VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Jul 30 2020 - 16:33:10 CDT

What are the differences between the two versions? Normally, I'm inclined
to think that if Joao changed some defaults, he had a good reason to, but I
can't comment further without knowing what changes you are seeing.

-Josh

On Thu, Jul 30, 2020 at 6:21 AM jrhau lung <jrhaulung_at_gmail.com> wrote:

> Dear VMD friends:
> Should the qwikmd file prepared by different versions of vmd be
> identical?
> I hope I am wrong, but for an identical protein pdb, same condition
> (explicit, 300k 0.15NaCl), the qwikmd files prepared by vmd1.9.4a12 and
> vmd1.9.4a29 appear having many different places.
> Would these differences generate identical simulation results? (This could
> be answered by analyze trajectory files downstream..Both vmd1.9.4 version
> could not repeat production simulation more than 3 in my system: ubuntu
> 16.04 LTS, NVIDIA-Linux-x86_64-440.82, cuda_9.0.176_384.81_linux.)
> Repeated production simulation more than 3 cycles could be achieved if
> using vmd1.9.3 with cuda8, which generate a qwikmd file has many places to
> those of vmd1.9.4 version)
> Understand these parameters one by one to tell which one makes the
> difference is what I have to do now.
>
>
> Jrhau
>
>
>
> jrhau lung <jrhaulung_at_gmail.com> 於 2020年7月27日 週一 下午5:19寫道：
>
>> Dear VMD friends:
>> An error was encountered in the initiation of the fifth cycle of a
>> 25ns production simulation.
>> When press down the finish button in the end of the fourth cycle, it
>> popup with "one or more files failed to be written, the new simulation
>> ready to run is". After hitting the "Start production simulation 5", an
>> application error message showed up as following,
>>
>> can't read "QWIKMD::advGui(protocoltb,MD,4,smd)": no such element in array
>> can't read "QWIKMD::advGui(protocoltb,MD,4,smd)": no such element in array
>> while executing
>> "if {$QWIKMD::advGui(protocoltb,$QWIKMD::run,$QWIKMD::state,smd) == 1 &&
>> $QWIKMD::state > 0} {
>> set do 1
>> }"
>> (procedure "QWIKMD::Run" line 115)
>> invoked from within
>> "QWIKMD::Run"
>> invoked from within
>> ".qwikmd.nbinput.f1.fcontrol.fcolapse.f1.run.button_Calculate invoke "
>> invoked from within
>> ".qwikmd.nbinput.f1.fcontrol.fcolapse.f1.run.button_Calculate instate
>> {pressed !disabled} {
>> .qwikmd.nbinput.f1.fcontrol.fcolapse.f1.run.button_Calculat..."
>> (command bound to event)
>>
>> Have try to modify the parameters in the X.qwikmd file but without
>> success,
>> Hope someone could help me to pass over this obstacle. Thanks
>>
>> Jrhau
>>
>