Re: [gmx-users] A question about deuteriu order parameters graph

Dear Javier Here is mdp file for MD run title        = cxcr7-DPPC Production MD ; Run parameters integrator    = md        ; leap-frog integrator nsteps        = 50    ; 2 * 50 = 1000 ps (1 ns) dt            = 0.002        ; 2 fs ; Output control nstxout        = 1000        ; save

[gmx-users] Extract van der waals surface atoms coordinates

Dear All   How can I extract van der waals surface atoms coordinates from MD Trajectory and write them to a file? Is it possible with gromacs? And with other tools? Any suggestion?   Thanks in advance-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] Problems with g_filter

Dear all I'm trying to use the follow command with a protein in DPPC and explicit water   g_filter -s md.tpr -f md.xtc -ol movie_filtered.pdb -fit -nf 5   Altough I selected protein group, the command export everything (water + protein + dppc).   How can I fix it?   Thanks in advance-- gmx-users

[gmx-users] Trajectory to matrix

Dear all I need to export all MD trajectory's data to a matrix. As column header I'd like to put each atom indentified by residue name and progressive number e.g. LYS-N1 In the rows I'd like to put z coordinate changing in time.   Any  suggestion?   Thanks-- gmx-users mailing listgmx-users@gr

[gmx-users] do_dssp segmentation fault

Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? Thank in ad-- gmx-users mailing listgmx-

Re: [gmx-users] Trajectory to matrix

  Where can I download the old version? Thanks Da: Mark Abraham A: Discussion list for GROMACS users Inviato: Martedì 22 Novembre 2011 9:32 Oggetto: Re: [gmx-users] Trajectory to matrix On 22/11/2011 7:27 PM, Alex Jemulin wrote: Dear all >I need to exp

[gmx-users] Cavity detection on membrane protein surface

Dear all, I'm studying a membrane protein. During MD some concavities appear and disappear on its surface. I'd like to isolate atoms and residues involved in these formations. Any suggestion? Which steps should I follow to automate the identification process?   Thanks in adavance-- gmx-users mai

[gmx-users] NVT Equilibration

Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md  ; leap-frog integrator nsteps  = 5  ; 2 * 5 = 100 ps dt  = 0.002  ; 2 fs tcoupl  = V-rescale ; modified Berendsen thermostat The syst

[gmx-users] NVT Equilibration

Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs tcoupl = V-rescale ; modified Berendsen thermostat The syst

[gmx-users] Convert to Sammon map

Dear All   I'd like to convert a gromacs RSMD matrix (xmp) to a Sammon map. Could you give me any suggestion?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Se

[gmx-users] Cluster analysis

Dear all   Could you give me any suggestion about how I can interpretate output result of g_cluster? Is there a detailed tutorial?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

[gmx-users] Convert xpm to matrix

Dear all,   I'd like to convert an xpm file to delimited CSV , because I need to import values in excel.   Any suggestion?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Ma

[gmx-users] Information about g_sas

Dear all   Which is the difference between hydropilic and hydrophobic sas? How can give an interpretation to g_sas xvg graph? What can I find out in it and how can use g_sas to analyze a trajectory?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] Information about boxX,boxY e boxZ

Dear All   I run a 1ns MD on a membrane protein and I get these values for box coordinate's Energy  Average   Err.Est.   RMSD  Tot-Drift --- Box-X    13.867  0.071   0.167634 

[gmx-users] Help with g_density

Dear All I run g_density on a membrane protein. Here are the results   http://elisacarli.altervista.org/densityhead.jpg http://elisacarli.altervista.org/tailsDensity.jpg   Could you help me to give an interpretation to my analysis?   Thank in advance-- gmx-users mailing listgmx-users@gromacs.

[gmx-users] Help with Principal component analysis

Dear all   I run a MD on a GPCR (transmembrane protein) Then I run a PCA on results and I found 3PC sufficient to explain variance. On the same PC I get big values for samples located both at Nter (extracellular) and Cter (intracellular) or for similar cases such as both Nter(extracellular) and L