From: sunyeping (sunyeping_at_aliyun.com)
Date: Thu Nov 26 2015 - 23:26:33 CST
When include "twoAwayX yes" in the conf file, I get the error:Reason: FATAL ERROR: Setting parameter twoAwayX from script failed!Actually it is not just for 2.11b1. Early version is the same. What's wrong?Yeping ------------------------------------------------------------------From:Jim Phillips <jim_at_ks.uiuc.edu>Time:2015 Nov 13 (Fri) 12:47To:namd-l <namd-l_at_ks.uiuc.edu>, 孙业平 <sunyeping_at_aliyun.com>Subject:Re: namd-l: Re: namd-l: Re: namd-l: NAMD 2.11b1 released2.11 does support twoAwayX/Y/Z. What are you seeing that suggests not?JimOn Fri, 13 Nov 2015, sunyeping wrote:> And 2.11 version does not seem to support "twoawayx/y/z" option.Yeping ------------------------------------------------------------------From:Jim Phillips <jim_at_ks.uiuc.edu>Time:2015 Nov 12 (Thu) 20:55To:namd-l <namd-l_at_ks.uiuc.edu>, 孙业平 <sunyeping_at_aliyun.com>Subject:Re: namd-l: Re: namd-l: NAMD 2.11b1 releasedIf you were limited by the CPU in 2.10 you're probably still limited by the CPU in 2.11. The largest increases are for energy evaluation and implicit solvent. Explicit solvent force evaluation is closer to 30%. We'll be working to reduce CPU dependence for 2.12.JimOn Thu, 12 Nov 2015, sunyeping wrote:> I have tried this new release of NAMD on my system which has two C2050 GPU. The simulation system contains more than 40,000 atoms but I don't see obvious speedup of the 2.11b1 compared to the CVS-2015-09-29 version. The speed are both around 0.11day/ns. So in what circumstance would the new version increase GPU performance? Yeping SunInstitute of Microbiology, Chinese Academy of Sciences------------------------------------------------------------------From:Tristan Croll <tristan.croll_at_qut.edu.au>Time:2015 Nov 12 (Thu) 10:12To:namd-l <namd-l_at_ks.uiuc.edu>, Jim Phillips <jim_at_ks.uiuc.edu>Subject:Re: namd-l: NAMD 2.11b1 releasedHi Jim,A doubling of CUDA performance is very exciting! Are the best speed-ups seen in smaller or larger systems?Thanks,Tristan________________________________________From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Jim Phillips <jim_at_ks.uiuc.edu>Sent: Wednesday, 11 November 2015 1:39 AMTo: namd-l_at_ks.uiuc.eduSubject: namd-l: NAMD 2.11b1 releasedDear NAMD users,NAMD 2.11b1 is available for download (since last night), with many newfeatures noted below. This is a beta release, so please test yoursimulations over the next few weeks and let us know of any issues. I amhoping for a short beta cycle with limited new code (and some newdocumentation) added before the final 2.11 release.Thank you all for your efforts and support.Jim+--------------------------------------------------------------------+| || NAMD 2.11b1 Release Announcement || |+--------------------------------------------------------------------+ November 10, 2015The Theoretical and Computational Biophysics Group at the University ofIllinois is proud to announce the public release of a new version ofNAMD, a parallel, object-oriented molecular dynamics code designed forhigh-performance simulation of large biomolecular systems. NAMD isdistributed free of charge and includes source code. NAMD developmentis supported by the NIH National Institute of General Medical Sciences.NAMD 2.11 has many advantages over NAMD 2.10, among these are:- GPU-accelerated simulations up to twice as fast as NAMD 2.10- Enhanced Tcl scripting of collective variables and "cv" command- Collective variables module improvements including to histogram bias- TclForces query total net forces for atom groups- Replica-exchange multiplexing (fewer partitions than replicas)- Tcl scripting multiple in-memory checkpoints- Improved Tcl scripting multi-copy interface documentation- Tcl scripting asynchronous multi-copy remote in-memory checkpoints- Tcl scripting asynchronous multi-copy remote trajectory output- Tcl scripting asynchronous multi-copy remote script evaluation- Tcl scripting asynchronous multi-copy central work queue support- Tcl scripting asynchronous multi-copy workflow-style programming- Improved minimization for Drude force field and rigid bonds- Improved long-range LJ correction with VDW force switching- Improved alchemical calculations with VDW force switching- Pressure calculation with fixed atoms on GPU works as on CPU- Improved scaling for GPU-accelerated particle-mesh Ewald calculation- Improved scaling for GPU-accelerated simulations- Improved scaling for multi-threaded "smp" builds- Prevent running smp builds with one thread per process- Support trajectory files larger than 2GB on Windows- Improved Intel Xeon Phi coprocessor support- Update to Charm++ 6.7.0 with improved multi-copy support- Ignore ioformat statement in CHARMM topology and parameter files- Psfgen improvements including long resids and insertion codes- Psfgen package available in NAMD Tcl interpreterDetails at http://www.ks.uiuc.edu/Research/namd/2.11/features.htmlNAMD is available from http://www.ks.uiuc.edu/Research/namd/For your convenience, NAMD has been ported to and will be installedon the machines at the NSF-sponsored national supercomputing centers.If you are planning substantial simulation work of an academic natureyou should apply for these resources. Benchmarks for your proposalare available at http://www.ks.uiuc.edu/Research/namd/performance.htmlThe Theoretical and Computational Biophysics Group encourages NAMD usersto be closely involved in the development process through reportingbugs, contributing fixes, periodical surveys and via other means.Questions or comments may be directed to namd_at_ks.uiuc.edu.We are eager to hear from you, and thank you for using our software!
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