<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi,<br>Once again, I appreciate all the responses.<br>1. To correct I just had in the previous email. I used GROMOS53ab not CHARMM. My apology.<br>2. At high temperaure, one of the helical turn in a alpha helix (3 residues) turns into a coil in GROMOS forcefield throughout the 20ns simulation. It was only slightly distorted in OPLSAA simulation in 20ns. <br>3. The RMSF (backbone) for those 3 residues: 0.3nm in GROMOS vs. 0.1 nm in OPLSAA.<br><br>As I mentioned, the protein is near its melting temperature, therefore, I am not surprised to see some helix to coil transition or helical distortions. As Justin has suggested, I probably will try to make a longer run to see what will happen.<br><br>Best,<br><br>Simon<br>--- On <b>Fri, 5/27/11, Peter C. Lai <i><pcl@uab.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left:
5px; padding-left: 5px;"><br>From: Peter C. Lai <pcl@uab.edu><br>Subject: Re: [gmx-users] oplsaa vs. charmm<br>To: "simon sham" <ssham44@yahoo.com><br>Cc: "gmx-users@gromacs.org" <gmx-users@gromacs.org><br>Date: Friday, May 27, 2011, 9:05 AM<br><br><div class="plainMail">On 2011-05-27 10:50:14AM -0500, simon sham wrote:<br>> Hi,<br>> I have recently done two simulations on a protein at high temperature near its melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA to double check the results. There are some differences in the structures between the forcefield used. I know different forcefields can give different results. All parameters in the simulations were the same except the forcefield. Is there anyway I can tell which forcefield gives more reliable results?<br>> <br><br>Also you never stated what RMSD/RMSFs between the two and if they are<br>significant to what you care to see (i.e. if you
expect, say, alpha<br>helix to random coil transition, what changes in the unfolding do you see<br>that make you suspect one forcefield is better than the other?). Also if this <br>is in a solvated system, the rest of the forcefield has been parameterized <br>with the implicit assumption that TIPS3P (Charmm-specific) water will be used <br>so make sure you have switched your water type when using CHARMM.<br><br>-- <br>==================================================================<br>Peter C. Lai | University of Alabama-Birmingham<br>Programmer/Analyst | BEC 257<br>Genetics, Div. of Research | 1150 10th Avenue South<br><a ymailto="mailto:pcl@uab.edu" href="/mc/compose?to=pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>(205) 690-0808
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