[gmx-users] Re: density profile

[Elisabeth]

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!
>>
>
>