From: HEMANTH H (hemanth.h_at_iitgn.ac.in)
Date: Mon Jun 29 2020 - 02:40:50 CDT
I assume that you are working on a Windows machine, because you had
mentioned D: drive.
I did this thinking that probably both working folder and executable files
should be in same drive.
Not necessary, as long as your paths specified in the input conf file are
proper. But again, it helps
Your NAMD executable is having some issues with one or more of the issues
mentioned below:
1. It is unable to locate the input file
2. Your input file is wrong.
Thanks and regards
Hemanth
On Mon, Jun 29, 2020 at 12:25 PM Ratnika Sharma <
ratnika.usbt.900510_at_ipu.ac.in> wrote:
> Thank you for your reply Sir.
> The Configuration file does exist in the same folder as is used for input
> protein pdb, psf etc and outputs.
> So, I will share the exact steps that I followed.
>
> I have downloaded NAMD and VMD.
> Installed them in D drive.
> Set the executable files of both in the env path.
> I wanted to simulate Lysozyme protein downloaded from RCSPDB, so i have
> downloaded pdb file and stored in folder named Lysozyme in the D drive only.
> However, I was having trouble specifying its path in command prompt, so i
> copied this folder to desktop. Still i faced the same issue.
> Then, I copied VMD and NAMD folders to C drive, program files and changed
> their env path again. I did this thinking that probably both working folder
> and executable files should be in same drive.
> Still faced the same error.
> Can you help me through this to understand what should be the actual
> locations of these folders because I seem to mix these steps?
>
>
> On Mon, Jun 29, 2020 at 7:36 AM HEMANTH H <hemanth.h_at_iitgn.ac.in> wrote:
>
>> Ms. Sharma,
>>
>> The log file is self explanatory. It says that the name of the
>> configuration file that you'd provided doesn't exist in your current
>> working directory. Kindly double check if your configuration file is
>> present in the directory.
>>
>> Thanks & Regards
>> Hemanth
>>
>> On Mon, 29 Jun 2020, 02:18 Ratnika Sharma, <ratnika.usbt.900510_at_ipu.ac.in>
>> wrote:
>>
>>> I'm trying to run NAMD Simulations. However, I'm getting the following
>>> error. Kindly help in troubleshooting.
>>>
>>> Charm++> Running on MPI version: 2.0
>>> Charm++> level of thread support used: MPI_THREAD_SINGLE (desired:
>>> MPI_THREAD_SINGLE)
>>> Charm++> Running in non-SMP mode: 1 processes (PEs)
>>> Charm++> Using recursive bisection (scheme 3) for topology aware
>>> partitions
>>> Converse/Charm++ Commit ID:
>>> v6.10.1-0-gcc60a79-namd-charm-6.10.1-build-2020-Mar-05-18422
>>> Charm++> Disabling isomalloc because mmap() does not work.
>>> CharmLB> Load balancer assumes all CPUs are same.
>>> Charm++> Running on 1 hosts (1 sockets x 2 cores x 2 PUs = 4-way SMP)
>>> Charm++> cpu topology info is gathered in 0.001 seconds.
>>> Info: NAMD 2.14b2 for Win64-MPI
>>> Info:
>>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>>> Info: for updates, documentation, and support information.
>>> Info:
>>> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
>>> Info: in all publications reporting results obtained with NAMD.
>>> Info:
>>> Info: Based on Charm++/Converse 61001 for mpi-win64
>>> Info: Built Thu, Jun 25, 2020 12:47:34 PM by jim on europa
>>> Info: Running on 1 processors, 1 nodes, 1 physical nodes.
>>> Info: CPU topology information available.
>>> Info: Charm++/Converse parallel runtime startup completed at 0.00300002 s
>>> Info: 3.11328 MB of memory in use based on GetProcessMemoryInfo
>>> Info: Configuration file is runme.namd
>>> FATAL ERROR: Unable to access config file runme.namd
>>> [Partition 0][Node 0] End of program
>>>
>>> I am new to this. Please tell me where to look for the possible error
>>> source.
>>> Thanks
>>>
>>
-- *Hemanth H 18310019* Research Scholar IIT Gandhinagar
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