Hi Mark,<br> 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<br>
came out fine and comparable with the literature data but at 200K the result is not fine. I have attached the result<br>at 200K, please find in the attachment. There you can see within 1ps there is very sharp decrease in the decay.<br>
I do not know why it is happening! Even at room temperature this result is wrong. Can you help me in the regard.<br>Your help will be highly appreciated. Thank you.<br><br>Yours sincerely,<br>Rama<br><br><div class="gmail_quote">
On Wed, Jun 30, 2010 at 8:30 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br><br>----- Original Message -----<br>From: Ramachandran G <<a href="mailto:gtrama@gmail.com" target="_blank">gtrama@gmail.com</a>><br>Date: Thursday, July 1, 2010 11:42<br>Subject: [gmx-users] amber/charmm force field and HB lifetime at low temperature<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi gromacs users:<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Using amber/charmm force field we simulated a solvated protein <br><br></div><div class="im">I've never heard of such a forcefield. What do you mean?<br>
<br>> system at different temperature(300,250 and 200K).<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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.<br>
<br></div>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.<div>
<div></div><div class="h5"><br><br>> 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? <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"></font><br></div></div><font color="#888888">Mark
</font><br>--<br>
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