From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Tue Sep 07 2010 - 11:23:35 CDT
Did you specify only two instances of atomNameResidueRange? If that's case,
no wonder that segments B, C and D were ignored.
Giacomo
---- ----
Dr. Giacomo Fiorin
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
giacomo.fiorin_at_temple.edu
---- ----
On Mon, Sep 6, 2010 at 6:26 PM, dhacademic <dhacademic_at_gmail.com> wrote:
> Hi Jerome and Giacomo,
>
> I have tried the following syntax (in colvars.conf file) according to the
> reply:
> atoms {
>
> psfSegID A A B B C C D D
> atomNameResidueRange CA 386-485
> atomNameResidueRange CA 628-763
> }
> And I still meet a similar output shown as follow. This time 236 atoms on
> segment A can be selected. However, the rest atoms on segment B, C, D are
> still ignored. It looks like that this atom definition error comes from to
> the bug of the version 2.7b1.
>
> #### my output file ####
> ....
> colvars: Initializing atom group "atoms".
> colvars: Warning: found more than one instance of "psfSegID".
> colvars: Atom group "atoms" defined, 236 atoms, total mass = 2834.6.
>
> colvars: # refPositionsFile = colvarb.pdb
> colvars: # refPositionsCol = B
> colvars: # refPositionsColValue = 1
> colvars: Error: the PDB file "colvarb.pdb" contains coordinates for
> only 87342 atoms, but 236 are needed.
> .....
>
> Best,
>
> Hao
>
>
>
> On Mon, Sep 6, 2010 at 3:10 PM, Giacomo Fiorin <giacomo.fiorin_at_temple.edu>wrote:
>
>> It would be best to use 2.7b2 or 2.7b3, in general.
>>
>> In the specific example, you used four psfSegID values but you specified
>> them separately: the correct syntax is to put them on the same line (one
>> psfSegID keyword with multiple values).
>>
>> Also, there may be only one atomNameResidueRange option for each psfSegID
>> value, not two of them as in your case. You should use something like
>> "psfSegID A A B B C C D D" to fix this.
>>
>> Giacomo
>>
>>
>> ---- ----
>> Dr. Giacomo Fiorin
>> ICMS - Institute for Computational Molecular Science - Temple University
>> 1900 N 12 th Street, Philadelphia, PA 19122
>> giacomo.fiorin_at_temple.edu
>> ---- ----
>>
>>
>>
>>
>> On Mon, Sep 6, 2010 at 11:29 AM, dhacademic <dhacademic_at_gmail.com> wrote:
>>
>>> my version is NAMD 2.7b1
>>>
>>>
>>>
>>> On Mon, Sep 6, 2010 at 11:14 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
>>>
>>>> Hi,
>>>>
>>>> First, for TMD, you probably need the restraint force, so you should
>>>> request outputAppliedForce, not outputSystemForce.
>>>>
>>>>
>>>> > (1) Do the "centers" and "targets" keywords mean the initial and final
>>>> RMSD
>>>> > of the system? I feel confused by reading the related part of the
>>>> > user-manual.
>>>>
>>>> They are the initial and final values of the center of the restraint
>>>> potential. If all goes well, the RMSD should follow.
>>>>
>>>>
>>>> > (2) I want to define 4 (segments) * 236 (per segment) = 944 atoms in
>>>> the
>>>> > input. However, only 237 atoms are defined according to the output
>>>> > file. Someone else used a similar way to define atoms within different
>>>> > segments
>>>> > (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12359.html).
>>>> What
>>>> > is wrong with my syntax?
>>>>
>>>> Not sure. What version of NAMD are you using? I wonder if this could
>>>> be an old bug that is now fixed.
>>>>
>>>> Cheers,
>>>> Jerome
>>>>
>>>
>>>
>>
>
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