Re: [gmx-users] lipid order parameter

Dear Gromacs users, I am looking for individual experimental (NMR) order parameter values for sn1 and sn2 chains at physiological temperature for DMPC in order to carry out the analysis of my trajectories and compare the results. I have got the values for sn-2 chain but unable to ge

Re: [gmx-users] Question about phospholipid monolayer on a water/air interface...

Hi Sergio, Hi My name is Sergio Garay, and I'm working on a simulation of a phospholipid monolayer on a water/air interface. To mimic that system I have constructed a rectangular box with a thick layer of water at the center, two monolayer of lipids (with their polar heads pointing toward water

Re: [gmx-users] Scripting Analysis tools in tcsh

Hello GMX users, (this may be more of a tcsh question, but here goes anyway). I'm trying to write a script to go through some trajectories and calculate hbonding. It looks like this: #!/bin/tcsh foreach number (1 2 3 4 5 6 7 8 9 10 11) g_hbond -f ../../FullMD/FullMD$number.trr -s ../..

Re: [gmx-users] Lipid Order Parameters - Calculating & Plotting

Hello GROMACS community, I was wondering if somebody could walk me through the process of calculating lipid order parameters (for a DMPC membrane), using the g_order analysis tool? I've got a 5 ns trajectory and would like to make one of the classic order parameter plots: i.e. On the y-axis: t

Re: [gmx-users] 2 beginner´s questions

Quoting [EMAIL PROTECTED]: Dear Gromacs community. I am just starting my first dynamics and wonder if you could help me with: 1. Want to use some graphical program to see the atoms moving. Can I use ngmx? What other programs are available? You can use VMD, also. 2. This is the near the end

Re: [gmx-users] PCA eigenvalue normalization

Have you checked if your peptide is "jumping" out of the box? Regards. Pedro Hello, I have performed PCA analysis, without mass weighting, on a peptide using g_covar and g_anaeig. The first principal component generally corresponds to the stretching of the peptide. I understand that ea

[gmx-users] dihedral PCA

Hi, I have read this topic in the users list... but, sorry!, it's still not clear to me: 1) I generated an [index].ndx with the format [ dih ] a b c d b c d e 2) In the program g_angle, which subset of atoms should I use in .trr and .tpr files? Regards. Pedro. -

Re: [gmx-users] FEP

Hi, are you using soft core portentials? Despite the theoretical drawbacks (see the previous discussion), the creation/annihilation of atoms was impossible (in my experience) without those potentials. Regards. Pedro. Hi all. I'm trying FEP In gromacs3.3. My system (3nm; 3nm; 3nm) consists o

Re: [gmx-users] FEP

Hi David, I am not an expert in FEP, but I have used that method to try to answer the following question: if there was a free energy difference between a system with a Na+ ion inserted by the best-potential method or randomly. I performed a series of MD runs (several lambdas) with annihilation

Re: [gmx-users] pressure scaling and hard drive space

Hi Brian, if you are using Berendsen pressure coupling (and your system is in the equilibration phase) try increasing tau-p. Regards. Pedro. Anyone know how to turn off those pesky "pressure scaling is greater than 1%" error messages? Instead of crashing, my simulations keep running with e