[gmx-users] Color in wheel

Dear GMX-users, In "wheel" (helical projection tool), can I make colors for some residues? Besides gray for hydrophobic residues, I also want to make positive charged residues in blue, and negative charged residues in red. Thank you for your help in advance. best, Hwankyu. _

[gmx-users] time constants for the Parrinello-Rahman/nose-hoover coupling

Dear GMX-users, I'm simulating lipid bilayer, and since fluctuation is important for the study of undulation and area compressibility (Ka), I'm also applying the Parrinello-Rahman and nose-hoover for the pressure and temperature couplings. When I use the Berendsen, time constants are like bel

[gmx-users] Measure contour area of bilayer undulation

Dear gmx-users, This is not a question about Gromacs, but I wonder if I can hear suggestions from here. I would like to measure contour area of bilayer undulation. If there is no undulation, area (area per lipid) can be easily calculated by dividing XY area by number of lipid. But, in the l

[gmx-users] How to make grids in lipid bilayer (to measure contour length)

Dear gmx-users, I'm trying to calculate contour length of huge lipid bilayer with undulation (non-projected area per lipid). In order to calculate that accurately, I would like to measure contour length in local areas of bilayer by making lots of grids in lipid bilayer. I'm wondering if ther

[gmx-users] Question about trjorder

Dear GMX-users, I'm using Gromacs 3.3.1, and trying to collect solvents within specific distance from a part of peptide. I typed "trjorder -f *.xtc -n *.ndx -s *.tpr -o -nshell -da 8 -na 12 -r 2.5". I correctly typed reference molecule, and the result of -nshell looks OK, but couldn't get the

[gmx-users] Calculation of the bending modulus (Kc) of bilayer using spectral intensity.

Dear gmx-users, I'm trying to measure the bending modulus (Kc) of lipid bilayer with different sizes. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q, but couldn't understand details. I wonder if I can hear more details and how to do th

[gmx-users] Re: Re: Calculations of area per lipid using g_sas

0 47.978 47.978 0 100100 0 38.3633 38.3633 0 -- Thanks, best, Hwankyu. Message: 5 Date: Tue, 10 Jul 2007 15:55:29 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re:

[gmx-users] Re: Calculations of area per lipid using g_sas

Dear Mark, I just measured the projected XY-area (simply XY-size of box), and used typical periodic boundary condition (In g_sas, default considers PBC). In the small system (128 lipid bilayer), there is no undulation, so projected area per lipid may be almost the same as non-projected area p

[gmx-users] Calculations of area per lipid using g_sas

Dear GMX users, I'm interested in calculating non-projected area/lipid of huge bilayer with undulations. I think that if the bigger solvent probes were used, the non-projected area per lipid may be reasonably calculated from the solvent accessible surface area because solvent probes cannot be

[gmx-users] Converting CHARMM trajectories (.trj) to GROMACS trajectories (.xtc)

Dear gmx-users, I would like to analyze CHARMM trajectories in GROMACS, and wonder if there are available scripts or tools to convert CHARMM traj to GROMACS traj (.xtc). I've searched the contributed software and forum sections, and it looks like there is a script for that, but couldn't find

[gmx-users] g_sdf

Dear Gromacs-users, I would like to use the analysis tool g_sdf, but couldn't find in the download section. If someone has the file, would you like to send me that ? Does it work with gromacs-3.3.1? Thank you very much for your help in advance. best, Hwankyu. _

[gmx-users] Coordinate and topology of TFE

Dear Gromacs-usrs, I searched trifluoroethanol (TFE) topology and coordinate developed by Fioroni et al. (J. Phys. Chem. B. 2000, 104:12347-12354) on the contribution section, but couldn't find them. Where can I find coordinate and topology files for TFE ? Thanks, best, Hwankyu.