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

[vivek sinha]

But mdrun doesnt update these information/new numbering in the topology
file. I mean the topology fie would be saying that there is a bond between
101 and 105 and if I removed those atoms, the mdrun would have assignmed
101 and 105 to some other atom and hence it can create problems.

Is this possible?


On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/15/14, 2:19 PM, vivek sinha wrote:
>
>> Hey Justin,
>> I think I understood the problem. When I removed the solvent from inside
>> CNT, I kept the numbering of atoms just like before without actually
>> making
>> a new strictly increasing order numbering. But now when I see that after
>> the energy minimization the new pdb file got arranged strictly by
>> increasing order.
>>
>> As an example. After deleting atoms inside the CNT, my .gro file did not
>> had the atom no 6292, but after energy minimisation the em.gro file
>> contains the atom no 6292. This must have created a renumbering of the
>> atoms. Not good I suppose.
>> Please suggest what to do?
>>
>> The concern is that whether to renumber the molecules after removing the
>> water from inside the CNT or not?
>>
>>
> The numbering in the input coordinate file is irrelevant.  The output of
> mdrun is always numbered consecutively from 1.
>
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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