VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Thu Jul 30 2020 - 18:44:45 CDT

Dear Peter and Josh;
     The qwikmd, psf and pdb files generated by 194a12 and 194a29 are added
in attached files. The psf and pdb files from run file folder should have
been solvated and are quite large. Hope the transfer could be reached.
Your kind help will be highly appreciated.
 bucf9rzln4-pqr-2X-fix195-460_QwikMD-194a29.pdb
<https://drive.google.com/file/d/1UJoN6XBKJ5v7GLCLMjY7XvSUpS-tPsXy/view?usp=drive_web>
 bucf9rzln4-pqr-2X-fix195-460_QwikMD-194a29.psf
<https://drive.google.com/file/d/1ARsZbiU1xLh_6YrhXfbFhfAojOPrhRop/view?usp=drive_web>
 bucf9rzln4-pqr-2X-fix195-460_QwikMD-194a12.pdb
<https://drive.google.com/file/d/1tWU8idLlAtWFDZuzQ1wuDc3aaRR_7Gl1/view?usp=drive_web>
 bucf9rzln4-pqr-2X-fix195-460_QwikMD-194a12.psf
<https://drive.google.com/file/d/1X4BEk6iv8KrZWyRfUTM1RuhAbMageGRb/view?usp=drive_web>

sincerely

Jrhau

Josh Vermaas <joshua.vermaas_at_gmail.com> 於 2020年7月31日 週五 上午5:33寫道：

> 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
>>>
>>