[gmx-users] Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off

Hello everyone, I'm running a simulation with Verlet scheme (for GPU). I've used cut-off method for van der Waals interactions and PME for electrostatic interactions. For energy minimization, I used steepest descent, conjugate gradient and l-bfgs sequentially. However, when I come to BFGS

[gmx-users] extracting from TRR

Dear GMX experts, How could I extract the only state from MD-simulation .TRR (or traj.xtc) file that has the lowest RMSD from the reference protein.pdb file? Please give me a line of code in UBUNTU or the script. Thank you in advance, Happy journey through the Universe, Niyaz -- Gromacs Users

Re: [gmx-users] gromacs-4.6.5 topol file error

i dont know how can create ions.mdp file for grompp command in gromacs . where can i found it?? On Thursday, September 25, 2014 11:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/25/14 2:15 PM, yaser wrote: i did it but i get this error again. If the file is, in fact in the working

Re: [gmx-users] HELP: g_velacc g_dos not match

On 2014-09-26 14:53, xy21hb wrote: dear all, it seems that the output of g_velacc, i.e. -o vel.xvg -os spec.xvg do not match that of g_dos, i.e. -vacf vel.xvg -dos spec.xvg, respectively, is there any reason for that? Are both files different? Maybe you can submit an issue at

[gmx-users] grompp help

hi gromacs user i have problem with grompp command in gromacs i cant find .mdp files and i cant pass step 4 in this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/04_ions.html im new in gromacs please help me to find a way to fix my problems.

Re: [gmx-users] grompp help

On 9/26/14 12:23 PM, Yaser Hosseini wrote: hi gromacs user i have problem with grompp command in gromacs i cant find .mdp files and i cant pass step 4 in this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/04_ions.html im new in gromacs please

Re: [gmx-users] extracting from TRR

On 9/26/14 6:42 AM, N. S. wrote: Dear GMX experts, How could I extract the only state from MD-simulation .TRR (or traj.xtc) file that has the lowest RMSD from the reference protein.pdb file? Please give me a line of code in UBUNTU or the script. Calculate the RMSD using g_rms, find the

Re: [gmx-users] Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off

On 9/26/14 5:34 AM, GAYATHRI S wrote: Hello everyone, I'm running a simulation with Verlet scheme (for GPU). I've used cut-off method for van der Waals interactions and PME for electrostatic interactions. For energy minimization, I used steepest descent, conjugate gradient and l-bfgs

Re: [gmx-users] grompp help

On this page, you see: An .mdp file is normally used to run energy minimization or an MD simulation, but in this case is simply used to generate an atomic description of the system. An example .mdp file (the one we will use) can be downloaded here

Re: [gmx-users] grompp help

thank you for replay when i want to download this file and i click on it its nothing happend and just the text page opend and its nothing to download. Sent from my iPad On Sep 26, 2014, at 19:56, Justin Lemkul jalem...@vt.edu wrote: On 9/26/14 12:23 PM, Yaser Hosseini wrote: hi

[gmx-users] GROM v0.6 Release Notes

Dear Gromacs users, GROM editor has been updated to version 0.6 and it includes New Features: Major Changes 1. Includes Spelling Suggestion of mdp parameters in context Menu. 2. Includes function to find parameter in Help file 3. Includes Line Number Area 4. Now supports .gro format Fixes

Re: [gmx-users] extracting from TRR

Dear Justin, Thank you very much for your respond. It seems however my poor English put me in a spot again. I do not need to find the lowest RMSD frame from a trajectory, it is too simple even for such a dummy as I am. I need to find a frame that has lowest RMSD regarding to another .pdb file.

Re: [gmx-users] extracting from TRR

Judging from what you wrote: Justin's answer is perfectly fine but your understanding of RMSD obviously is not. RMSD is not a quantity of one structure only. Rather, it is defined as root mean square deviation (kind of a measure of difference) between two structures one from another. If one of

Re: [gmx-users] grompp help

On 9/26/14 12:50 PM, yaser wrote: thank you for replay when i want to download this file and i click on it its nothing happend and just the text page opend and its nothing to download. Right-click - Save As... -Justin -- == Justin A.

Re: [gmx-users] extracting from TRR

Dear Matthias, I am very new ( about 1 month only) to MD and Dr. Justin A. Lemkul is well-known expert in MD, the author of excellent Gromacs tutorials. Certainly, I do not understand well even basics of Gromacs. And namely this is the reason why I have subscribed to gromacs.org_gmx-users

[gmx-users] FEP residue mutation tutorial

Dear gromacs users, Is there a tutorial/guide or something for beginners to perform FEP for amino acid mutations on gromacs? Thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and

Re: [gmx-users] grompp help

thank you i did it. Sent from my iPad On Sep 26, 2014, at 23:42, Justin Lemkul jalem...@vt.edu wrote: On 9/26/14 12:50 PM, yaser wrote: thank you for replay when i want to download this file and i click on it its nothing happend and just the text page opend and its nothing to

[gmx-users] position restrains while pull simulation

Dear gmx-users, I am doing a pull simulation in CG MARTINI and following the tutorial: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html My systems contains POPC and cardiolipin (grouped as Lipid in index file), protein, water and ions. I want to position