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

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Mar 25 2019 - 11:44:08 CDT

Most or all of the free energy functionality in AMBER is somewhat different
than in NAMD.

For geometrical transformations most users use Colvars - there are a number
of tutorials on this.

For alchemical transformations there are also tutorials. Unfortunately,
NAMD only supports XPLOR format inputs for these kinds of calculations,
though there are now tools (such as ParmEd) for converting between formats
that may help.

HTH,
BKR

On Sun, Mar 24, 2019 at 3:51 PM Braden Kelly <bkelly08_at_uoguelph.ca> wrote:

> 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
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__m3g.iqm.unicamp.br_packmol_home.shtml&d=DwMFAg&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=bmYT7SFHq2qTybxVX6auD7OQAIVVJAMzw-0naUITwHc&s=wcMWx9ERNnZ06ruYZ8PzQVMlcoTuQ8qq5GJ1fTzSgWY&e=>
> Packmol - Initial configurations for Molecular Dynamics
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__m3g.iqm.unicamp.br_packmol_home.shtml&d=DwMFAg&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=bmYT7SFHq2qTybxVX6auD7OQAIVVJAMzw-0naUITwHc&s=wcMWx9ERNnZ06ruYZ8PzQVMlcoTuQ8qq5GJ1fTzSgWY&e=>
> 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
>
>

This archive was generated by hypermail 2.1.6 : Wed Sep 18 2019 - 23:20:52 CDT