[gmx-users] Re: gromacs with CMAP

David van der Spoel spoel at xray.bmc.uu.se
Tue Jun 29 06:48:39 CEST 2010

On 2010-06-29 03.48, Da-Wei Li wrote:
>> Hi, all
>> I recently download the git version and test the CMAP. However, very
>> strange result I get. I want to use CMAP support in my own
>> coarse-grained force field.
>> Basically, I construct a ALA-ALA-ALA system and turn off all energy
>> terms except bond length, bond angle and CMAP to do some test. The
>> CMAP is only applied to phi,psi of central residue with a constant
>> value of -5 (unit is kj/mol, right?) on a 24*24 grid. The result Rama
>> plot is not a uniformed distribution as expected but avoid  27 regular
>> distributed region ! (Sorry I can't attach a figure due to size limit).
> Can someone help me out?

Maybe the angle potential also implicitly imposes limits to the phi/psi 
available space? Try turning it off.

>> best
>> dawei

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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