AMBER Archive (2009)

Subject: Re: [AMBER] implicit solvent (GB version2) MD simulation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 10 2009 - 10:57:57 CDT

GB simulations of peptides can have many issues. I suggest that you need to
read beyond the tutorials, which are just meant to show you some of the
technical things. There are many papers on peptide simulations using GB
models, and you probably want to read those, and follow protocols from ones
that successfully address scientific problems similar to what you want to
do.

On Fri, Jul 10, 2009 at 11:53 AM, workalemahu berhanu
<wgberhanu_at_gmail.com>wrote:

> Dear amber users
> I was doing implicit solvent (GB version2) MD simulation on my peptide
> and the peptide with the ligand but the RMSD is not getting
> stabilized. I run it at different simulation times to see if it is
> getting stabilized (from 100ps to 10 ns).
> I am suspecting that there could be a problem with my approach? I
> followed tutorial 1 for the DNA
> The peptide is first minimized according to:
> Minimisation
> &cntrl
> imin = 1,
> maxcyc = 1000,
> ncyc = 500,
> ntb = 0,
> igb = 2
> cut = 12
> /
> The input file for the simulation is:
> MD run Generalised Born, 12 angstrom cut off
> &cntrl
> imin = 0, ntb = 0,
> igb = 2, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 50000000, dt = 0.001,
> cut = 12.0
> /
> If you notice any mistake in the method I am using, please tell me.
> With best regards
> Thank you
> Workalemahu
>
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