VMD-L Mailing List

From: Timothy Click (tclick_at_nctu.edu.tw)
Date: Tue Jun 05 2018 - 21:38:29 CDT

Thanks for the replies. They are most helpful.

On a side note, is it possible to have NAMD run in parallel? I’ve noticed that, on my 4-core iMac (27-in., late 2012, macOS High Sierra 10.13.5), NAMD occasionally runs two processes with 2 threads/process, but I was wondering whether I could specify the number of cores for bond or dihedral optimization? 

--
Cordially,
Timothy H. Click, Ph.D.
Department of Biological Science and Technology
Institute of Bioinformatics and Systems Biology
National Chiao Tung University
Dong District, Hsinchu, Taiwan 30062
> On Jun 4, 2018, at 11:26, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:
> 
> Glad it worked!  
> 
> There’s a NAMD pair interaction bug that seems to only crop up in 2.12 for Macs.  I’m waiting for the official 2.13 release to test again.
> 
> Best,
> JC
> 
>> On Jun 3, 2018, at 11:20 PM, Timothy Click <tclick_at_nctu.edu.tw> wrote:
>> 
>> This seems to work. Thanks.
>> 
>> Yet, I am curious as to why NAMD 2.12 doesn’t play nicely (although I can run an independent job successfully)?
>> 
>> --
>> Cordially,
>> 柯明 Timothy H. Click, Ph.D.
>> Department of Biological Science and Technology
>> Institute of Bioinformatics and Systems Biology
>> National Chiao Tung University
>> 208 Lab Building 1, 75 Bo-Ai St.
>> Dong District, Hsinchu, Taiwan 30062
>> (R.O.C.)
>> +886-3-5712121 x56997
>> tclick_at_nctu.edu.tw
>> 
>>> On Jun 3, 2018, at 09:07, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:
>>> 
>>> Can you try NAMD 2.11?  
>>> 
>>> Best,
>>> JC
>>> 
>>>> On Jun 1, 2018, at 8:24 AM, <tclick_at_nctu.edu.tw> <tclick_at_nctu.edu.tw> wrote:
>>>> 
>>>> I am attempting to run FFTK on a Mac (macOS 10.13.4, 32 Gb). Charge optimization works well, but when I attempt to perform bond optimization, it hangs on me. I start with a round of simulated annealing (T: 25, Tsteps: 25, Iter: 40). Initially, NAMD runs but after a couple of iterations [e.g., Optimizing(Iter:2)], it hangs and doesn’t advance any further. I have encountered this problem with a different molecules, but I am successful in my endeavors if I run in Linux. I am using VMD 1.9.4a 2017-12-21 and NAMD 2.12 on both the Mac and on Linux.
>>>> 
>>>> Any suggestions on how to correct this?
>>>> 
>>>> -- 
>>>> Timothy H. Click, Ph.D.
>>>> Dept. of Biological Sciences and Technology
>>>> National Chiao Tung University
>>>> 
>>>> 
>>>> <Mail Attachment>
>>> 
>>> 
>> 
> 
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