Re: [gmx-users] Problem with reading AMBER trajectories

2013-10-25 Thread anu chandra
Hi, Sorry for the late reply. I have tried all the possibilities with filename extension as mentioned in the VMD molfile details. As said, VMD uses .crd or .crdbox filename extensions for reading Amber trajectories. I have tried with both the options ( ie. with .crd and .crdbox extensions) , but u

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-25 Thread Michael Shirts
Hi, all- At this point, any fixes are going to be in the 5.0 version, where the integrators will be a bit different. If you upload your system files to redmine.gromacs.org (not just the .mdp), then I will make sure this gets tested there. On Fri, Oct 25, 2013 at 10:14 AM, Guillaume Chevrot wrot

Re: [gmx-users] Lie method for binding free energy calculations

2013-10-25 Thread Andrea Spitaleri
Hi, You can email me we have a tool for mmpbsa with gromacs Andrea Messaggio inviato dal mio ASUS MeMO Pad Justin Lemkul ha scritto: On 10/25/13 11:43 AM, Sajad Ahrari wrote: > is AMBER facilities the only way of approaching MM-PBSA calculations? could > you > lead me to any other software m

Re: [gmx-users] Lie method for binding free energy calculations

2013-10-25 Thread Justin Lemkul
On 10/25/13 11:43 AM, Sajad Ahrari wrote: is AMBER facilities the only way of approaching MM-PBSA calculations? could you lead me to any other software more friendly with Gromacs MD output? See what Google tells you. -Justin -- == Justin A. L

Re: [gmx-users] Lie method for binding free energy calculations

2013-10-25 Thread Justin Lemkul
On 10/25/13 11:32 AM, Sajad Ahrari wrote: thanks for replying. are these features available under Gromacs? and is there any tutorial or related material I can grasp to stand up for start? My umbrella sampling tutorial covers generating a PMF. MM/PBSA is just a post-processing technique, re

Re: [gmx-users] Lie method for binding free energy calculations

2013-10-25 Thread Justin Lemkul
On 10/25/13 11:07 AM, Sajad Ahrari wrote: Hello dears searching through literature, many cases of LIE method application for BFE calculation of small molecules are on hand . but I couldn't find any report of using this method for interaction of small peptides and proteins. I wanted to know

[gmx-users] Lie method for binding free energy calculations

2013-10-25 Thread Sajad Ahrari
Hello dears  searching through literature, many cases of LIE method application for BFE   calculation of small molecules are on hand . but I couldn't find any report of using this method for interaction of small peptides and proteins. I wanted to know if the protocol prepared in Justin tutorial

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-25 Thread Guillaume Chevrot
Dear Xavier, 2013/10/12 XAvier Periole > > Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? > > FYI, I tried 10 and 1 and the energy drift is exactly the same. > Similar flags apply to temperature and pressure and I believe might > seriously affect energy conserva

Re: [gmx-users] GPU-gromacs

2013-10-25 Thread Carsten Kutzner
On Oct 25, 2013, at 4:07 PM, aixintiankong wrote: > Dear prof., > i want install gromacs on a multi-core workstation with a GPU(tesla c2075), > should i install the openmpi or mpich2? If you want to run Gromacs on just one workstation with a single GPU, you do not need to install an MPI library

[gmx-users] GPU-gromacs

2013-10-25 Thread aixintiankong
Dear prof., i want install gromacs on a multi-core workstation with a GPU(tesla c2075), should i install the openmpi or mpich2? -- 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

Re: [gmx-users] Optimizing performance mac osx

2013-10-25 Thread Mark Abraham
On Fri, Oct 25, 2013 at 11:19 AM, Tiago Gomes wrote: > Hi, > > I am relatively new to the gromacs environment and would like to optimize > performance for my mac pro (osx 10.6.8) > with 8 cores (16 in hyper-theading). I´ve read that one can use > the g_tune_pme, i guess with np = 16. Don´t know if

[gmx-users] 2D umbrella sampling simulation

2013-10-25 Thread Christopher Neale
unfortunately not. It will be done eventually though: to follow the progress of that feature, check out: http://redmine.gromacs.org/issues/1346 If you have to do that, there is a patch that I posted on that same redmine page (posts 8 and 9) to allow this in gromacs 4.0.5. Chris. -- original me

[gmx-users] Wall potential for a membrane-simulation

2013-10-25 Thread Marianne Schulte
  Hi everyone! I'm new to Gromacs and trying to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40) abov

[gmx-users] Optimizing performance mac osx

2013-10-25 Thread Tiago Gomes
Hi, I am relatively new to the gromacs environment and would like to optimize performance for my mac pro (osx 10.6.8) with 8 cores (16 in hyper-theading). I´ve read that one can use the g_tune_pme, i guess with np = 16. Don´t know if using mpirun or gromacs compiled mpi would be faster. I guess si

Re: [gmx-users] Gromos54a8

2013-10-25 Thread rajat desikan
Thank you so much, Djurre. I will do some tests with protein-membrane systems in mind and share it with the community. I will see if I can reproduce the results in the 54A8 paper. On Fri, Oct 25, 2013 at 1:01 PM, Djurre de Jong-Bruinink < djurredej...@yahoo.com> wrote: > Dear Rajat Desikan, > I

Re: [gmx-users] Gromos54a8

2013-10-25 Thread Djurre de Jong-Bruinink
Dear Rajat Desikan, I recently ported the 54A8 to Gromacs format. However I did not have the time yet to extensively test it or compare it to published results. I did the porting by hand (the differences between 54A7 and 54A8 are modest), which is of course more error prone. I'll send you the f