[gmx-users] Re: density profile

[Dr. Vitaly Chaban]

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