VMD-L Mailing List

From: Tianhua Feng (tfeng_at_ualberta.ca)
Date: Fri Jul 17 2015 - 16:45:38 CDT

Dear all

There is a problem when I using the NAMD Energy Plugin, vision 1.4. When I
use the command "-ofile energy.txt", I want to output several groups of
datas in the for loop. But there will only be one group data when I open
"energy.txt". The txt file is rewritten again and again but not be written
continuously. What should I do?

#####Here is my program:

set start 1
set end 5
for {set x $start} {$x <= [expr $end-1]} {incr x} {
for {set y [expr $x +1]} {$y <= $end} {incr y} {
set s1 [atomselect top "resid $x"]
set s2 [atomselect top "resid $y"]
namdenergy -vdw -elec -sel $s1 $s2 -ofile energy.txt -exe
~/WORK/NAMD_2.10_MacOSX-x86_64-multicore\ 2/namd2
}
}

##### In the energy file:
Frame Time Elec VdW Total
0 0 -17.6203 -0.9105 -18.5308

# you can see there is one group of data.

Best regrets
Fitch

On Thu, Jul 16, 2015 at 12:08 PM, Yasaman Ghadarghadr <
y.ghadarghadr_at_gmail.com> wrote:

> Dear John,
>
> Thank you so much. It worked just fine.
>
> Regards,
>
> Yasaman
>
>
>
>
>
> *Yasaman GhadarPostdoctoral Research Associate Chemistry
> DepartmentWashington State UniversityPullman, WA, 99164*
>
> On Thu, Jul 16, 2015 at 7:57 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> The described issue affects some users with certain revs of
>> MacOS X Yosemite on some (but not all) Macs. I have posted a
>> couple of times about the following workaround:
>>
>> A short-term workaround for the MacOS X Yosemite 10.10.x update problems
>> that
>> have recently cropped up on certain varieties of Mac laptops.
>>
>> The solution is to set an environment variable to tell VMD not to
>> use the MacOS-provided file browser window, and to instead use the
>> FLTK-based file chooser. This is done by setting the environment variable
>> "VMDFILECHOOSER" to the value "FLTK". This can be done in VMD itself
>> in the text console, in the user's .vmdrc file, in the global .vmdrc
>> file in the VMD.app bundle, or by setting the environment variable in the
>> user's Unix shell .bashrc, etc.
>>
>> To set the variable in VMD or .vmdrc etc, run this command:
>> set env(VMDFILECHOOSER) FLTK
>>
>> To set the variable in bash, add this to .bashrc etc:
>> VMDFILECHOOSER=FLTK
>> export VMDFILECHOOSER
>>
>> After the environment variable is set, VMD will use the alternative
>> file selector window in the graphical interface, and this should prevent
>> the problems you've been encountering.
>>
>> Let me know if the workaround is successful for you.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Wed, Jul 15, 2015 at 12:14:31PM -0700, Yasaman Ghadarghadr wrote:
>> > Dear all,
>> >
>> > I have encountered the same problem as stated in
>> > [1]
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24265.html and
>> > have followed the discussion however I have not found any solution.
>> I was
>> > wondering if the solution has ever been posted?
>> >
>> > My Mac-OS version is 10.10.4.
>> >
>> > Thank you for your time,
>> >
>> > -Yasaman
>> >
>> > Yasaman Ghadar
>> > Postdoctoral Research Associate
>> > Chemistry Department
>> > Washington State University
>> > Pullman, WA, 99164
>> >
>> > References
>> >
>> > Visible links
>> > 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24265.html
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>
>