Re: [gmx-users] k-means clustering in GROMACS

Nikos Sgourakis wrote: Dear GROMACS users, Here I have implemented the k-means clustering algorithm in the original GROMACS module, gmx_cluster.c (called by the wrapper g_cluster). k-means is a heuristic algorithm that finds the partition of n points (conformations) in k groups (clusters), suc

[gmx-users] Centering using trjconv

Hello All. I am simulating t4 lysozyme with NAG. I have added a short peptide label to lysozyme which binds calcium ions. During the simulation there is some drift. I am attempting to re-center the protein+label+NAG+Ca ion. I am using trjconv and have setup an index file that contains only these

Re: [gmx-users] PMF calculation

> Dear all, > I am working on a tripeptide and would like to calculate Potential > Mean Force for the tripeptide. Suggestions to calculate PMF are > awaited. How about looking for PMF in the manual and reading what it has to say there? Mark ___ gmx-use

Re: [gmx-users] Re: question about dihedral angle in *.itp file

> Thank you very much for your answer! > I have check manual in chapter4. I am still confused about this sentence. Which sentence? Please either quote it, or refer precisely to it with a reference. Nobody is going to read the whole of chapter 4 to find the one relevant sentence that is confusing y

[gmx-users] PMF calculation

Dear all, I am working on a tripeptide and would like to calculate Potential Mean Force for the tripeptide. Suggestions to calculate PMF are awaited. Regards, Chetana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/lis

[gmx-users] Re: question about dihedral angle in *.itp file

Thank you very much for your answer! I have check manual in chapter4. I am still confused about this sentence. As we know, each dihedral was counted only once(?) in the program. however, if several torsional dihedral angles with different parameters can be defined on the same set of atoms i, j, k,

[gmx-users] k-means clustering in GROMACS

Dear GROMACS users, Here I have implemented the k-means clustering algorithm in the original GROMACS module, gmx_cluster.c (called by the wrapper g_cluster). k-means is a heuristic algorithm that finds the partition of n points (conformations) in k groups (clusters), such that the sum of the d

[gmx-users] GROMACS AMBER DNA TERMINUS

Dear All, I am using Gromacs 3.1.1 with the AMBER port. After following the instructions on the ffamber web-page, pdb2gmx works fine. But according to point 6: "... However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains

Re: [gmx-users] REMD demuxing

Hello, Instead of using system calls, you may also use the pymacs python interface by Daniel Seelinger: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/dseelig/pymacs.html You can access all information in an xtc file in an object-oriented manner. Nikos Andrea C. Vaiana wrote: Hello

Re: [gmx-users] How can I generate a FCC unit cell?

> Hi gmx-users, > I need to generate a FCC unit cell (in fact a face centered cubic lattice) > in order to produce a nanocristal. I would like to know if is possible > to make this using directly GROMACS. In affirmative case, as I can make > it? Setting up the contents of your periodic cell is not

Re: [gmx-users] REMD demuxing

Andrea C. Vaiana wrote: Hello everyone, I'm trying to find a better way of demuxing REMD runs, I wrote a python script to do this but it is very slow because it relies on system calls to trjconv in order to read/write frames. I checked the documentation and mailing lists, it seems that this sh

Re: [gmx-users] How can I generate a FCC unit cell?

Eudes Fileti wrote: Hi gmx-users, I need to generate a FCC unit cell (in fact a face centered cubic lattice) in order to produce a nanocristal. I would like to know if is possible to make this using directly GROMACS. In affirmative case, as I can make it? Thanks in advance __

[gmx-users] How can I generate a FCC unit cell?

Hi gmx-users, I need to generate a FCC unit cell (in fact a face centered cubic lattice) in order to produce a nanocristal. I would like to know if is possible to make this using directly GROMACS. In affirmative case, as I can make it? Thanks in advance ___ Eud