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

Justin Lemkul jalemkul at vt.edu
Sun Jul 13 18:16:09 CEST 2014

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 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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