Re: [gmx-users] cross correlations

Thanks a lot Sir for your help. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote: > Hi Bipin, > > Read them in as a vector of numbers and divide them into sqrt(len(vector)) > rows to get yourself a nice square correlation matrix. > > Cheers, > > Tsjerk > > On Jun 24, 2011 3:28 PM, "bipi

Re: [gmx-users] cross correlations

Hello, I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but after plotting the correlation, I have observed that it is of 537X537,instead of179X179.Please suggest me how to get correlation between the C-alpha atoms only. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrot

Re: [gmx-users] cross correlations

Hi Bipin, You have three coordinates per residue, hence a 3Nx3N matrix. Cheers, Tsjerk On Jun 25, 2011 4:40 PM, "bipin singh" wrote: Hello, I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but after plotting the correlation, I have observed that it is of 537X537,instead

[gmx-users] About the %SS values in the output of do_dssp

Dear All, I have simulated 6 peptides (with 7 AA each capped in N and C termini) in water and trehalose. During all the simulation time, the six peptides have b-sheet conformations. I would like to calculate the average % of secondary structure for the 6 peptides over the course of run. So I have

Re: [gmx-users] About the %SS values in the output of do_dssp

sa wrote: Dear All, I have simulated 6 peptides (with 7 AA each capped in N and C termini) in water and trehalose. During all the simulation time, the six peptides have b-sheet conformations. I would like to calculate the average % of secondary structure for the 6 peptides over the course

[gmx-users] Simulation of Primed DNA

Dear Experts, Hi from a beginner in Gromacs, I am trying to simulate i-motif so I have primed all the four chains and manually created a phosphodiester bond between two i-motif units. all the with Amber/Gromos ff the problem is : Fatal error: Atom P in residue DT 1 was not found in rtp entry DT

Re: [gmx-users] Simulation of Primed DNA

raghav singh wrote: Dear Experts, Hi from a beginner in Gromacs, I am trying to simulate i-motif so I have primed all the four chains and manually created a phosphodiester bond between two i-motif units. all the with Amber/Gromos ff the problem is : Fatal error: Atom P in residue DT 1 wa

[gmx-users] Periodic Images - clarification

Dear users, I apologize for asking the same question. but I wanted a clarification regarding this I had done a simulation for 100ns which had minimum image violation after 27ns. I have asked this question several times and people have suggested me not to use the results. But I just wanted to know

[gmx-users] (no subject)

Hi,   Upon running g_helix_d -s md.tpr -n md.ndx -f md.trr I got the following output: Fatal error: rnr==0. Please tell me how can I proceed? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac