WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM?

From: Amin Dehkharghani (amin.dehkharghani_at_gmail.com)
Date: Sun Mar 01 2015 - 14:58:08 CST

I have a system with these specifications:

Motherboard: Microsystems X9DA7-E
CPU: 2 X Intel Xeon(R) CPU E5-2670
Graphics Card: Quadro K2000
OS: Ubunto 14.04 64bit

I want to run molecular dynamics simulations in this system as fast and
optimized as possible, and I have the following questions:

*1) Which version of NAMD should I install from the following list? *
Version Nightly Build (2015-03-01) Platforms:

   - Linux-x86_64-multicore
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1258>
(64-bit
   Intel/AMD single node)
   - Linux-x86_64-multicore-CUDA
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1259>
(NVIDIA
   CUDA acceleration)
   - Source Code
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1257>

Version 2.10 (2014-12-11) Platforms:

   - Linux-x86_64-multicore
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1316>
(64-bit
   Intel/AMD single node)
   - Linux-x86_64
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1310>
(64-bit
   Intel/AMD with ethernet)
   - Linux-x86_64-TCP
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1311>
(TCP
   may be better on gigabit)
   - Linux-x86_64-ibverbs
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1312>
(InfiniBand
   via OpenFabrics OFED, no MPI needed)
   - Linux-x86_64-ibverbs-smp
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1315>
(InfiniBand
   plus shared memory, no MPI needed)
   - Linux-x86_64-multicore-CUDA
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1314>
(NVIDIA
   CUDA acceleration)
   - Linux-x86_64-ibverbs-smp-CUDA
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1313>
(NVIDIA
   CUDA with InfiniBand)
   - Linux-x86_64-multicore-MIC
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1323>
(Intel
   Xeon Phi coprocessor acceleration)
   - Linux-x86_64-netlrts
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1320>
(Multi-copy
   algorithms)
   - MacOSX-x86_64
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1318>
(Mac
   OS X for 64-bit Intel processors)
   - MacOSX-x86_64-netlrts
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1319>
(Multi-copy
   algorithms)
   - Win64
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1321>
(Windows
   7, 8, etc.)
   - Win64-CUDA
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1322>
(NVIDIA
   CUDA acceleration)
   - Win64-MPI
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1317>
(Windows
   HPC Server)
   - Source Code
   <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=313890&AccessCode=6402234159568766164291427013894&ArchiveID=1309>

*2) Do I need to install any additional drivers and softwares in addition
to ubunto itself (nvidia drivers, cuda, ...)?*

I look forward to your response as soon as possible,

Best Regards,
---------------------------------------------------------------------------
Amin Dehkharghani
School of Mechanical Engineering
Sharif University of Technology

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