From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Oct 25 2010 - 02:18:07 CDT
Aha, of course. If I'm only interested in the minimization part, do I even
have to calculate the forces or is it enough to calculate only th energies?
(I'm guessing only energies are enough)
Best regards,
Ajasja
On Fri, Oct 22, 2010 at 17:30, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> TclForces should work during minimization as long as you also calculate the
> correct energy to go along with the force (i.e., the added force is the
> negative gradient of the added energy). The minimizer relies on energies
> during its line searches.
>
> -Jim
>
>
>
> On Thu, 21 Oct 2010, Ajasja Ljubeti~M wrote:
>
> Dear all,
>>
>> I am currently running a rigid multidimensional dihedral scan of a spin
>> label. I generate the conformations using VEGA ZZ and than extract the
>> energies with namd using:
>>
>> while { ![coorfile read] } {
>> # Set firstTimestep so our energy output has the correct TS.
>> firstTimestep $ts
>> # Compute energies and forces, but don't try to move the atoms.
>> run 0
>>
>> incr ts 1
>> }
>>
>> Would it be possible to run a relaxed dihedral scan in a similar manner.
>> I tried putting "minimize 100" after each "run 0", which works in a
>> manner.
>> After adjusting *DCDfreq* to 101 I get only minimal structures in the DCD.
>> (By the way - it seems that *outputEnergies *has no efect on the number of
>> energies printed during minimization)
>>
>> I would like to be able to restrain the dihedral being scanned. I think
>> that
>> neither tclForces or the ABF module work during minimization. Can
>> extraBonds
>> or *consref *be changed between runs? Are there any other options?
>>
>> (As a last resort I can always write N seperate pdb files.)
>>
>> Best regards,
>> Ajasja
>>
>
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