[CP2K:4391] amber torsion energy

Teodoro Laino teodor... at gmail.com
Thu May 2 11:18:03 CEST 2013


Thanks Letif and apologies for the delay.
The issue was indeed a bug and the fix is in the SVN. Should you encounter other discrepancies, please, do not hesitate to report them.
best,
Teo

On Apr 22, 2013, at 8:54 PM, Letif Mones <letif... at gmail.com> wrote:

> Hi Teo,
> 
> I am sending the following files: amber and cp2k inputs, amber restart file and amber topology file (dmpoh_vacuum.atop). I also attached another topology file (dmpoh_vacuum_mod.atop) in which I halved the dihedral force constants. With this latter cp2k gives the right answer.
> 
> Regards,
> 
> Letif
> 
> 
> 
> 
> On 22 Apr 2013, at 17:53, Teodoro Laino wrote:
> 
>> Dear Letif,
>> 
>> thanks for reporting this issue. All parameters should be converted at the moment they are read. We also had few examples to check the numerics and I remember they were matching with Sander they were OK.
>> Do you have an input file (including all relevant files) that shows this problem?
>> 
>> Thanks,
>> Teo
>> 
>> On Apr 22, 2013, at 5:23 PM, Letif Mones <letif... at gmail.com> wrote:
>> 
>>> Hi,
>>> 
>>> I did a molecular mechanical calculation in cp2k using an amber topology file (force field: amber99). When I checked the bonded energy terms I found that the bond and angle terms are correct but the dihedral energy is twice as the energy calculated by sander. I think the reason is that in the amber FF the form of the torsion potential is: K / 2 * [ 1 + cos[ M*PHI - PHI0 ] ] while cp2k uses the form of  K * [ 1 + cos[ M*PHI - PHI0 ] ].
>>> So should not the torsion force constant read from an amber topology file be multiplied by 0.5 (and the improper one too as it has the same form)?
>>> 
>>> Letif
>>> 
>>> 
>>> -- 
>>> You received this message because you are subscribed to the Google Groups "cp2k" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com.
>>> To post to this group, send email to cp... at googlegroups.com.
>>> Visit this group at http://groups.google.com/group/cp2k?hl=en.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>> 
>>> 
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com.
>> To post to this group, send email to cp... at googlegroups.com.
>> Visit this group at http://groups.google.com/group/cp2k?hl=en.
>> For more options, visit https://groups.google.com/groups/opt_out.
>> 
>> 
> 
> <amber.inp><cp2k.inp><dmpoh_vacuum_mod.atop><dmpoh_vacuum.atop><dmpoh.rst>-- 
> You received this message because you are subscribed to the Google Groups "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at http://groups.google.com/group/cp2k?hl=en.
> For more options, visit https://groups.google.com/groups/opt_out.
> 
> 




More information about the CP2K-user mailing list