[gmx-users] amber/charmm force field and HB lifetime at low temperature

Mark Abraham mark.abraham at anu.edu.au
Thu Jul 1 05:30:38 CEST 2010

----- Original Message -----
From: Ramachandran G <gtrama at gmail.com>
Date: Thursday, July 1, 2010 11:42
Subject: [gmx-users] amber/charmm force field and HB lifetime at low	temperature
To: gmx-users at gromacs.org

> Hi gromacs users:
>      Using amber/charmm force field we simulated a solvated protein 

I've never heard of such a forcefield. What do you mean?

> system at different temperature(300,250 and 200K).
> I used TIP5P water model and applied NVT ensemble . We analyzed the hydrogen bond life time correlation function(HBCF) to study the protein water interactions. At 300K, the result looks good and comparable with the literature data. But at 250 and 200K, during the initial 0-2ps, HBCF decay is very fast before it start to relax.

Forcefields are typically parameterized on data around laboratory conditions, so trying to make observations on systems whose conditions are  significantly far from those is doubtful. I don't have any real idea what "decay is very fast before it start to relax" means, either.

> This problem does not arise when i tried with other force field which came along with gromacs package(like GROMOS,OPLS..) I don't know where i am making mistakes; patching the amber and charmm force fields to gromacs package lead to this problem? 


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