VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sun Jun 03 2018 - 22:26:04 CDT

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>
>>
>>
>