Re: [gmx-users] Energy from a subgroup of molecules

On 4/11/19 5:39 PM, paul buscemi wrote: Thank you for the response, Mark. I do use the rerun tactic, and this is not too bad for a small number of molecules but is there a way to include the index information within the mdrun (rerun ) … something like gmx mdrun -s adsorb.ener_gp.tpr -r

Re: [gmx-users] Energy from a subgroup of molecules

Thank you for the response, Mark. I do use the rerun tactic, and this is not too bad for a small number of molecules but is there a way to include the index information within the mdrun (rerun ) … something like gmx mdrun -s adsorb.ener_gp.tpr -rerun adsorb,npt.trr - n use_only.ndx ? o

Re: [gmx-users] gromacs instillation

Yes I'm using the quick and dirty Installation On Thu, Apr 11, 2019 at 12:55 PM RAHUL SURESH wrote: > Are you following the quick and dirty Installation or modify your > compilation? > > On Thu 11 Apr, 2019, 11:20 PM RAHUL SURESH, > wrote: > > > > > > > On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed,

Re: [gmx-users] Different versions of gromacs

Thnxx sir On Thu 11 Apr, 2019, 8:46 PM Justin Lemkul > More specifically, versions within a release series that only differ by > patch number (e.g. 2016.x, 2018.x, etc) are designed to be compatible. I > would not personally do different processes in the same project with > different major versio

Re: [gmx-users] gromacs instillation

Are you following the quick and dirty Installation or modify your compilation? On Thu 11 Apr, 2019, 11:20 PM RAHUL SURESH, wrote: > > > On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed, wrote: > >> I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each >> terminal I run source /usr/lo

Re: [gmx-users] gromacs instillation

On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed, wrote: > I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each > terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs. > I kind of confused which one I should modify > If that is your executable directory, then the

Re: [gmx-users] gromacs instillation

I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs. I kind of confused which one I should modify On Thu, Apr 11, 2019 at 10:08 AM p buscemi wrote: > when you open a new terminal you need to run " so

Re: [gmx-users] Different versions of gromacs

More specifically, versions within a release series that only differ by patch number (e.g. 2016.x, 2018.x, etc) are designed to be compatible. I would not personally do different processes in the same project with different major versions. -Justin On 4/10/19 10:56 PM, Bratin Kumar Das wrot

Re: [gmx-users] atom types of hydrogens

On 4/10/19 4:12 AM, boshra.moradi.61 wrote: در 2019-04-09 20:08، Justin Lemkul نوشته است: On 4/9/19 11:26 AM, boshra.moradi.61 wrote:   Dear all, i'm new om gromacs and my molecule is D-glucosamine.i introduced it via inserting in aminoacids.rtp file.my question is how nominate four H-at

Re: [gmx-users] Protein dipole moments

On 4/10/19 1:02 AM, Emran Heshmati wrote: What are the physical meaning of <|M|^2> and <|M|>^2 in the outputs of gmx dipoles command ?? Any help is welcome. The notation suggests the average of the squared dipoles and the square of the average dipoles, respectively. Check the source code to

Re: [gmx-users] gromacs instillation

when you open a new terminal you need to run " source" again, but you probably know this by now or add the path to your /etc/.profile to make the change permanent Sent from Mailspring (https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect

Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

Hi Szilárd, Many thanks, now it is clear to me also how the tests are verified. This means, I can trust my energy calculation now. Thanks again, Steffi -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.k

[gmx-users] Glycam06 force field

Hello Gromacs users, Anyone is here familiar with Glycam06 Force Field for carbohydrates and tried building sugar molecules using the tool do_glycans, I have some questions. -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L

Re: [gmx-users] Atom name mismatch between gro and top file

Simply change the order of the atoms in the gro file to match the topology file. The order of the atoms is not in itself what is important, ie they can really be in any order, it's that the names and order match between coordinate - topology file and then within the topology file. This error also