I have downloaded NAMD 2.9 for Win64-MPI. I downloaded the .zip file, extracted it and tried to run the program. But it gave the following error message "msmpi.dll file is missing". I am sure that this msmpi.dll file was not extracted during installation (I have extracted all the files twice to confirm this).
I am using Dell 660S desktop with Windows 7 OS. From the message it seems clear that the problem is not with NAMD, but with the system architecture. What I suspect is that I have downloaded a program which is not meant to be run on my system. But then there's only one version of 64 bit NAMD available for download. I don't know what 'MPI' means. Am I doing something wrong?
I just wish to run NAMD faster using 64 bit version rather 32 bit version. Have I downloaded the right version of program? Win32 version of NAMD runs exactly fine on my system.
@ Prakash Sambavekar There is nothing complicated in installation of NAMD. Just extract the archive to a convenient location (say for example in C drive) and rename the folder to NAMD instead of NAMD_2.2_Win32-i686. This will save time when you run configuration file from commandline prompt. You would require VMD for preparation of system for simulation as well as for analyzing trajectories. You can follow excellent tutorial at http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html.
Initially working in NAMD seems to hard, but it becomes easier once you get used to commandline environment. Please see the attached file that shows NAMD running process. The image explains that. first you need to reach the location where your configuration file and other files (like parameter, psf, coordinate files etc) are located. for example in my figure configuration file is located in D drive in sub folder name 20-A \ rECEPTOR\equilibrate\new-folder. Once you get till here you need to specify location of your namd exe file. I have extracted NAMD in C drive in folder named NAMD that contain namd2.exe. finally you need to provide how many processors you wish to use to run NAMD by specifying +p4 (It means that i wish to use 4 processors for calculation) you better manage your own computational resources as per your requirement. finally specify name of configuration file (Equilibrate_reseraction.conf is name of my configuration file). > Equilibrate_reseraction.log specfies that all the computed data will be saved in log file named Equilibrate_reseraction.log file.
Hopefully it serves the purpose...
Happy MD...
Make sure that the fire wall does not block msmpi or namd2 on the
first start, if not You should install ms-mpi from this link, because perhaps you didn't install this library on your PC.
http://www.microsoft.com/download/en/details.aspx?id=14737
First of all thank you very much Tomasz Molcan for your kind suggestion. You are absolutely correct in trouble-shooting my problem. As you said i downloaded msmpi library from your provided link and installed it and NAMD is working very effectively. and yes... you rock buddy... you saved my day... thanx again
@ Carlos Aguilar, Suggestion of Tomasz Molcan works. Let me know if you have difficulty in NAMD.
@ Prakash Sambavekar There is nothing complicated in installation of NAMD. Just extract the archive to a convenient location (say for example in C drive) and rename the folder to NAMD instead of NAMD_2.2_Win32-i686. This will save time when you run configuration file from commandline prompt. You would require VMD for preparation of system for simulation as well as for analyzing trajectories. You can follow excellent tutorial at http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html.
Initially working in NAMD seems to hard, but it becomes easier once you get used to commandline environment. Please see the attached file that shows NAMD running process. The image explains that. first you need to reach the location where your configuration file and other files (like parameter, psf, coordinate files etc) are located. for example in my figure configuration file is located in D drive in sub folder name 20-A \ rECEPTOR\equilibrate\new-folder. Once you get till here you need to specify location of your namd exe file. I have extracted NAMD in C drive in folder named NAMD that contain namd2.exe. finally you need to provide how many processors you wish to use to run NAMD by specifying +p4 (It means that i wish to use 4 processors for calculation) you better manage your own computational resources as per your requirement. finally specify name of configuration file (Equilibrate_reseraction.conf is name of my configuration file). > Equilibrate_reseraction.log specfies that all the computed data will be saved in log file named Equilibrate_reseraction.log file.
Hopefully it serves the purpose...
Happy MD...
Dr. Raman
Is the configuration file folder and the the files which we have extracted are different?
Or the configuration files are the one which we defines for running any simulation?
I have just started learning about it. So I still have a doubts and difficulties understanding about it
I have similar problem in running NAMD, but in my own case it display fatal error message " No simulation config file specified on command line" despite the fact that I have installed the mpi_x64.msi.
@ Mustafa Alhaji Isa : Please follow my earlier answer with figure... YOu will find answer there.. As per your story, it seems that you have not specified the path of configuration file (.conf file) while running the simulation.
Thanks Dr Meshram, I have already successful overcome the problem and run the simulation.
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