Re: [gmx-users] generating movie file

On 1/27/18 7:12 AM, Vidya R wrote: I want to include the movie file in my ppt (using MS office). Rendering a movie requires you to create some useful representation of the system, color properly, add labels to things or represent whatever is meaningful, then encode that in a movie format.

Re: [gmx-users] Replica exchange checkpoint error

Hello Mark It makes sense to me , I have already restarted my simulations, hopefully it will write up cpt as it supposed to do. Best regards Riotto Sent from my Samsung Galaxy smartphone. Original message From: Mark Abraham Date: 28/1/18 1:17

Re: [gmx-users] Replica exchange checkpoint error

Yes On Sat, Jan 27, 2018, 15:10 金 瑞涛 wrote: > Hello Dhaniram > > Thanks for repling me! Is -append option a default option? > > Best regards > > Riotto > > > > Sent from my Samsung Galaxy smartphone. > > > Original message > From: Dhaniram Mahato

Re: [gmx-users] Replica exchange checkpoint error

Hi, They got opened immediately. Fifteen minutes before the checkpoint file. Mark On Sat, Jan 27, 2018, 15:09 金 瑞涛 wrote: > Hello Mark > > Thanks for repling me, i am wondering if it is file system problem, why > the other files like trr, xtc and log file were still

Re: [gmx-users] Replica exchange checkpoint error

Hello Dhaniram Thanks for repling me! Is -append option a default option? Best regards Riotto Sent from my Samsung Galaxy smartphone. Original message From: Dhaniram Mahato Date: 27/1/18 3:14 pm (GMT+10:00) To: gmx-us...@gromacs.org Subject: Re:

Re: [gmx-users] Replica exchange checkpoint error

Hello Mark Thanks for repling me, i am wondering if it is file system problem, why the other files like trr, xtc and log file were still updated? Best regards Riotto Sent from my Samsung Galaxy smartphone. Original message From: Mark Abraham

Re: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

Hello Have you tried different pressure coupling type? Maybe a semi-isotropic one will solve the problem if you chose z-axis as your pulling vector direction. Best regards Riotto Sent from my Samsung Galaxy smartphone. Original message From: Shrinath Kumar

Re: [gmx-users] Compiling Gromacs 2018 using Intel 2018.1 compiler on OSX 10.13.3

Hi, We haven't tried to build with icc on Mac, but as you say the problem is likely with that version of icc there. The icc 18 compiler works fine on Linux and Windows... Check for an updated version, or use gcc. Mark On Fri, Jan 26, 2018, 18:32 Zhiyi Wu wrote: > Hi,

[gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

Hi, I'm doing umbrella sampling and running into the above error. I can't really increase the box size as that would make the system too big nor can I use pull-geometry = direction-periodic as I need to use NPT. But I'm confused on why I get this error in the first place because my periodic box

Re: [gmx-users] Using libgromacs in a CMake project built on the fly?

Hi, In theory, one can compose CMake projects like that, but we have not tried to make that work with GROMACS. A better approach is probably to use a CMake external project to build GROMACS and thereby install it into the build tree. That installation has a FindGROMACS.cmake file that your main

Re: [gmx-users] Replica exchange checkpoint error

Hi, That sounds most likely a file system has decided to go missing by the time the first checkpoint file is written after fifteen minutes. As such, all you can do is try again and complain to the cluster admins if it keeps happening. Mark On Fri, Jan 26, 2018, 04:09 金 瑞涛

Re: [gmx-users] generating movie file

I want to include the movie file in my ppt (using MS office). On Sat, Jan 27, 2018 at 11:19 AM, Alex wrote: > No, there are other tools for that (e.g. pymol + avidemux). > > I too was wondering if trjconv could produce an mp4 and add Morgan > Freeman's voice as narration