From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 28 2016 - 02:12:14 CST
No more needed, I came across what is needed
fp
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Dec 26, 2016 at 11:17 AM
Subject: Re: namd-l: NAMD 2.12 released
To: NAMD <namd-l_at_ks.uiuc.edu>, Jim Phillips <jim_at_ks.uiuc.edu>
Dear Jim:
I was looking without success for instructions about the long waited
- QM/MM simulation via interfaces to ORCA and MOPAC
Does it come already precompiled or (likely) has to be compiled?
Thanks
francesco pietra
On Fri, Dec 23, 2016 at 7:57 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> Dear NAMD users,
>
> NAMD 2.12 is available for download. Most of the fixes since 2.12b1 have
> been to the colvars module and the new QM/MM capability.
>
> This release (along with 2.12b1) includes new kernels for both NVIDIA GPUs
> and Intel Xeon Phi Knight's Landing (KNL) processors (not co-processor
> accelerators). If necessary, the old GPU kernels can be selected with
> "useCUDA2 no" and "usePMECUDA no", and multi-threaded optimizations
> disabled with "useCkLoop 0". Avoid the Intel 17.0 compiler when building
> for KNL due to apparent vectorization bugs. For details please see
> http://www.ks.uiuc.edu/Research/namd/2.12/features.html
>
> Please note that there is a change in the adaptive biasing force (ABF)
> system force conventions in the collective variables module. For details
> see http://colvars.github.io/totalforce.html
>
> Thank you all for your efforts and support.
>
> Jim
>
>
> +--------------------------------------------------------------------+
> | |
> | NAMD 2.12 Release Announcement |
> | |
> +--------------------------------------------------------------------+
>
> December 22, 2016
>
> The Theoretical and Computational Biophysics Group at the University of
> Illinois is proud to announce the public release of a new version of
> NAMD, a parallel, object-oriented molecular dynamics code designed for
> high-performance simulation of large biomolecular systems. NAMD is
> distributed free of charge and includes source code. NAMD development
> is supported by the NIH National Institute of General Medical Sciences.
>
> NAMD 2.12 has many advantages over NAMD 2.11, among these are:
>
> - GPU-accelerated simulations up to three times as fast as NAMD 2.11
>
> - Improved vectorization and new kernels for Xeon Phi Knight's Landing
>
> - Improved scaling for large implicit solvent simulations
>
> - Improved scaling for multi-threaded "smp" builds
>
> - Communication thread sleeps in single-process-per-replica smp runs
>
> - Divide GPUs among replicas on host with "+devicesperreplica n"
>
> - Shared-memory parallel calculation of collective variables
>
> - Tcl scripting of collective variables thermodynamic integration
>
> - Constraints on probability distributions of collective variables
>
> - Collective variables module improvements including to histogram bias
>
> - Extended adaptive biasing force on-the-fly free energy estimator
>
> - Dynamic lambda scaling for alchemical work calculations
>
> - Scaling of bonded terms in alchemical free energy calculations
>
> - Properly scaled alchemical Lennard-Jones long-range corrections
>
> - Multigrator pressure and temperature control method
>
> - Retry after spurious EXDEV (Invalid cross-device link) output errors
>
> - Ability to modify grid force scaling without restarting
>
> - Ability to reload molecular structure without restarting
>
> - Optional Python scripting interface
>
> - QM/MM simulation via interfaces to ORCA and MOPAC
>
> - Update to Charm++ 6.7.1
>
>
> Details at http://www.ks.uiuc.edu/Research/namd/2.12/features.html
>
> NAMD is available from http://www.ks.uiuc.edu/Research/namd/
>
> For your convenience, NAMD has been ported to and will be installed
> on the machines at the NSF-sponsored national supercomputing centers.
> If you are planning substantial simulation work of an academic nature
> you should apply for these resources. Benchmarks for your proposal
> are available at http://www.ks.uiuc.edu/Research/namd/performance.html
>
> The Theoretical and Computational Biophysics Group encourages NAMD users
> to be closely involved in the development process through reporting
> bugs, 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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