[gmx-users] Re: density profile

[Dr. Vitaly Chaban]

On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth <katesedate at 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 added to the
> other side due to PBC. as a result the density profile does not exactly go
> down to zero but tends to zero anyways. I was wondering if this is
> considered a liquid-vapor interface?
>


YES






>  or it is still liquid-vacuum?
>
> thanks!
>
>
> On 1 April 2013 14:43, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>
>> 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 <vvchaban at gmail.com>wrote:
>>
>>>
>>>
>>>
>>> On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth <katesedate at 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
>>>> current NVT recipe molecules tend to fill up the free zone no matter how
>>>> much pressure was applied in the previous NPT runs?
>>>>
>>>>
>>>
>>> You cannot get a profile just because you have NO LIQUID and NO
>>> INTERFACE upon these conditions. Gas fills all the available space, there
>>> is no such thing as gas/gas interface.
>>>
>>> And yeah... Forget about NPT and learn the Gibbs phase rule.
>>>
>>>
>>> Dr. Vitaly Chaban
>>>
>>>
>>>
>>>
>>>
>>>
>>>>
>>>> On 1 April 2013 14:22, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth <katesedate at 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. I am
>>>>>> wondering how I can obtain the density profile if I am going to get another
>>>>>> uniformly distributed box after this NVT run?
>>>>>>
>>>>>>
>>>>>
>>>>> Here we come to the question what your system is composed of... Based
>>>>> on the density profile, this is not a (conventional) liquid... Polymer,
>>>>> non-Newtonian liquid ... or what?
>>>>>
>>>>> If molecules tend to fill vacuum, it can only mean that the matter you
>>>>> are simulating is above critical point.
>>>>>
>>>>> What is your T and what are the particles in your box?
>>>>>
>>>>>
>>>>> Dr. Vitaly Chaban
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> I am expecting to see how density changes with Z at the solvent
>>>>>> -vacuum interface....
>>>>>>
>>>>>> Please advise me on this,,
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>>
>>>>>> On 1 April 2013 13:14, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>>>>>>
>>>>>>> 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 <katesedate at gmail.com>wrote:
>>>>>>>
>>>>>>>> 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 <vvchaban at gmail.com>wrote:
>>>>>>>>
>>>>>>>>> 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 <katesedate at gmail.com>wrote:
>>>>>>>>>
>>>>>>>>>> Hi Vitaly,
>>>>>>>>>>
>>>>>>>>>> I did NVT simulations and tried to obtain density profile at
>>>>>>>>>> interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is
>>>>>>>>>> the density profile in the box not the interface. Box size is 3 nm and
>>>>>>>>>> Before NVT runsI extended Z to 6 nm. Please see the attached profile.
>>>>>>>>>> Thanks!
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>