[gmx-users] converting .xpm to .eps

2013-12-19 Thread Nidhi Jatana
Dear Sir/Madam I generated the atomic density plot using g_densmap by giving the following command: g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm The calculation completed successfully but when I am trying to convert .xpm file to .eps file using xpm2ps command, its giving error and aborts.

Re: [gmx-users] MM/GBSA and MM/PBSA in gromacs module

2013-12-19 Thread bipin singh
You may want to look at the below article. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 On Tue, Dec 17, 2013 at 8:22 AM, dxl...@hotmail.com wrote: Ｉ have the same question， too！ At 2013-12-16 22:48:06,Arunima Shilpi writetoas...@gmail.com wrote: Dear Sir I

Re: [gmx-users] RMSD per residue

2013-12-19 Thread Justin Lemkul
On 12/19/13 6:03 AM, Saman Shahriyari wrote: Dear users I am trying to have the RMSD per residue profile of my trajectory. i approached this by using g_rmsf tool with -od and -res options. although i can have such profile, but it seems that the average structure of my trajectory is being

Re: [gmx-users] OPLS force field issue....

2013-12-19 Thread Justin Lemkul
On 12/18/13 10:13 PM, Sidath Wijesinghe wrote: could you please give me a hint about a suitable method for this task? You can make just about anything work. 1. pdb2gmx with .rtp entries for each of your molecules, with appropriately named (unique) atoms 2. g_x2top can also process each

[gmx-users] entropy term in binding free energy calculation

2013-12-19 Thread sunyeping
Dear all, I am trying to calculate the entropy term of binding free energy using gromacs MD simulation. A strategy I can think of is: to do MD of the complex, the receptor and the ligand respectively and get the trajectories of the three species, and to calculate the entropy of the three

[gmx-users] bead-spring polymer and silver NP

2013-12-19 Thread MarcoB
Dear all, I am Marco Bernabei from the university of Barcelona. I am quite a new users of gromacs and need some help if possible with the following issues: 1) I have a configuration of a (the coordinates produced by a different program) of a silver nanoparticle (silver atoms interacts through

Re: [gmx-users] Implicit solvation: nonpolar term?

2013-12-19 Thread Justin Lemkul
On 12/19/13 5:47 PM, rdwducl wrote: Hello, I am using GBSA/OBC implicit solvation with an ACE-type approximation for the nonpolar term. Having looked at the GROMACS code, it would appear to be using the following form for the nonpolar free energy: sum_i 4*pi*tension*(R_i + R_s)^2 *

Re: [gmx-users] Implicit solvation: nonpolar term?

2013-12-19 Thread rdwducl
Thanks for the reply Justin but I'm confused. Why must the atoms be bonded? Ultimately I plan to model micellisation whereby surfactants, which only interact with each other via non-bonded terms, are driven to aggregate by this nonpolar term... -- View this message in context:

Re: [gmx-users] Implicit solvation: nonpolar term?

2013-12-19 Thread Justin Lemkul
On 12/19/13 6:14 PM, rdwducl wrote: Thanks for the reply Justin but I'm confused. Why must the atoms be bonded? Ultimately I plan to model micellisation whereby surfactants, which only interact with each other via non-bonded terms, are driven to aggregate by this nonpolar term... I'm

Re: [gmx-users] Implicit solvation: nonpolar term?

2013-12-19 Thread Robert Darkins
On 19/12/13 23:31, Justin Lemkul wrote: On 12/19/13 6:14 PM, rdwducl wrote: Thanks for the reply Justin but I'm confused. Why must the atoms be bonded? Ultimately I plan to model micellisation whereby surfactants, which only interact with each other via non-bonded terms, are driven to