[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT

[vivek sinha]

What changes in topology file should I do? Just the number of water
molecules?
But I have also changed the atom number of each molecule while removing the
molecules from inside.

In other words my new .gro file also has the atom numbers in increasing
order with no gap.



On Mon, Jul 14, 2014 at 1:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/13/14, 12:10 PM, vivek sinha wrote:
>
>> Hi All,
>> I solvated the CNT but then I wanted to remove the water molecules from
>> inside the CNT. I made a C++ script and have removed but the topology file
>> is still not updated. How can I update the topology file?
>> Thanks,
>> Vivek Sinha
>>
>> PS: I have update the topology after complete solvation but not after
>> removing the H2O molecules. Please help me!
>>
>>
> You'll have to update it yourself.  It's simple to do.  Use grep to count
> the number of waters, then use a text editor to change the topology.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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