[gmx-users] Re: gromacs with CMAP

[Da-Wei Li]

It is because I want to apply cmap to my own stuff. I can define my
own 2D grid potential and apply to two sequential dihedral angles by
add one line in the topol file.  However, the testing result is really
unexpected.

dawei

On Tue, Jun 29, 2010 at 8:53 AM, Per Larsson <per.larsson at sbc.su.se> wrote:
> Hi,
>
> I do not fully understand what you are trying to do, but currently CMAP is only
> available for the standard amino acid residues present in the rtp-file for the
> Charmm-forcefield, and the values for the grid are specified in the cmap.itp-file.
>
> Do you use something else?
>
> /Per
>
>
> 29 jun 2010 kl. 14.45 skrev Da-Wei Li:
>
>> HI, David,
>>
>> thanks for your advise. I remove the bond angle force and get same
>> result. It is really strange. If I set +5 on all the 24*24 grid, I
>> just get a inverted distribution and if I set 0 on all grid, I will
>> get a uniformed distribution. It is like that 27 regions are force to
>> have zero cmap potential. I cannot attach figure due to size limit the
>> list. I have sent the figure to you directly.
>>
>> best,
>>
>> dawei
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