Re: [gmx-users] can we analyse Gromacs trajectory with jupyter?

Great to hear that. Hopefully it can support .xtc format soon, since the .trr file is really huge. On 06/24/2016 04:36 PM, Hai Nguyen wrote: Hi, cpptraj is able to read TRR format too. cpptraj can read a pdb file as Topology, so no need to do any conversion to " an equivalent AMBER

Re: [gmx-users] Gromacs 5.1 build for windows 8. Cygwin compatibility with CUDA/GPU acceleration.

Hi, On Fri, Jun 24, 2016 at 3:16 PM wrote: > I have spend the past week trying to figure out how to compile GROMACS for > windows. I spend a lot of time on the web and everyone pointed to the use > of cygwin for building in windows. > Unless you can find "CUDA

Re: [gmx-users] Gromacs 5.1 build for windows 8. Cygwin compatibility with CUDA/GPU acceleration.

why not install it in Linux instead of wasting time install it in Windows. On 06/24/2016 03:12 PM, timothy.du...@louisville.edu wrote: I have spend the past week trying to figure out how to compile GROMACS for windows. I spend a lot of time on the web and everyone pointed to the use of

[gmx-users] Gromacs 5.1 build for windows 8. Cygwin compatibility with CUDA/GPU acceleration.

I have spend the past week trying to figure out how to compile GROMACS for windows. I spend a lot of time on the web and everyone pointed to the use of cygwin for building in windows. I was pursuing the email list and found a thread which brought up my issue with enabling GPU acceleration. The

Re: [gmx-users] can we analyse Gromacs trajectory with jupyter?

Hi, Not that I know of. From the point of view of someone who already has a GROMACS trajectory, the underlying cpptraj tool has support for reading .gro and .pdb, but not .xtc or .tng, and you'd also have to decide whether you need to produce an equivalent AMBER topology to help analyze your

Re: [gmx-users] Block averaging

On 6/24/16 6:23 AM, sun wrote: Sir If I do averaging of no. of clusters in case of protein (increased no. of clusters as compared to pro-lig complex) at regular intervals of time, It will be sufficient to assess if my simulation is converged? In my case clustering in addition to secondary

[gmx-users] Parameters file for CHARMM 27 Force Field

Dear Gromacs users, I am writing CHARMM27 parameters for a new molecule. Where can I get a parameter file for the CHARMM27 ? where all parameters for all the atoms are available similar file for OPLS/AA force filed can be found in below link.

Re: [gmx-users] Block averaging

Sir If I do averaging of no. of clusters in case of protein (increased no. of clusters as compared to pro-lig complex) at regular intervals of time, It will be sufficient to assess if my simulation is converged? In my case clustering in addition to secondary structure are conclusive parameters.

Re: [gmx-users] Gromacs Orca QMMM segfault

INdeed, ORCA is not maintained at the moment. At least not by me, partially because it is not opensource (AFAIK). The interface with gaussian is still working though. So my (poor) advice is either to keep using an older version of gromacs, or switch to gaussian, depending on the functionality

[gmx-users] can we analyse Gromacs trajectory with jupyter?

Hello: I recently found that Amber introduced jupyter (http://jupyter.org/) for MD simulation result analysis. One can analyze it through webpage and plot the result nicely with Python and R. One can even display the structure and trajectory in a webpage through WebGL technology. Here are

Re: [gmx-users] Saving trajectory with different output time steps

Hi, You can use trjconv with the -skip flag to get your desired output. On 24 Jun 2016 9:19 a.m., "Sanket Ghawali" wrote: > Dear Gromacs user, > > I have 100ns trajectory in which the output steps are written every 5ps. I > would like to save the same trajectory of

[gmx-users] Saving trajectory with different output time steps

Dear Gromacs user, I have 100ns trajectory in which the output steps are written every 5ps. I would like to save the same trajectory of 100ns with the output steps written at every 500ps. Is there any options available to do so ? Or do i need to perform the production run again making changes to