Re: [gmx-users] mpirun

Hi, I deleted the old one and moved another one using box.com since scp doesn't work, but I got the same results. Any ideas? /Elsaid On Tue, Nov 10, 2015 at 3:02 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/9/15 7:59 PM, Elsaid Younes wrote: > >> Hi, >

Re: [gmx-users] mpirun

g_dyndom_d > g_helixorient g_mindist_d g_pme_error g_rms_dg_select > g_tcaf_d g_xrama make_editrjcat > >> > >> > >> Elsaid, > >> > >> Regarding Justin’s suggestion, on Uppmax I believe the full path would > be: &

Re: [gmx-users] mpirun

Hi, Thank you for your response. When writing gmx, it gives the command not found. (Note I use windows) Elsaid On Mon, Nov 9, 2015 at 3:31 PM, Justin Lemkul wrote: > > > On 11/9/15 5:23 AM, Said wrote: > >> Hi, >> >> I have a gateway access to uppmax. I could have copied

Re: [gmx-users] mpirun

Hi, it gives me file input/output error 1aki.pdb. Elsaid On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes <elk...@gmail.com> wrote: > Thank you! > > On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores <samuelflor...@gmail.com> > wrote: > >> Oh that makes sense! >&g

[gmx-users] rm command.

Hi, Can anyone please tell me how to remove a file from directory? rm doesn't work. for example: rm/prss/sss/topol.top There are three files of it. /Elsaid -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] X11 forwarding!

Hi all, I can not do ssh over X, although my sshd-config is: # Package generated configuration file # See the sshd_config(5) manpage for details # What ports, IPs and protocols we listen for Port 22 # Use these options to restrict which interfaces/protocols sshd will bind to #ListenAddress ::

[gmx-users] Scripts to the gromacs

Hey all, I wish I can find a way to help me writing a script to the gromacs. I mean by scripts "the commands that one writes to gramacs terminals and the choices, which are prompted after command's processing, all collected in one file" I do simulation like lysozyme in water tutorial. Looking

Re: [gmx-users] Extend the simulation

) Performance:5.5544.321 /Elsaid On Sun, Feb 21, 2016 at 3:56 AM, Elsaid Younes <elk...@gmail.com> wrote: > Sorry > Once, I added .tpr to the md_0_1 then it gave me the above message then I > did as you said without .tpr. > That error was obtained: > > F

[gmx-users] Extend the simulation

Hi all, I need to extend a previous simulation, and its directory is the same with all inputs and outpts. That simulation can not be complete due to the maximum time of the job which is limited by the server. I use gromacs 5, when using the command gmx convert-tpr, an error is obtained. Command

Re: [gmx-users] Extend the simulation

Hi, If I have this file md_0_1_prev.cpt What is the text exactly? It asks for topol.tpr On 2/20/16 5:32 PM, Elsaid wrote: >* The simulation has the time, which is time of the wanted simulation. But the *>* job was killed by the server. * If the simulation terminated prior to completion, you

Re: [gmx-users] Extend the simulation

Still asks for topol.tpr? Can I have that file /Elsaid On 2/20/16 6:49 PM, Elsaid Younes wrote: >* Hi, *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks *>* for topol.tpr * I gave you the command-line options that are new to the mdrun command line. Run

Re: [gmx-users] Extend the simulation

Hi, The mdrun I did was gmx mdrun -deffnm md_0_1 I write the command mdrun -cpi md_0_1_prev.cpt -append I tried to use -noappend, but still doesn't work. /Elsaid On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elk...@gmail.com> wrote: > Still asks for topol.tpr? Can I have

Re: [gmx-users] Extend the simulation

Ok, How can I use md_0_1.tpr instead of topol.tpr /Elsaid On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes <elk...@gmail.com> wrote: > Hi, > > The mdrun I did was gmx mdrun -deffnm md_0_1 > I write the command > mdrun -cpi md_0_1_prev.cpt -append > I tried to use -noa

Re: [gmx-users] Extend the simulation

It says: No previous checkpoint file present, assuming this is a new run. Reading file md_0_1.tpr, VERSION 5.0.4 (single precision) Changing nstlist from 10 to 20, rlist from 1 to 1.03 then start.. /Elsaid On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes <elk...@gmail.com> wrote: >

Re: [gmx-users] Extend the simulation

because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- /Elsaid On Sun, Feb 21, 2016 at 3:38 AM, Elsaid Younes <elk...@gmail.com>

Re: [gmx-users] Gromacs installation.

..After all Gromacs can not start. On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes <elk...@gmail.com> wrote: > Hi all, > > I have installed gromacs like the quick and dirty installation. I have a > 16.04 version of ubuntu. I can not start it. > I used to

[gmx-users] Gromacs installation.

Hi all, I have installed gromacs like the quick and dirty installation. I have a 16.04 version of ubuntu. I can not start it. I used to do the same procedure in ubuntu 15.10, and it worked fine. /Elsaid -- Gromacs Users mailing list * Please search the archive at