Re: [gmx-users] Normal Mode Analysis

Hi, I don't know exactly what went wrong when I tried to patch the file. There was a > on line 18 in the fix file, actually. I checked it. With the file you sent me, gmxdump works fine. Thank you very much for your help. Best regards, Franzi --- Franziska Hoffgaard PhD Student Bioinformatics &

Re: [gmx-users] Normal Mode Analysis

Hi thanks for your reply. I tried patching as you described it, but I got the error message: patch: `>' expected at line 18 of patch Franzi --- Franziska Hoffgaard PhD Student Bioinformatics & Theo. Biology Group TU Darmstadt 2009/5/26 Berk Hess > Hi, > > I just saw that 4.0 uses a new

Re: [gmx-users] Normal Mode Analysis

Hi, as I wrote in the first message, I tried renaming it with the extension .trj and yielded segmentation faults. I also tried it with the extension .trr and got the error message: trn version: VERSION 4.0.4 --- Program gmxdump_d, VERSION 4.0.4

[gmx-users] Normal Mode Analysis

Hi, I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis of a small protein in water. As a result I would like to have the hessian matrix in a readable format, that I can use for further computations. As I have read in the manuals/tutorials/mailing-lists I minimized the