Re: [gmx-users] powercut command

On 4/13/17 3:14 PM, Anshul Lahariya wrote: i am performing a md of protein ligand complex for 10 ns. i am using gromacs 5.1.4 on my lappy with 16 gb ram without gpu. Running MD of large systems on a laptop is a bad idea. It's not the cause of the error, but you're likely to overheat the

Re: [gmx-users] powercut command

i am performing a md of protein ligand complex for 10 ns. i am using gromacs 5.1.4 on my lappy with 16 gb ram without gpu. i was performing all the steps without error but found an error in mdrun. kindly help me to stable my system. {i am following the protein - ligand complex tutorial of bevan

Re: [gmx-users] powercut command

On 4/13/17 11:25 AM, Anshul Lahariya wrote: i was failed to diagnose. plzz help me Start here: http://www.catb.org/esr/faqs/smart-questions.html As I already said, no one on this list can tell anything about your system because you have provided no useful diagnostic information or

Re: [gmx-users] powercut command

i was failed to diagnose. plzz help me On Thu, Apr 13, 2017 at 5:30 PM, Justin Lemkul wrote: > > > On 4/13/17 7:59 AM, Anshul Lahariya wrote: > >> Now i perform a new md, there is a problem with this error >> >> >> [anshu@dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0 >>

Re: [gmx-users] powercut command

On 4/13/17 7:59 AM, Anshul Lahariya wrote: Now i perform a new md, there is a problem with this error [anshu@dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0 :-) GROMACS - gmx mdrun, 2016.2 (-: GROMACS is written by: Emile Apol

Re: [gmx-users] powercut command

Now i perform a new md, there is a problem with this error [anshu@dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0 :-) GROMACS - gmx mdrun, 2016.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar

Re: [gmx-users] powercut command

okkk,,, thank u justin sir On Thu, Apr 13, 2017 at 3:51 PM, Justin Lemkul wrote: > > > On 4/13/17 6:19 AM, Anshul Lahariya wrote: > >> now i got this error >> >> >> Program: gmx mdrun, version 2016.2 >> Source file: src/gromacs/mdlib/constr.cpp (line 167) >> >> Fatal error:

Re: [gmx-users] powercut command

On 4/13/17 6:19 AM, Anshul Lahariya wrote: now i got this error Program: gmx mdrun, version 2016.2 Source file: src/gromacs/mdlib/constr.cpp (line 167) Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file

Re: [gmx-users] powercut command

now i got this error Program: gmx mdrun, version 2016.2 Source file: src/gromacs/mdlib/constr.cpp (line 167) Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable

Re: [gmx-users] powercut command

For md.xtc output -x flag is there. -o flag gives the md.trr as output. This is what Gromacs is complaining. File name 'md_1_0.xtc' cannot be used for this option. Only the following extensions are possible: On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya

Re: [gmx-users] powercut command

thankss tasneem. let me try. On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya wrote: > powercut take place and md stops, so i want to continue my md > > > > > [root@dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g > md_1_0.log -o md_1_0.xtc -cpi

Re: [gmx-users] powercut command

powercut take place and md stops, so i want to continue my md [root@dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append :-) GROMACS - gmx mdrun, 2016.2 (-: GROMACS is

Re: [gmx-users] powercut command

gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt -cpo 10ns.cpt -append There is problem in the command that you have given in your first mail. gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -x 10ns.xtc -cpi 10ns.cpt -append You did not provided the -x flag. This was the

Re: [gmx-users] powercut command

Lincs warning usually occurs for the system that not minimized. You can try to minimize your system before running the real simulation. Other option would be use -maxwarn flag but please use it only if you know that these warnings are not important. > On 13 Apr 2017, at 11:10, Anshul Lahariya

Re: [gmx-users] powercut command

please give the exact command and error message. On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya wrote: > dear das sir, > > -cpi was already added to the command but my problem is not solved > > On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya < >

Re: [gmx-users] powercut command

dear das sir, -cpi was already added to the command but my problem is not solved On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya wrote: > error says, xtc file is not used for this option . plzz use trr, cpt, tng > > > help me out > > On Thu, Apr 13, 2017 at 11:29

Re: [gmx-users] powercut command

error says, xtc file is not used for this option . plzz use trr, cpt, tng help me out On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb wrote: > please put this command line > gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt -o > md_1_0.xtc > > good luck > >

Re: [gmx-users] powercut command

Hi, On Thu, Apr 13, 2017 at 7:43 AM Anshul Lahariya wrote: > My md was running. Suddenly power supply was cuts due to some reason and my > my MD stops.. > To continue my MD, I use command:- > Use the same command, but add -cpi whatever.cpt > > > gmx mdrun -v -s

Re: [gmx-users] powercut command

This is a error that i got during mdrun. plzzz help.. Program: gmx mdrun, version 2016.2 Source file: src/gromacs/mdlib/constr.cpp (line 167) Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the

Re: [gmx-users] powercut command

Thank u so much #Devashish Das On Thu, Apr 13, 2017 at 11:30 AM, Devashish_Das wrote: > Please use to resume: > > gmx mdrun -v -deffnm 10ns -cpi 10ns.cpt > > > > > On Thu, Apr 13, 2017 at 11:12 AM, Anshul Lahariya < > anshullahariy...@gmail.com> wrote: > > > My md

Re: [gmx-users] powercut command

Please use to resume: gmx mdrun -v -deffnm 10ns -cpi 10ns.cpt On Thu, Apr 13, 2017 at 11:12 AM, Anshul Lahariya < anshullahariy...@gmail.com> wrote: > My md was running. Suddenly power supply was cuts due to some reason and my > my MD stops.. > To continue my MD, I use command:- > > > gmx

Re: [gmx-users] powercut command

please put this command line gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt -o md_1_0.xtc good luck On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya < anshullahariy...@gmail.com> wrote: > My md was running. Suddenly power supply was cuts due to some reason and my > my MD

[gmx-users] powercut command

My md was running. Suddenly power supply was cuts due to some reason and my my MD stops.. To continue my MD, I use command:- gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt -cpo 10ns.cpt -append but shows error. Error in user input: Invalid command-line options