[gmx-users] Re: density profile

[Dr. Vitaly Chaban]

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:

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> On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth <katesedate at gmail.com> wrote:
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>> 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?
>>
>>
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> 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.
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> Dr. Vitaly Chaban
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>> On 1 April 2013 14:22, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
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>>> 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
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>>>>
>>>> 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!
>>>>>>>>
>>>>>>>
>>>>>>>
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