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

[Ramachandran G]

Hi Mark,
    Thanks for your reply. I used charmm forcefield to study a solvated
protein using TIP5P water model applying NVT ensemble. I did hydrogen-bond
correlation function to understand the diffusivity of water near the
protein. At 300K the result
came out fine and comparable with the literature data but at 200K the result
is not fine. I have attached the result
at 200K, please find in the attachment. There you can see within 1ps there
is very sharp decrease in the decay.
I do not know why it is happening!  Even at room temperature this result is
wrong. Can you help me in the regard.
Your help will be highly appreciated. Thank you.

Yours sincerely,
Rama

On Wed, Jun 30, 2010 at 8:30 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- 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?
>
> Mark
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100712/e22f58cd/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: HB-200K.pdf
Type: application/pdf
Size: 32784 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100712/e22f58cd/attachment.pdf>