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<div>Sorry, meant to post this on the bb.</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 02. April 2013 um 11:50 Uhr<br/>
<b>Von:</b> "lloyd riggs" <lloyd.riggs@gmx.ch><br/>
<b>An:</b> vvchaban@gmail.com<br/>
<b>Betreff:</b> Aw: Re: [gmx-users] Re: density profile</div>
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<div>How would you set up a gas/gas interface, say modeled after a large gas planet or upper atmosphere, without effects from garvity and pressures in the 10K plus ATM? In such a system the gases behave almost like liquids, but most effects are from extreems of conditions. Actaul interfaces though I assume would include large amounts of mixing right at the atomic level interface, but I have no clue how far this would extend. If you remove rotational effects, I am willing to bet you can model a gas/gas interface at the atomic level with extreem conditions, which might be an aset in some fileds/areas of research. Minus gravitational effects though, I do not know if they could work properly. You can however set up a ligid gas interface by introducing box systems with differences in force at a plain across the midpoint equal to gas/liquid interfaces, or gradients of force, etc...but in all cases I assume a minimal amount of programming might be necessary. Opinions/answers anyone?</div>
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<div>Stephan Watkins</div>
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<div style="margin: 0 0 10.0px 0;"><b>Gesendet:</b> Montag, 01. April 2013 um 20:43 Uhr<br/>
<b>Von:</b> "Dr. Vitaly Chaban" <vvchaban@gmail.com><br/>
<b>An:</b> Elisabeth <katesedate@gmail.com>, gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] Re: density profile</div>
<div>There is a wonderful data page devoted to methane in wikipedia...<br/>
<br/>
It follows from this webpage that you will get a perfect density profile if<br/>
you decrease your T down to 150K...<br/>
<br/>
<br/>
On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban <vvchaban@gmail.com>wrote:<br/>
<br/>
><br/>
><br/>
><br/>
> On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth <katesedate@gmail.com> wrote:<br/>
><br/>
>> You are right. I compressed my alkane system under NPT at 400 K at 100<br/>
>> bar. The normal boiling point is below 425 K. So it seems there in no way<br/>
>> one can obtain profiles obove boiling point of liquid given than with the<br/>
>> current NVT recipe molecules tend to fill up the free zone no matter how<br/>
>> much pressure was applied in the previous NPT runs?<br/>
>><br/>
>><br/>
><br/>
> You cannot get a profile just because you have NO LIQUID and NO INTERFACE<br/>
> upon these conditions. Gas fills all the available space, there is no such<br/>
> thing as gas/gas interface.<br/>
><br/>
> And yeah... Forget about NPT and learn the Gibbs phase rule.<br/>
><br/>
><br/>
> Dr. Vitaly Chaban<br/>
><br/>
><br/>
><br/>
><br/>
><br/>
><br/>
>><br/>
>> On 1 April 2013 14:22, Dr. Vitaly Chaban <vvchaban@gmail.com> wrote:<br/>
>><br/>
>>><br/>
>>><br/>
>>><br/>
>>> On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth <katesedate@gmail.com> wrote:<br/>
>>><br/>
>>>> Hi Vitaly,<br/>
>>>><br/>
>>>> The problem was with cpt file since it re sets the last line of gro. I<br/>
>>>> removed the -f flag and now the Z direction is extended. However, I see<br/>
>>>> that molecules tend to fill up the upper zone (free space) rapidly. I am<br/>
>>>> wondering how I can obtain the density profile if I am going to get another<br/>
>>>> uniformly distributed box after this NVT run?<br/>
>>>><br/>
>>>><br/>
>>><br/>
>>> Here we come to the question what your system is composed of... Based on<br/>
>>> the density profile, this is not a (conventional) liquid... Polymer,<br/>
>>> non-Newtonian liquid ... or what?<br/>
>>><br/>
>>> If molecules tend to fill vacuum, it can only mean that the matter you<br/>
>>> are simulating is above critical point.<br/>
>>><br/>
>>> What is your T and what are the particles in your box?<br/>
>>><br/>
>>><br/>
>>> Dr. Vitaly Chaban<br/>
>>><br/>
>>><br/>
>>><br/>
>>><br/>
>>>><br/>
>>>> I am expecting to see how density changes with Z at the solvent -vacuum<br/>
>>>> interface....<br/>
>>>><br/>
>>>> Please advise me on this,,<br/>
>>>><br/>
>>>> Thanks!<br/>
>>>><br/>
>>>><br/>
>>>> On 1 April 2013 13:14, Dr. Vitaly Chaban <vvchaban@gmail.com> wrote:<br/>
>>>><br/>
>>>>> I think if you use checkpoint files, the program does not read either<br/>
>>>>> MDP, or GRO, or TOP, or anything except CPT.<br/>
>>>>><br/>
>>>>><br/>
>>>>> Dr. Vitaly Chaban<br/>
>>>>><br/>
>>>>><br/>
>>>>><br/>
>>>>><br/>
>>>>> On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth <katesedate@gmail.com>wrote:<br/>
>>>>><br/>
>>>>>> Hi vitaly,<br/>
>>>>>><br/>
>>>>>> The initial structure is indeed extended but the final output.gro is<br/>
>>>>>> not. I think its because I am using the cpt file from the previous NPT runs<br/>
>>>>>> as input for the new runs? Do I have to remove the -t flag?<br/>
>>>>>><br/>
>>>>>><br/>
>>>>>> On 1 April 2013 12:47, Dr. Vitaly Chaban <vvchaban@gmail.com> wrote:<br/>
>>>>>><br/>
>>>>>>> Hi Elisabeth -<br/>
>>>>>>><br/>
>>>>>>> The only explanation is that you actually DID NOT extend the box in<br/>
>>>>>>> Z direction. Look at the last line of confout.gro.<br/>
>>>>>>><br/>
>>>>>>> g_density -d Z gives you a [local] density versus Z coordinate.<br/>
>>>>>>><br/>
>>>>>>><br/>
>>>>>>> Dr. Vitaly Chaban<br/>
>>>>>>><br/>
>>>>>>><br/>
>>>>>>><br/>
>>>>>>><br/>
>>>>>>> On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth <katesedate@gmail.com>wrote:<br/>
>>>>>>><br/>
>>>>>>>> Hi Vitaly,<br/>
>>>>>>>><br/>
>>>>>>>> I did NVT simulations and tried to obtain density profile at<br/>
>>>>>>>> interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is<br/>
>>>>>>>> the density profile in the box not the interface. Box size is 3 nm and<br/>
>>>>>>>> Before NVT runsI extended Z to 6 nm. Please see the attached profile.<br/>
>>>>>>>> Thanks!<br/>
>>>>>>>><br/>
>>>>>>><br/>
>>>>>>><br/>
>>>>>><br/>
>>>>><br/>
>>>><br/>
>>><br/>
>><br/>
><br/>
--<br/>
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