On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth katesed...@gmail.com wrote:
Hi Vitaly,
I realize that when one extends the Z direction the resulting interface is
liquid-vacuum, but I see that even at T below boiling point some molecules
still leave the interface and enter the empty zone and are
Sorry, meant to post this on the bb.
Gesendet:Dienstag, 02. April 2013 um 11:50 Uhr
Von:lloyd riggs lloyd.ri...@gmx.ch
An:vvcha...@gmail.com
Betreff:Aw: Re: [gmx-users] Re: density profile
How would you set up a gas/gas interface, say modeled after a large gas planet or upper atmosphere
Hi Elisabeth -
The only explanation is that you actually DID NOT extend the box in Z
direction. Look at the last line of confout.gro.
g_density -d Z gives you a [local] density versus Z coordinate.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth katesed...@gmail.com wrote:
Hi
Hi vitaly,
The initial structure is indeed extended but the final output.gro is not. I
think its because I am using the cpt file from the previous NPT runs as
input for the new runs? Do I have to remove the -t flag?
On 1 April 2013 12:47, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Hi
I think if you use checkpoint files, the program does not read either MDP,
or GRO, or TOP, or anything except CPT.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth katesed...@gmail.com wrote:
Hi vitaly,
The initial structure is indeed extended but the final output.gro is not.
On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
I think if you use checkpoint files, the program does not read either MDP,
or GRO, or TOP, or anything except CPT.
I would have to check the code to be sure, but that is certainly not true
in the case of the .mdp
It is something very new for me.
If structure, etc are not read from CPT files, why does one need them for...
On Mon, Apr 1, 2013 at 7:21 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
I think if you use checkpoint
Justin -
I am sure mdrun reads coordinates from -cpi state.cpt
Vitaly
On Mon, Apr 1, 2013 at 7:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 1, 2013 at 1:29 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
It is something very new for me.
If structure, etc are not read
Hi Vitaly,
The problem was with cpt file since it re sets the last line of gro. I
removed the -f flag and now the Z direction is extended. However, I see
that molecules tend to fill up the upper zone (free space) rapidly. I am
wondering how I can obtain the density profile if I am going to get
On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.com wrote:
Hi Vitaly,
The problem was with cpt file since it re sets the last line of gro. I
removed the -f flag and now the Z direction is extended. However, I see
that molecules tend to fill up the upper zone (free space) rapidly.
On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth katesed...@gmail.com wrote:
You are right. I compressed my alkane system under NPT at 400 K at 100
bar. The normal boiling point is below 425 K. So it seems there in no way
one can obtain profiles obove boiling point of liquid given than with the
There is a wonderful data page devoted to methane in wikipedia...
It follows from this webpage that you will get a perfect density profile if
you decrease your T down to 150K...
On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
On Mon, Apr 1, 2013 at 8:29 PM,
Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.
You must use NVT only. Otherwise, the cell will compress in XY directions
to compensate its inability to compress in Z direction.
Here
Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
compressibility in Z then? I was hoping to run NPT to secure a fixed
pressure.
I also wanted to know if surface tension can be also calculated under NVT
(if NPT fails for this puporse)
Thanks!
On 31 March 2013 14:01, Dr.
Hi Elisabeth -
On Sun, Mar 31, 2013 at 8:28 PM, Elisabeth katesed...@gmail.com wrote:
Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
compressibility in Z then? I was hoping to run NPT to secure a fixed
pressure.
Please, read about Gibbs phase rule... This is your
15 matches
Mail list logo
