[gmx-users] Re: density profile

[Elisabeth]

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?


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