[gmx-users] Re: density profile

[Dr. Vitaly Chaban]

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!
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>