 -
iunrea 24 iunwri 25 iuncrd 26 kunit 27 nsavcc 1000 -
hoover reft 303.0 tmass @tmass -
pcons pint pref 1.0 pmass @pmass pgamma 0.0 -
ihtfrq 0 ieqfrq 0 ntrfrq 500 -
iasors 1 iasvel 1 iscvel 0 ichecw 0 -
echeck 100.

I want to know what ensemble it is? If it is NVT,if so,why the volume of the water box great changed? However, I have two model one keep the volume good,the another one not? Why?

Re: Water box change volume
Yong Mao #33933 05/16/14 02:02 AM
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pressure.doc

Re: Water box change volume
Kenno #33934 05/16/14 11:31 AM
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If I use the NPT ensemble,how the volume of the water box changed? I just found the water box changed very much, I am afraid it's wrong here.

Re: Water box change volume
Yong Mao #33936 05/16/14 03:23 PM
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I strongly recommend to pick up a basic thermodynamics textbook. Some minimal notions of thermodynamics are required to work in the field of MD. More info here and here.

Edit: how much did the volume change, and can you attach full input and a relevant section of your output? It may or may not be a system setup problem - you're giving far too few details.

Last edited by Kenno; 05/16/14 03:26 PM.
Re: Water box change volume
Yong Mao #33937 05/16/14 03:56 PM
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Calculate the density in gm/cc of your initial box, based on it's volume and the number of water molecules.


Rick Venable
computational chemist

Re: Water box change volume
Yong Mao #34017 06/06/14 05:40 PM
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What is @pmass set to? If it's nonzero, then this is an NPT calculation and the box volume is allowed to change in order to achieve the desired pressure (speaking very loosely - the details are in the references that have already been recommended to you).

BTW, this suspiciously looks to me like an input script from CHARMMing ... there is a specific forum for CHARMMing-related questions.


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