Re: rmsd colvars atom definition

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Apr 10 2020 - 03:05:35 CDT

Hi Francesco,

if you are trying to select the C alpha, I assume their name is CA. What is
N1?

There is so far no way to select by residue name, however for that kind of
task I'd recommend preparing the input using the Dashboard in VMD.

Best,
Jerome

On Fri, 10 Apr 2020 at 09:56, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Hello
> I am looking for advice on defining <atomNameResidueRange> for rmsd
> colvars. As shown below, I could define one atom only. To this concern, I
> tried also <atomNameResidueRange P N1 2820-2821>
> which was not accepted.
>
> Moreover, is it possible to define residue names in place of atom names?
>
>
>> colvar {
>> name colvar1 # needed to identify the variable
>> lowerBoundary -2.0
>> upperBoundary 2.0 ;# force will kick in when rmsd exceeds 2 A
>>
>>
>> lowerWall -1.5 ;# a lttle higher than lowerBoundary
>> upperWall 1.5 ;# a little lower than upperBoundary
>>
>> lowerWallConstant 100.0 ;# force constant in kcal/mol
>> upperWallConstant 100.0
>> outputTotalForce yes # reports also colvar system force
>>
>>
>> rmsd {
>> atoms {
>> # add all the C-alphas within residues 2820-2821 of segment AN7
>> psfSegID AN7
>> atomNameResidueRange N1 2820-2821
>> }
>> # refPositionsFile sphere20_CEA_box_ion.pdb
>> }
>> ref PositionsCol X, Y, Z
>> }
>>
>> colvar {
>> name colvar2 # needed to identify the variable
>> lowerBoundary -2.0
>> upperBoundary 2.0 ;# force will kick in when rmsd exceeds 2 A
>>
>> lowerWall -1.5 ;# a lttle higher than lowerBoundary
>> upperWall 1.5 ;# a little lower than upperBoundary
>>
>> lowerWallConstant 100.0 ;# force constant in kcal/mol
>> upperWallConstant 100.0
>>
>> outputTotalForce yes # reports also colvar system force
>>
>>
>> rmsd {
>> atoms {
>> # add all the C-alphas within residues 2869-2875 of segment AN8
>> psfSegID AN8
>> atomNameResidueRange N1 2869-2875
>> }
>> refPositionsFile sphere20_CEA_box_ion.pdb
>> }
>> # refPositionsCol X, Y, Z
>> }
>>
>> harmonic {
>>
>> name AN7_harmonic
>>
>> colvars { colvar1 }
>>
>> centers 0.0
>>
>> forceConstant 10.0
>> }
>>
>> harmonic {
>>
>> name AN8_harmonic
>>
>> colvars { colvar2 }
>>
>> centers 0.0
>>
>> forceConstant 10.0
>> }
>>
>
> Thanks
> francesco pietra
>

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