VMD-L Mailing List

From: SHRAVANI NETHI . (p20160500_at_hyderabad.bits-pilani.ac.in)
Date: Mon May 20 2024 - 06:40:34 CDT

Dear VMD users,
I have been working on clay simulations with NAMD.
The simulation box consists of Montmorillonite (clay) and water.
As per the CLAYFF force field, the clay atoms are defined as a group of
atoms with no bonds except for O-H. Only non bonded interactions are
defined.
As a result, the clay atoms in the o/p dcd files were seen as not wrapped
and appear at different edges of the simulation box due to PBC conditions.
I need to wrap the clay atoms into single molecule.
I tried following pbc wrap
pbc wrap -center com -centersel "resname CLY" -compound residue -all
but I could neither wrap all clay atoms together not make the com of CLY as
box center with all water wrapped around it.
Any suggestion will be highly appreciated.
-
Shravani N
Ph.D Scholar
BITS-Pilani, Hyderabad Campus 

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