From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 10 2017 - 21:10:21 CDT
The syntax of the colvarbias command that Josh quoted:
eval colvarbias [concat changeconfig $replica(colvarbias)]
has *not* changed.
Perhaps what changed is how the replica dictionary is filled in, i.e. the
problem is in the script.
Giacomo
On Thu, Aug 10, 2017 at 5:17 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:
> Z is the name of the harmonic restraint.
>
> For reference, the colvar is in a different file:
>
> harmonic {
> name Z
> colvars COMDistance
> forceConstant { 0.0125 } centers { 0.0 }
> }
>
> But the replica(colvarbias.$i) is how the script tells namd to update that
> replica's properties. I wondered if something has changed in how namd
> interprets that data.
>
> Thanks!
> JC
>
> On Thu, Aug 10, 2017, 1:58 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
>> The old way would have been through something like "eval colvarbias [cat
>> changeconfig somestuff here]". I ran into problems once when I neglected to
>> change the name of the harmonic bias I wanted to change (I call all of mine
>> harm), accidentally using the collective variable the harmonic was trying
>> to bias as the name instead. Is "Z" the name of your collective variable or
>> the harmonic that biases the collective variable?
>>
>> -Josh
>>
>> On 08/10/2017 11:54 AM, Giacomo Fiorin wrote:
>> Hi JC, how is this code calling Colvars? I don't see any Tcl command
>> that does call it in there.
>>
>> The primary method for changing parameters for a bias should be through
>> the "cv" command. Deleting the bias and re-creating it with the new
>> configuration would be the way to go.
>>
>> Giacomo
>>
>> On Thu, Aug 10, 2017 at 1:07 PM, JC Gumbart <gumbart_at_physics.gatech.edu<
>> mailto:gumbart_at_physics.gatech.edu>> wrote:
>> Has something changed in newer versions of NAMD with regards to how
>> inputs are fed to different replicas in colvars?
>>
>> Specifically, the input below worked fine in earlier versions (2.10 I
>> think?), but in 2.12, the center and forceConstant both get set to the same
>> value, namely that for the center.
>>
>> > proc replica_bias { i } {
>> > set c [expr 5.5 + $i*0.5]
>> > set klist { 10 10 10 10 10 10 5 5 5 5 5 5 5 5 5 5 5 5 5 5 }
>> > set k [expr [lindex $klist $i]*0.05*0.05]
>> > return [list Z "centers \{$c\} forceConstant \{$k\}"]
>> > }
>>
>> And then this is how that proc is used:
>> > set replica(colvarbias) [replica_bias $replica(index)]
>> > for { set i 0 } { $i < $replica(num_neighbors) } { incr i } {
>> > set replica(colvarbias.$i) [replica_bias $replica(index.$i)]
>> > set replica(colvarbias.$i) [replica_bias $replica(index.$i)]
>> > }
>>
>>
>> Thanks!
>> JC
>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_Q3TBQU&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=le65FX1fWXGgd_kx40_8XmBrxibpHje2LVmb5ZXwlKY&s=ejCJmH0xLQz-6niH-chFQO7oupkeVnQmzanCeRwDg6s&e=>
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%
>> 2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%
>> 7C8314221259fd42dbbd7a08d4e018e602%7Ca0f29d7e28cd4f5484427885aee7
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>> TfWISdnTlqBko%3D&reserved=0
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__na01.safelinks.protection.outlook.com_-3Furl-3Dhttp-253A-252F-252Fgoo.gl-252FQ3TBQU-26data-3D02-257C01-257CJoshua.Vermaas-2540nrel.gov-257C8314221259fd42dbbd7a08d4e018e602-257Ca0f29d7e28cd4f5484427885aee7c080-257C0-257C0-257C636379844930020633-26sdata-3D8L89QqKCxfU6eQHAfuug45uDZNPVjMTfWISdnTlqBko-253D-26reserved-3D0&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=le65FX1fWXGgd_kx40_8XmBrxibpHje2LVmb5ZXwlKY&s=lNY-a33ikqwInk-sa3mzEA_5Vb3C_YKAobjZNpWW_dA&e=>
>> >
>> https://github.com/giacomofiorin
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_giacomofiorin&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=le65FX1fWXGgd_kx40_8XmBrxibpHje2LVmb5ZXwlKY&s=Zh5zXfsgRslsJeJtrroupym0Vn0vrRf7lQdwK16swWs&e=>
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.
>> com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%
>> 7C8314221259fd42dbbd7a08d4e018e602%7Ca0f29d7e28cd4f5484427885aee7
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>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__na01.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fgithub.com-252Fgiacomofiorin-26data-3D02-257C01-257CJoshua.Vermaas-2540nrel.gov-257C8314221259fd42dbbd7a08d4e018e602-257Ca0f29d7e28cd4f5484427885aee7c080-257C0-257C0-257C636379844930020633-26sdata-3D4p-252FVXyHfOnhkmFwh9djZRJRJgmVZTLNc1UAxI6v9tU8-253D-26reserved-3D0&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=le65FX1fWXGgd_kx40_8XmBrxibpHje2LVmb5ZXwlKY&s=_fV9RaFM5zoDjEN54QzaoFLV-funRJZM1GMXMKU5MOM&e=>
>> >
>>
>>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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