[gmx-users] oplsaa vs. charmm
ssham44 at yahoo.com
Fri May 27 18:28:33 CEST 2011
Once again, I appreciate all the responses.
1. To correct I just had in the previous email. I used GROMOS53ab not CHARMM. My apology.
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.
3. The RMSF (backbone) for those 3 residues: 0.3nm in GROMOS vs. 0.1 nm in OPLSAA.
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.
--- On Fri, 5/27/11, Peter C. Lai <pcl at uab.edu> wrote:
From: Peter C. Lai <pcl at uab.edu>
Subject: Re: [gmx-users] oplsaa vs. charmm
To: "simon sham" <ssham44 at yahoo.com>
Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Date: Friday, May 27, 2011, 9:05 AM
On 2011-05-27 10:50:14AM -0500, simon sham wrote:
> 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?
Also you never stated what RMSD/RMSFs between the two and if they are
significant to what you care to see (i.e. if you expect, say, alpha
helix to random coil transition, what changes in the unfolding do you see
that make you suspect one forcefield is better than the other?). Also if this
is in a solvated system, the rest of the forcefield has been parameterized
with the implicit assumption that TIPS3P (Charmm-specific) water will be used
so make sure you have switched your water type when using CHARMM.
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | BEC 257
Genetics, Div. of Research | 1150 10th Avenue South
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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