AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Feb 26 2009 - 10:24:40 CST

yes, do that. think about whether you want to include GB solvation or just
gas phase energies are ok (probably gas phase in your case)
when you strip the water and write the traj file in ptraj, make sure to
specify nobox. make sure to use a prmtop file made witout water. also make
sure your patches are up to date.

On Thu, Feb 26, 2009 at 11:19 AM, Lake, Thomas <thomas.lake08_at_imperial.ac.uk
> wrote:

> Hello,
>
> I am trying to plot the energy vs time of a peptide during a MD
> simulation. Since I want the energy of the peptide without solvent, I
> strip the water molecules using ptraj. I'm not sure how to then obtain
> the energy. I'm wondering if I should input the mdcrd file into sander
> using the imin=5 option?
>
> Any help would be appreciated
>
> Regards
>
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