[gmx-users] Setting rcon according to system

Dear gmx comunity, I have been running my system without any problems with 100 processors. But I decided to make some of the bonds of my main molecule constrains. My molecule is not an extended chain, it is a molecular hydrated ion, in particular the uranyl cation with 5 water molecules forming a

[gmx-users] How to use rcon based on my system.

Dear gmx comunity, I have been running my system without any problems with 100 processors. But I decided to make some of the bonds of my main molecule constrains. My molecule is not an extended chain, it is a molecular hydrated ion, in particular the uranyl cation with 5 water molecules forming a

Re: [gmx-users] pdb generator

well if you use Linux then you can use GVim to do highlight and do simple changes on one type only then use find and replace option. That what I do when I have more than one type. It needs one hour practice then you will be ok. Or you can write a script for such things. Best On Tue, Nov 13, 2018

Re: [gmx-users] pdb generator

You should know how many atoms in each residue then how many residues of XXX you have then you can see. Suggestion, if possible use sperate pdb files then use solvation option to produce your system .gro or pdb. This will help you in editing each pdb then get your correct gromacs input files.

Re: [gmx-users] pdb generator

Hello Momin The best tool I have found for dealing with cif files, including exporting to pdb, is Mercury. You can download it for free from: https://www.ccdc.cam.ac.uk/Community/csd-community/freemercury/ Hope this helps Victor El mar., 13 nov. 2018 a las 8:04, Momin Ahmad () escribió: >

Re: [gmx-users] pdb generator

Hi, I use Avogadro and it is easy to change LIG to anything you want. I just use find and replace option which takes less than a minute. Best Ali On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad wrote: > Hi, > > is there a tool where i can use for example a .cif file (or .xyz) file > to generate a

Re: [gmx-users] pdb generator

Hi Ali, my problem is that there is not only one molecule but two different molecules which build up a crystaline structure. For example i have 10 XXX and 100 YYY in the .pdb file. Cheers Momin Am 13.11.18 um 16:12 schrieb Ali Ahmed: Hi, I use Avogadro and it is easy to change LIG to

[gmx-users] Do need to recompile GROMACS with hardware changes

To Distribution: Do you need to recompile GROMACS with any hardware changes, i.e. 1 GPU to 8 GPU or 16 GPUs. My coworker says he saw this requirement in the documentation. But with the new release 2018.4, it's not there. Can anyone confirm? Many thanks for any responses. -Darin Darin S

[gmx-users] pdb generator

Hi, is there a tool where i can use for example a .cif file (or .xyz) file to generate a .pdb file with correct classification? For example Avogadro classifies all atoms as LIG and i cannot change it. Is there also another tool which can be used to generate large scale crystal structures

Re: [gmx-users] pdb generator

Hi Ali, thanks for you help. How can you distinguish between a C atom from residue XXX and another C atom from residue YYY when there are about 2000 atoms in the file. Did you write a script for that? If there doesnt exist a tool with a GUI to solve this then i will have to write my own

Re: [gmx-users] Subject: Re: Group WAT referenced in the .mdp file was not found in the index file

Hi, If you want to engage in discussion, please don't subscribe to the digest, because you can no longer reply to your own discussion in a way that means people understand the context. Mark On Tue, Nov 13, 2018 at 1:13 AM Rahma Dahmani wrote: > Hi Justin, > Thanks for your response, > I am

Re: [gmx-users] dssp excutable-error

Hi, Have you followed the advice in gmx help do_dssp about setting the environment variables? Did you install the correct version of dssp? Mark On Mon, Nov 12, 2018 at 11:43 PM marzieh dehghan wrote: > Dear all > I installed dssp software on ubuntu version 12.04 in the /usr/local/bin, > when

Re: [gmx-users] Global minimum

Hi, That's not a relevant thing. In statistical mechanics you have an ensemble of configurations. Mark On Mon, Nov 12, 2018 at 12:11 AM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > > How do we get the global minimum from a MD simulation? Is there any method >

Re: [gmx-users] Insert Molecules Settings

Hi, The tools look first in the working directory for such files, so copy it there and modify however suits you. Mark On Mon, Nov 12, 2018 at 2:42 PM tca1 wrote: > I sent this message on Friday, but I didn't see it show up in my > digest, so I'm trying again. Here's the previous text: > > >

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 28 - start the simulation of the last stopping point.

Hi, Those were not the commands you issued. What commands did you issue? Mark On Fri, Nov 9, 2018 at 7:12 AM Edjan Silva wrote: > Dear Paul, > > Thank you for your help. However, when you run the command: > > $ gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr > $ gmx mdrun

[gmx-users] ali.mof...@mail.utoronto.ca

Hello. I am trying to install GROMACS and when I enter 'make'', I get this response. What can I do to fix this? checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... configure: error: unsafe srcdir value: '/mnt/c/Users/Ali

Re: [gmx-users] Error: Cannot set thread affinities on the current platform

Hi, Unfortunately Cygwin isn't a supported platform for GROMACS. Setting such affinities is very important for performance, but doing so on cygwin requires doing things outside of Cygwin, I believe. There are some blog posts around that might help. Mark On Sun, Nov 11, 2018 at 6:45 PM Neena

Re: [gmx-users] LINCS warning

Hi, I can't tell whether that's a periodicity artefact in your visualization, or the topology is indeed junk. You will likely need to inspect the output of the tool that generated it. Rarely do these things "just work." Mark On Sun, Nov 11, 2018 at 3:01 AM Farial Tavakoli wrote: > Dear Mark >

Re: [gmx-users] Running GPU issue

Hi, It can share. Mark On Mon, Nov 12, 2018 at 10:19 PM Kovalskyy, Dmytro wrote: > Hi, > > > > To perform GPU with Gromacs does it require exclusive GPU card or Gromacs > can share the video card with X-server? > > > Thank you > > > Dmytro > -- > Gromacs Users mailing list > > * Please

Re: [gmx-users] Unable to generate .rtp file from gro and pdb file.

Hi, Your topology had 5 GEL and 2 PE, which means you have 7 things that could be a problem. Start with 1 so you find out where the problem is. Mark On Mon, Nov 12, 2018 at 10:40 PM Karpurmanjari Kakati < ch18resch01...@iith.ac.in> wrote: > Hi, > I didn't understand, what you exactly meant.

Re: [gmx-users] Periodic saving of checkpoint file

Hi, Looks OK. The details don't matter, as you are anyway changing ensemble. Mark On Thu, Nov 8, 2018 at 2:39 AM Nicolas Cheron < nicolas.cheron.bou...@gmail.com> wrote: > Hi Mark, > > Thank you for your answer. I didn't know this option. From what I have > read, eneconv is for reading

Re: [gmx-users] Do need to recompile GROMACS with hardware changes

Hi, On Tue, Nov 13, 2018 at 8:15 AM Darin Lory-External < darin.l...@regeneron.com> wrote: > To Distribution: > > Do you need to recompile GROMACS with any hardware changes, i.e. 1 GPU to > 8 GPU or 16 GPUs. > No. You might require a recompilation if the generation of the hardware changes, or

Re: [gmx-users] Setting rcon according to system

Hi, Possibly. It would be simpler to use fewer processors, such that the domains can be larger. What does mdrun think it needs for -rcon? Mark On Tue, Nov 13, 2018 at 7:06 AM Sergio Perez wrote: > Dear gmx comunity, > > I have been running my system without any problems with 100 processors.

Re: [gmx-users] ali.mof...@mail.utoronto.ca

Hi, It looks like the configure that is part of the FFTW build that you requested from GROMACS does not like your build location. Perhaps that's because your username has a space in it and configure can't handle that. Unfortunately GROMACS can't fix that, so I suggest you try to build from some

Re: [gmx-users] Building Gromacs

Hi, On Mon, Nov 12, 2018 at 3:46 PM Jasper Jordan wrote: > I was sure that a month ago when I started down the path of building and > making Gromacs available for our user community, that I read a statement > that whenever there is a hardware change, you need to rebuild Gromacs. I > took this

Re: [gmx-users] Question about nsttcouple

Hi, Sorry, it looks like the documentation is wrong in that case. Developers are fond of doing fancy things and not remembering all the things that depend on it. I imagine that nsttcouple gets 10 chosen, and only later is nstlist changed. The interpretation and behaviour of nstlist have