[gmx-users] Re: gromacs with CMAP

[Da-Wei Li]

hi, all

Finally figured out that it was because all numbers in the cmap.itp
file must be separated by only one space,otherwise the program will
read in a "zero". I would suggest this to be fixed in the release
version.

have a nice day.

dawei

On Tue, Jun 29, 2010 at 9:05 AM, Da-Wei Li <lidawei at gmail.com> wrote:
> 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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>