Re: Solvate with methanol and acetone using free energy methods in NAMD?

From: Braden Kelly (bkelly08_at_uoguelph.ca)
Date: Sun Mar 24 2019 - 14:49:40 CDT

You can use packmol to set up the initial structure. After that it is just a typical Amber/NAMD simulation.

http://m3g.iqm.unicamp.br/packmol/home.shtml
Packmol - Initial configurations for Molecular Dynamics<http://m3g.iqm.unicamp.br/packmol/home.shtml>
PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar ...
m3g.iqm.unicamp.br

Braden
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Defrese, Matthew <matthew.defrese_at_uky.edu>
Sent: Sunday, March 24, 2019 2:03 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Solvate with methanol and acetone using free energy methods in NAMD?

Hello,

We are looking to model a system consisting of ligand binding to a synthetic polymer in varying solvent conditions such as water, acetone, methanol and their mixtures. Is there a straightforward way of solvating a box with these types of solvents in NAMD?

Is setting up and running free energy calculations in NAMD similar or equivalent to AMBER in terms of user friendliness? As all of our input files are in AMBER format, would there be any impediment to using these files in NAMD?

Thank you for any assistance,

- Matt Defrese

Graduate Student, Marsac Lab, Dept. of Pharmaceutical Sciences

College of Pharmacy, University of Kentucky

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