[gmx-users] Re: density profile

[Dr. Vitaly Chaban]

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!
>>>
>>
>>
>