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Research, Family and Life
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Mingjun Yang's Blog: AMBER on clustervison
http://mingjun.blogspot.com/2007/03/amber-on-clustervision-set-up-amber-on.html
Research, Family and Life. Wednesday, 28 March 2007. This is a brief introduction on AMBER for clustervision users (clustervision1.shef.ac.uk). 1 set up amber on clustervision. In your home directory, put the following lines into .bashrc file. 2 run amber (serial and parallel). One will need at least three files for running a simulation with AMBER:. Coordinate file, which contains the Cartesian coordinates of all atoms. Parameter file, which tells how to run the simulation. Or qsub parallel.sh. You will ...
Mingjun Yang's Blog: From amber to gromacs
http://mingjun.blogspot.com/2008/01/from-amber-to-gromacs-there-is-useful.html
Research, Family and Life. Tuesday, 8 January 2008. From amber to gromacs. There is a useful tool to use amber potential in gromacs. Http:/ chemistry.csulb.edu/ffamber/. There some changes might need to apply before using a pdb file with pdb2gmx program. For exmaple, we build a peptide with sequence (use amber03 force field). NARG ARG GLU GLU TRP TRP ASP ASP ARG ARG GLU GLU TRP TRP ASP CASP. The atom types in the pdb file are slightly different from that listed in ffamber (ffamber03.rtp):. CA - - CA.
Mingjun Yang's Blog: February 2011
http://mingjun.blogspot.com/2011_02_01_archive.html
Research, Family and Life. Tuesday, 15 February 2011. The cluster (know as clustervsion.shef.ac.uk) can only be accessible within the firewall of Sheffield University. 18 dual core AMD Opteron 275 (12) and Opteron 285 (6) ( 4 CPUs each) nodes. Dual core AMD Opteron 275 font end. 16 GB memory per node. Submit job to clustervision. Before you submit any job to the cluster, you need to load the sge module with command. 1 Serial job submission. 2 Parallel job submission. Pe mpich mx 4. 3 check your job.
Mingjun Yang's Blog: February 2007
http://mingjun.blogspot.com/2007_02_01_archive.html
Research, Family and Life. Wednesday, 28 February 2007. The amber 9.0 has been compiled on clustervision1 using Intel Fortran compiler and mpich2. It is located at /usr/local/bin/amber. First you need to set the environment variable AMBERHOME to /usr/local/bin/amber either by putting the following line in your .bashrc. Or simply run this command for one-time use. One simple Perl script for running parallel sander have been attached. System("export MPICH PROCESS GROUP=no");. Pe mpich mx 2. 然 而，虽然已经...
Mingjun Yang's Blog: ACML library on clustervision
http://mingjun.blogspot.com/2007/06/acml-library-on-clustervision.html
Research, Family and Life. Tuesday, 19 June 2007. ACML library on clustervision. If there is any problems caused by compilation of LAPACK and BLAS on clustervision (AMD opteron CPU), a simple way is to use ACML library provided by AMD on the following website. Http:/ developer.amd.com/acml.aspx. Posted by Mingjun Yang. Subscribe to: Post Comments (Atom). Born in China. Assistant Professor in Department of Chemistry, University of Copenhagen. PhD from University of Edinburgh in 2006.
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Be intoxicated by my girlie and one-of-a-kind designs. Tuesday, June 16, 2009. IVORY (made of bone). Posted by Ming Julep. Posted by Ming Julep. Sunday, May 4, 2008. Posted by Ming Julep. Posted by Ming Julep. Posted by Ming Julep. Saturday, May 3, 2008. Posted by Ming Julep. 925 silver rose charms. Posted by Ming Julep. Posted by Ming Julep. Czech glass bell flowers. Posted by Ming Julep. Czech glass bell flowers. Posted by Ming Julep. Posted by Ming Julep. Posted by Ming Julep. 14k gold ear wires.
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Mingjun Yang's Blog
Research, Family and Life. Tuesday, 15 February 2011. The cluster (know as clustervsion.shef.ac.uk) can only be accessible within the firewall of Sheffield University. 18 dual core AMD Opteron 275 (12) and Opteron 285 (6) ( 4 CPUs each) nodes. Dual core AMD Opteron 275 font end. 16 GB memory per node. Submit job to clustervision. Before you submit any job to the cluster, you need to load the sge module with command. 1 Serial job submission. 2 Parallel job submission. Pe mpich mx 4. 3 check your job.
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