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

Justin Lemkul jalemkul at vt.edu
Wed Jul 16 02:37:06 CEST 2014

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 A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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