[CP2K:3531] restraint dihedral

Jacopo Sgrignani sgr... at gmail.com
Mon Oct 17 15:39:25 CEST 2011


Dear Pablo
The input files are in the tar archive.
Actually, I found a post in this list about a similar problem with AMBER
prmtop files.
Then I tried to put the number (456) of the molecule analysing the output of
the MOLECULE print_key (it is the .mol file in the tar archive).
However the message is that the constrainted atoms are not in the 456
molecule.
Maybe I'm reading the molecule number in a wrong place.


Thanks again

Jacopo
2011/10/17 Campomanes Ramos Pablo <pablo.ca... at epfl.ch>

>  Dear Jacopo,
>
> I think that the message is clear. The code cannot find the MOLNAME defined
> for constraints, and therefore I assume that constraints are not applied.
> However, it is difficult to guess where your problem is (pdb, topology
> file...) without having a look at your input(s) file(s)... Could you please
> post them here?
>
> Regards,
> Pablo.
>
>  ------------------------------
> *From:* cp... at googlegroups.com [cp... at googlegroups.com] on behalf of Jacopo
> Sgrignani [sgr... at gmail.com]
> *Sent:* Monday, October 17, 2011 1:44 PM
> *To:* cp... at googlegroups.com
> *Subject:* Re: [CP2K:3530] restraint dihedral
>
>  Thanks Pablo for your suggestion, I'm trying this solution.
> However I have a problem with the keyword MOLNAME or MOLECULE<http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE.html#list_MOLECULE>,
> actually
> I tried both the keyword MOLECULE with the resid number from the PDB input
> file, and
> the keyword MOLNAME with the resname fromthe pdb, but they don't seem to be
> the right solutions.
> Actually using MOLECULE with the resname the simulation start but in the
> output I find this warning:
>
>
>  *** 13:22:30 WARNING in topology_constraint_util:print_warning_molname
> ***
>  *** MOLNAME (ASD) was defined for constraints, but this molecule      ***
>  *** name is not defined. Please check carefully your PDB, PSF (has
> ***
>  *** priority over PDB) or input driven CP2K coordinates. In case you may
> ***
>  *** not find the reason for this warning it may be a good idea to print
> ***
>  *** all molecule information (including kind name) activating the
> ***
>  *** print_key MOLECULES specific of the SUBSYS%PRINT section.
> Then I used also the MOLECULES print_key but the number of the molecule
> where the constrainted atoms are, it is
> the same of the resid number in the PDB.
>
> Can somebody help me? Is it this waring important or the costraint is
> applied?
>
> Thanks again
>
> Jacopo
>
> 2011/10/16 Campomanes Ramos Pablo <pablo.ca... at epfl.ch>
>
>>  Dear Jacopo,
>>
>> I think you can easily solve your problem if you have a look at:
>>
>>
>> http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE/RESTRAINT.html
>>
>> Best regards,
>> Pablo.
>>
>> -----------------------------------------------
>> *Pablo Campomanes *
>>
>>
>> Tel:++41-(0)21-693-0326
>> Fax: ++41-(0)21-693-0320
>> Email: pablo.ca... at epfl.ch
>>
>>
>>  Laboratory of Computational
>> Chemistry and Biochemistry
>> BCH 4118 EPF Lausanne
>> CH-1015 Lausanne
>> ------------------------------------------------
>>
>>  ------------------------------
>> *From:* cp... at googlegroups.com [cp... at googlegroups.com] on behalf of Jacopo
>> Sgrignani [sgr... at gmail.com]
>> *Sent:* Sunday, October 16, 2011 4:09 PM
>> *To:* cp... at googlegroups.com
>> *Subject:* [CP2K:3528] restraint dihedral
>>
>>    Dear All
>>
>> I would like to know the best way to restrict a dihedral angle during a
>> simulation.
>>
>> Without any experience about this, I tried to use a fictitious Colvar
>> putting two walls to define the space that the dihedral can freely explore.
>>  Then, the program asks for a value of the SCALE variable during the
>> metadynamics calculation, and I set this to 0.
>>
>>
>>
>> However, I'm not sure that this is the correct solution to my problem.
>>
>>
>>
>> Can somebody suggest me other solutions?
>>
>>
>>
>> Thanks
>>
>>
>>
>> Jacopo
>>
>>
>>
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