I think I found a workaround my own problem: I initially placed everything in a box that includes all present molecules within its borders and solvated it. Then I redefined the box and ran an energy minimisation step. The em.gro file looks as if everything is solvated fine inside the new box which has molecule_1 at its center.
----- Original Message ----- From: "gromacs org gmx-users-request" <gromacs.org_gmx-users-requ...@maillist.sys.kth.se> To: "gromacs org gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> Sent: Thursday, December 27, 2018 1:32:20 PM GMT +02:00 Athens, Beirut, Bucharest, Istanbul Subject: gromacs.org_gmx-users Digest, Vol 176, Issue 69 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: how to restart a job in grmacs (sp...@iacs.res.in) 2. Re: how to restart a job in grmacs (SHAHEE ISLAM) 3. Question on gmx editconf, pbc and NPT (Sebastian Muraru) 4. Re: how to restart a job in grmacs (sp...@iacs.res.in) 5. Re: how to restart a job in grmacs (SHAHEE ISLAM) 6. electrostatic and LJ energy (Dr Tushar Ranjan Moharana) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Dec 2018 16:28:53 +0530 From: sp...@iacs.res.in To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] how to restart a job in grmacs Message-ID: <20181227162853.horde.xoxxxhf68ivvyq27yoz5...@mailweb.iacs.res.in> Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530 ? ? From: SHAHEE ISLAM <islamsha...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] how to restart a job in grmacs ? ? ? To: gmx-us...@gromacs.org > hi, > i have run a simulation for 10 ns but after 4 ns due to power off the > job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi > md_0_10ns.cpt,continue the left simulation.Now after normal > termination of 10 ns how i wll do the next 5 ns simulation after this > 10 ns. > thanking you > shahee > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@gromacs.org. Hi You can extend the job by generating a new tpr file? gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr? then restart the job? gmx mdrun -s new.tpr -cpi state.cpt ?This will continue the run from 10 ns. Sunipa ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- ------------------------------ Message: 2 Date: Thu, 27 Dec 2018 16:41:21 +0530 From: SHAHEE ISLAM <islamsha...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to restart a job in grmacs Message-ID: <cajz7at9ygwciw8tn4hyog+51qdky6eqkvpegamjygupyw2-...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" thank you so much for your reply. -extend 5000 what does it signify.if the time step is 2 fs then by simply multiplying these two it will give 10 ns. thanking you On 12/27/18, sp...@iacs.res.in <sp...@iacs.res.in> wrote: > ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- > ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530 > ? ? From: SHAHEE ISLAM <islamsha...@gmail.com> > Reply-To: gmx-us...@gromacs.org > Subject: [gmx-users] how to restart a job in grmacs > ? ? ? To: gmx-us...@gromacs.org > >> hi, >> i have run a simulation for 10 ns but after 4 ns due to power off the >> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi >> md_0_10ns.cpt,continue the left simulation.Now after normal >> termination of 10 ns how i wll do the next 5 ns simulation after this >> 10 ns. >> thanking you >> shahee >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests >> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or send a mail to gmx-users-requ...@gromacs.org. > > Hi > You can extend the job by generating a new tpr file > gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr > then restart the job > gmx mdrun -s new.tpr -cpi state.cpt > ?This will continue the run from 10 ns. > Sunipa > ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. ------------------------------ Message: 3 Date: Thu, 27 Dec 2018 13:12:46 +0200 (EET) From: Sebastian Muraru <sebastian.mur...@grabtop.upb.ro> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Question on gmx editconf, pbc and NPT Message-ID: <1457525096.48541545909166873.javamail.r...@webmail.chim.upb.ro> Content-Type: text/plain; charset=utf-8 Hi there! Please help me figure something out. I have a setup made out of two molecules and I would like to investigate when happens when they meet (graphene + biomolecule). One of them is fixed by position restraints, one of them is mobile. When running a simulation under NPT conditions I assumed pressure is applied so that everything is 'slightly guided' towards the center of the simulation box (given a high enough pressure value). Would that assumption be correct? Or is pressure presumably applied on the faces of the simulation box? Thus, I figured, since I want to check what happens when the molecules meet, I want molecule_1 to be in the center of the simulation box and have molecule_2 slightly guided towards it. However, given that the distance between the molecules is known and fixed, placing the box so that molecule_1 is at the center leaves a part of molecule_2 out of the box through the top face. I assumed this would not be a problem during a simulation due to pbc being on, thus allowing the part of molecule_2 that's out of the box to reenter through the bottom layer. However, I also need to go through a solvation step and that I think this complicates things because a part of molecule_2 will not be in solvent. Would you know a workaround for this issue? I try to avoid making the box taller / bigger. Thanks and a Happy Upcoming New Year to the Gromacs Community! ------------------------------ Message: 4 Date: Thu, 27 Dec 2018 16:47:39 +0530 From: sp...@iacs.res.in To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] how to restart a job in grmacs Message-ID: <20181227164739.horde.cg717yibka2pua0otamy...@mailweb.iacs.res.in> Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- ? ? Date: Thu, 27 Dec 2018 16:41:21 +0530 ? ? From: SHAHEE ISLAM <islamsha...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to restart a job in grmacs ? ? ? To: gmx-us...@gromacs.org > thank you so much for your reply. > -extend 5000 what does it signify.if the time step is 2 fs then by > simply multiplying these two it will give 10 ns. > thanking you > > On 12/27/18, sp...@iacs.res.in <sp...@iacs.res.in> wrote: >> ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- >> ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530 >> ? ? From: SHAHEE ISLAM <islamsha...@gmail.com> >> Reply-To: gmx-us...@gromacs.org >> Subject: [gmx-users] how to restart a job in grmacs >> ? ? ? To: gmx-us...@gromacs.org >> >>> hi, >>> i have run a simulation for 10 ns but after 4 ns due to power off the >>> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi >>> md_0_10ns.cpt,continue the left simulation.Now after normal >>> termination of 10 ns how i wll do the next 5 ns simulation after this >>> 10 ns. >>> thanking you >>> shahee >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests >>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>> or send a mail to gmx-users-requ...@gromacs.org. >> >> Hi >> You can extend the job by generating a new tpr file >> gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr >> then restart the job >> gmx mdrun -s new.tpr -cpi state.cpt >> ?This will continue the run from 10 ns. >> Sunipa >> ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a >> mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@gromacs.org. Hi -extend 5000 means you want to extend 5000 ps or 5 ns extra after 10 ns. So your final trajectory will be for 15 ns. Sunipa ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- ------------------------------ Message: 5 Date: Thu, 27 Dec 2018 16:52:17 +0530 From: SHAHEE ISLAM <islamsha...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to restart a job in grmacs Message-ID: <cajz7at_7dcazgsmxa4l_sj-hkuzhtmbtcq_03cn8zie7mtx...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" thank you is the trajectory wil be from 0-15 ns or it will be from 10-15 ns. On 12/27/18, sp...@iacs.res.in <sp...@iacs.res.in> wrote: > ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- > ? ? Date: Thu, 27 Dec 2018 16:41:21 +0530 > ? ? From: SHAHEE ISLAM <islamsha...@gmail.com> > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] how to restart a job in grmacs > ? ? ? To: gmx-us...@gromacs.org > >> thank you so much for your reply. >> -extend 5000 what does it signify.if the time step is 2 fs then by >> simply multiplying these two it will give 10 ns. >> thanking you >> >> On 12/27/18, sp...@iacs.res.in <sp...@iacs.res.in> wrote: >>> ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- >>> ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530 >>> ? ? From: SHAHEE ISLAM <islamsha...@gmail.com> >>> Reply-To: gmx-us...@gromacs.org >>> Subject: [gmx-users] how to restart a job in grmacs >>> ? ? ? To: gmx-us...@gromacs.org >>> >>>> hi, >>>> i have run a simulation for 10 ns but after 4 ns due to power off the >>>> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi >>>> md_0_10ns.cpt,continue the left simulation.Now after normal >>>> termination of 10 ns how i wll do the next 5 ns simulation after this >>>> 10 ns. >>>> thanking you >>>> shahee >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests >>>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>> or send a mail to gmx-users-requ...@gromacs.org. >>> >>> Hi >>> You can extend the job by generating a new tpr file >>> gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr >>> then restart the job >>> gmx mdrun -s new.tpr -cpi state.cpt >>> ?This will continue the run from 10 ns. >>> Sunipa >>> ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a >>> mail to gmx-users-requ...@gromacs.org. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests >> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or send a mail to gmx-users-requ...@gromacs.org. > > Hi > -extend 5000 means you want to extend 5000 ps or 5 ns extra after 10 ns. So > your final trajectory will be for 15 ns. > > Sunipa > > ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. ------------------------------ Message: 6 Date: Thu, 27 Dec 2018 17:01:10 +0530 From: Dr Tushar Ranjan Moharana <tusharranjanmohar...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] electrostatic and LJ energy Message-ID: <CAH6CjFgO_HOb8-L4riJStqAib0a2Xaaccm=fzjzbhcsudhf...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" You can use gmx energy (g_energy). Follow the online manual at http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-energy.html Regards -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 176, Issue 69 ****************************************************** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.