[gmx-users] Re: Covariance file format

Hi Tsjerk, Coffee is always magical, I tell you. Just a sniff in the air and it makes things clear. So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992? By any chance we don't obtain a file I. Which the first column wud have alpha atom one second column would have 2nd aloha

[gmx-users] Angle Distribution

Dear All, Do you know how can I calculate angular distribution of all angles in my system? Shall I specify in one index group all e.g. 80 atoms so g_angle will calculate all possibile distributions and plot it as a sum? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.groma

[gmx-users] Re: Angle Distribution

The other issue... I am using tables as an input in my protein coarse grained model based on atomistic simulations. I used Boltzmann inversion and fitted the curve into the 6th order polynomial then in angle_a*.xvg I used -f ' (x) so the derivative of my polynomial. My question: Do I need to use i

[gmx-users] ANN: mdtraj 0.3 released

I am pleased to announce the release of mdtraj 0.3. Description mdtraj is a library for loading, saving, and manipulating molecular dynamics trajectories in the python programming language. It supports the RCSB PDB, Gromacs XTC and TRR, CHARMM / NAMD DCD, AMBER binpos, AMBER NetCD

[gmx-users] D-aminoacids in input file

Dear gmx users, I have D amino acids in my input .pdb file. The force field which I aim to use, is CHARMM. I am wondering if I need to modify aminoacids.rtp file? Or it would be OK if I use the same parameters as L aminoacids for D aminoacids? Thanks for your suggestions. They would be apprec

Re: [gmx-users] Re: Covariance file format

Hi Ankita, No, the file contains the 3Nx3N covariance matrix, row by row, split over triplets, mass weighted if you did the analysis mass-weighted. But for C-alpha only there is no difference between mass-weighted and non-mass-weighted, except for global scaling. Cheers, Tsjerk On Mon, Jul 1,

[gmx-users] Re: Covariance file format

Hi Tsjerk, Thank you very much. It was extremely helpful. Kind regards Ankita On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > Hi Ankita, > > No, the file contains the 3Nx3N covariance matrix, row by row, split over > triplets, mass weighted if you did the analysis mass-weighted. But for >

Re: [gmx-users] D-aminoacids in input file

Hi Shima, You can use the same parameters. There is no difference other than the position of atoms. Cheers, Tsjerk On Mon, Jul 1, 2013 at 9:52 AM, Shima Arasteh wrote: > Dear gmx users, > > I have D amino acids in my input .pdb file. The force field which I aim to > use, is CHARMM. I am wond

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

I have run TPI using three versions (4.0.4, 4.5.4 and 4.6.1) and three different insertions particles: CH4 (uncharged), Cl- (negative) and Na+ (positive). All TPI were run on the same simulations of SPC water and the three particles taken from GROMOS force-field. Reaction-field was used for electro

[gmx-users] Computational slow downs when using oscillatory electric field

Hello, I am using the oscillatory electric field function in gromacs 4.6.1. I have experienced slow downs in computation efficiency (50% decrease or more) between the oscillatory electric field simulations and simulations with no applied electric field. Has anyone experience similar decreases i

Re: [gmx-users] Computational slow downs when using oscillatory electric field

I would expect the applied-field code got no work during the lead-up to 4.6, but I can see no obvious reason why it should run slowly. Please use diff on your .log files and gmxcheck on your .tpr files to see what can be learned about what is actually different. Mark On Mon, Jul 1, 2013 at 6:44 P

[gmx-users] energy groups for specific parts of the molecule

Dear Gromacs  users, I ran  a simulation between 6 molecules of Hypericin and  26 base pair long DNA, so for energy_grps I set HYP and DNA. Is there any way to get van der Waals and coulomb energy's of the interaction between hypericin and  a specific parts of  the DNA(phosphate groups for examp

Re: [gmx-users] energy groups for specific parts of the molecule

On 7/1/13 7:00 PM, Hovakim Grabski wrote: Dear Gromacs users, I ran a simulation between 6 molecules of Hypericin and 26 base pair long DNA, so for energy_grps I set HYP and DNA. Is there any way to get van der Waals and coulomb energy's of the interaction between hypericin and a specific

[gmx-users] TRACE OF RMSD COMPARISON MATRIX

Hello users, I'm using g_rms to compare my actual trajectory obtained from simulation with the filtered trajectory (along given set of eigenvectors), this gives me an RMSD comparison matrix in xpm format where the values of the plot are not clear. Is there any way which can help me to get the valu

Re: [gmx-users] TRACE OF RMSD COMPARISON MATRIX

Following link might be helpful: http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html -g -- Gaurav Goel Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India On 02-Jul-2013, at 10:45 AM, Richa Singh w