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6 Jan 2021: New mek-quake. From CUC3. This is a large cluster system to be used by the Wales and Vendruscolo groups.

6 Jan 2021: New project ideas. From Raspberry Pi in the Chemistry Library. Share your ideas for projects using Raspberry Pis here:.

New mek-quake. From Docswiki. This is a large cluster system to be used by the Wales and Vendruscolo groups.

As this is a new server, you will need to login once from each machine you use. ... log into the new repository to make sure it's working. svn ls $SVN/trunk.

6 Jan 2021: PATHSAMPLE. From CUC3. A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis. PATHSAMPLE is currently documented for two versions, 2.0 and 2.1. Tutorials. These tutorials are under

6 Jan 2021: We also welcome new project ideas and recommendations for extra modules.

6 Jan 2021: 6. next step: creation new binary file points.min; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database.

PATHSAMPLE. From Docswiki. A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis. PATHSAMPLE is documented here. Tutorials. These tutorials are under development. Please correct any

6 Jan 2021: It is robust tool, especially if you are starting of with a new set of code.

6. next step: creation new binary file points.min; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database.

6 Jan 2021: Catherine 14:50, 28 March 2006 (BST). There is now an RSS feed for the sector IT news, providing updates of the messages of the day for the workstations and clusters.

A post script file with be saved as well as a new session file.

6 Jan 2021: up restart run in the current directory' echo 'Number of steps completed='$oldsteps echo 'Number of additional steps requested='$1 echo 'Total number of steps after restart='$steps # CREATING THE NEW ... Prints the top of the data file up to (but not

aux file from a latex compilation and creates a new bib file called references.bib which contains only the entries required by the corresponding.

6 Jan 2021: OpenSSH (SSH client) DONE. Pan (news client) DONE. Pine (mail/news client) DONE. ... rasmol (molecular visualisation) DONE. TeX/LaTeX (document preparation system) DONE. Thunderbird (mail/news client) DONE.

up restart run in the current directory' echo 'Number of steps completed='$oldsteps echo 'Number of additional steps requested='$1 echo 'Total number of steps after restart='$steps # CREATING THE NEW ... Prints the top of the data file up to (but not

6 Jan 2021: Where to put them. One can go on the new backup server but the primary ought to be close to the workstations.

6. next step: creation new binary file points.ts; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database.

6 Jan 2021: New backup system. I want to buy a new backup server with about 6Tb of space, move the backups onto that, and make them user-accessible. ... New archive system. The other two old backup servers would immediately be free for reuse.

In that sense, mercurial is very similar to the other new generation version management systems as git or bazaar. ... Also good. Since all new code that you write has bugs, you have a choice.

6 Jan 2021: a symbolic link to the file's new location and leaving all other files untouched.

6 Jan 2021: In order to do so, new OPTIM keywords, DEBUG, DUMPNEBEOS, and DUMPNEBXYZ need to be added to print the NEB interpolated energy and coordinates in the files neb.xyz.31267.<n>,

For an example that is working look at newtip.f90. If you need to add a new potential, here are the steps you need to do:. ... See INERTIANTIP in newtip.f90 as an example. Edit subroutine COMPUTEINERTIA to add the call to your new inertia routine.

6 Jan 2021: DUMPINT 100 RESTORE GMIN.dump STEPS 15000 SAVE 100. The number of steps in the new data file should always be greater than in the original. ... In the new format, there is an extra line in the dump file which details the number of structures saved in the

24663 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> $$$$$$ New timer profile $$$$$ List time 0.00959 Other: 0.00000 Electrostatic & VDW 0.00004 Other: 0.00000 Nonbond force 0.01572

6 Jan 2021: Aux basis: aTZ Basis type as indicated. New mid-bond set used: 3s3p3d2f1g.

New backup system. I want to buy a new backup server with about 6Tb of space, move the backups onto that, and make them user-accessible. ... New archive system. The other two old backup servers would immediately be free for reuse.

6 Jan 2021: 1 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane.

However, when you have the path.info file(s) from OPTIM you may not want to use them to start a new database -- instead, you can add them (one at a ... Systematically increasing the number of connections per minimum. Starting from an existing KTN, with

Please notify me if you find errors or new commands to add to this list (total length under 65 characters).

6 Jan 2021: odata.<n> -- OPTIM input file. odata.new.<n> -- files generated by OPTIM for restarting from that point (non-CHARMM varieties of OPTIM).

Then someone's going to have fftw2 loaded and forget about it, and suddenly find they can't load a new compiler. ... A few months later I tried a variant of this by installing the new 64-bit cluster tardis without 32-bit Portland modules.

In order to do so, new OPTIM keywords, DEBUG, DUMPNEBEOS, and DUMPNEBXYZ need to be added to print the NEB interpolated energy and coordinates in the files neb.xyz.31267.<n>,

DUMPINT 100 RESTORE GMIN.dump STEPS 15000 SAVE 100. The number of steps in the new data file should always be greater than in the original. ... In the new format, there is an extra line in the dump file which details the number of structures saved in the

The next step would be to simply merge the two pdb files such that the new pdb file contains information about only two strands which we are interested in. ... Paste these two parts one after the other into a new pdb file TGmismatch.pdb.

To keep things organised, create a new directory in your current working directory (e.g FE_<THRESH>_<TEMP>) and copy the relevant output from the free energy calculation there. ... To construct the free energy disconnectivity graph you will need a new

Can be very useful for visualizing your system and for rapidly implementing and testing new ideas. ... rough outline of the subroutines that need to be changed to add a new model to GMIN.

1 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane.

This new reorganised file we give the rather unimaginative name of lowest_to_highest_distances_tot. ... Assuming all of the connections were successfully made, all we need to do now is to merge these new connected databases together.

odata.<n> -- OPTIM input file. odata.new.<n> -- files generated by OPTIM for restarting from that point (non-CHARMM varieties of OPTIM).

The best permutation is returned in the LPERM array. SAVEPERM is set to NEWPERM with the new permutation applied. ... Updates to permutation vector and coordinates (l870-l912). ALLPERM is updated with the new swaps.

If you are unsatisfied with the topology, it's time to try a new connection scheme. ... permissions? JOBSPERNODE/PBS vs CPUS again? "Operation not permitted". "error code returned by host stdio - 1." -> close the terminal and open a new one!

6 Jan 2021: 5.5-dev. Branched from trunk on the 25-Mar-10. New program: res2disp added. ... Kernel integrals constructed in CamCASP. New propagator module: Implements the ALDA(X) kernel in the manner described in Bukowski et al.

6 Jan 2021: If you do module avail after loading the use.own module, you'll see there's a new section: /home/${USER}/privatemodules.

job). Also, it would be helpful once you've done this if you add your new cofactor to the group8 list.

mkdir. mkdir newdir newdir2. This will create two new directories, newdir and newdir2.

CHARMM to calculate the order parameters charmm_new < order_parameters.inp > charmm.out.

Where to put them. One can go on the new backup server but the primary ought to be close to the workstations.

Setting up CGMIN. Copy the metenk.crd file you have just created into a new directory, and rename it input.crd. ... We now need to create a new file, data, which contains the GMIN keywords we would like to use.

1 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane.