Re: [gmx-users] GROMACS parallel set up Questions.

Mark Abraham wrote: Subhrangshu Supakar wrote: Dear All, I have a few questions about installing gromacs in a parallel set up: I am planning to use a parallel system consisting of 4 x3650 boxes connected to each other with a gigabit switch and the same OS installed in all the three. The MPI wo

Re: [gmx-users] GROMACS parallel set up Questions.

Subhrangshu Supakar wrote: Dear All, I have a few questions about installing gromacs in a parallel set up: I am planning to use a parallel system consisting of 4 x3650 boxes connected to each other with a gigabit switch and the same OS installed in all the three. The MPI would be LAM/MPICH and

[gmx-users] GROMACS parallel set up Questions.

Dear All, I have a few questions about installing gromacs in a parallel set up: I am planning to use a parallel system consisting of 4 x3650 boxes connected to each other with a gigabit switch and the same OS installed in all the three. The MPI would be LAM/MPICH and the boxes will use their own HD

Re: [gmx-users] combining differently-generated force-fields

[EMAIL PROTECTED] wrote: I don't have a problem, per se, but would like to discuss the problems that may, or may not, arise when mixing force fields. It is clear to me why one would not want to calculate the free energy of binding for two proteins, one using the amber ff and the other using th

Re: [gmx-users] Building simple alcohol topologies

Mark Abraham wrote: Jussi Lehtola wrote: Hi, I've been trying to find all-atom topologies and atom coordinates for 1-alcohols (from ethanol to 1-decanol, possibly also n-alcohols) to be used in MD simulations for electronic structure calculations. However I haven't found any, also I haven't fo

[gmx-users] combining differently-generated force-fields

I don't have a problem, per se, but would like to discuss the problems that may, or may not, arise when mixing force fields. It is clear to me why one would not want to calculate the free energy of binding for two proteins, one using the amber ff and the other using the opls ff; also it is

Re: [gmx-users] adding missing hydrogen in PDB files

Vigneshwar Ramakrishnan wrote: Hi All, I am a newbie to GROMACS, so pardon me if I am wrong. I think pdb2gmx can handle this with amber forcefields. We just need to use the right nomenclature. I think the .hdb files for amber ff in GROMACS are already equipped with the necessary info. I a

Re: [gmx-users] adding missing hydrogen in PDB files

Hi All, I am a newbie to GROMACS, so pardon me if I am wrong. I think pdb2gmx can handle this with amber forcefields. We just need to use the right nomenclature. I think the .hdb files for amber ff in GROMACS are already equipped with the necessary info. I am not sure why one must use an externa

Re: [gmx-users] DCCM

[EMAIL PROTECTED] wrote: Dear Gromacs Users, My apologies for putting forward a naive question. Actually, I'm a little confused, is covariance matrix the same as correlation matrix ?? Names for such procedures vary quite a bit with the kind of field you work in - I've known scientists, engin

Re: [gmx-users] Building simple alcohol topologies

Jussi Lehtola wrote: Hi, I've been trying to find all-atom topologies and atom coordinates for 1-alcohols (from ethanol to 1-decanol, possibly also n-alcohols) to be used in MD simulations for electronic structure calculations. However I haven't found any, also I haven't found any guides on how

[gmx-users] DCCM

Dear Gromacs Users, My apologies for putting forward a naive question. Actually, I'm a little confused, is covariance matrix the same as correlation matrix ?? I had been thinking of carryingout DCCM analysis for my trajectories (20ns each), one for a WT protein and the other a mutant version. I t

[gmx-users] Building simple alcohol topologies

Hi, I've been trying to find all-atom topologies and atom coordinates for 1-alcohols (from ethanol to 1-decanol, possibly also n-alcohols) to be used in MD simulations for electronic structure calculations. However I haven't found any, also I haven't found any guides on how to construct such file

Re: [gmx-users] adding missing hydrogen in PDB files

In terms of external software, check out OpenBabel: http://openbabel.org/wiki/Main_Page There's also the H++ server, which employs Babel as part of its algorithm: http://biophysics.cs.vt.edu/H++/index.php I believe H++ can handle nucleic acids. You could also do all of this with Gromacs, if you

[gmx-users] adding missing hydrogen in PDB files

Hi All I have been trying to simulate a DNA tetramer d()_2 using gromacs with amber ports. I have downloaded the X-ray structure from www.rcsb.org/pdb which has several missing hydrogen atoms. Can anybody advise how to plug in the missing atoms, e.g. with softwares or otherwise to proc

Re: [gmx-users] oxaloacetate and atp

Quoting "E.M." <[EMAIL PROTECTED]>: > Greetings. > > I was wondering if any of you have a library file for oxaloacetate > compatible with > the atp files of any force field?. Your quick input would be greatly > appreciated, > also I was wondering, how to include these not standard molecules so I

[gmx-users] oxaloacetate and atp

Greetings. I was wondering if any of you have a library file for oxaloacetate compatible with the atp files of any force field?. Your quick input would be greatly appreciated, also I was wondering, how to include these not standard molecules so I can create an initial system?. Thanks for th

Re: [gmx-users] Re: upgrade version - "make distclean"?

Low Soo Mei wrote: Thanks David and Mark for your helpful comments. Just to follow up, make uninstall works very well - I executed it in the directory that was untarred from the source 3.3.2 tarball, and it removed all the 3.3.2 files in both that directory and the /usr/local/gromacs (default