[gmx-users] Ris: compatibility between ff14SB and GLYCAM_06j-1 force field
Inviato dal mio dispositivo mobile Huawei Dear Louise, Did you check if the lipids you need are available with lipid17 force field? It is an Amber - based one and it is compatible with ff14SB. Notably, it has the same scaling factors of ff14SB. Hope this helps, Tommaso Messaggio originale Oggetto: [gmx-users] compatibility between ff14SB and GLYCAM_06j-1 force field Da: Louise Lassalle A: gromacs.org_gmx-users@maillist.sys.kth.se CC: Hello, I get a compatibility error between ff14SB and GLYCAM_06j-1 with gromacs 2018.4. I prepared my model (protein with co factors and lipids) via tleap and when I tried to convert to gromacs file with ParmEd I got this error: "Structure has mixed 1-4 scaling which is not supported by Gromacs". Does the next version of gromacs will be able to solve this problem? I need the ff14SB version for some atoms of the HEME and the GLYCAM for the lipids (HTG, LMG and SQD). What could be an equivalent of GLYCAM ? Thank you, Louise Lassalle -- 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 visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] compatibility between ff14SB and GLYCAM_06j-1 force field
Hello, I get a compatibility error between ff14SB and GLYCAM_06j-1 with gromacs 2018.4. I prepared my model (protein with co factors and lipids) via tleap and when I tried to convert to gromacs file with ParmEd I got this error: "Structure has mixed 1-4 scaling which is not supported by Gromacs". Does the next version of gromacs will be able to solve this problem? I need the ff14SB version for some atoms of the HEME and the GLYCAM for the lipids (HTG, LMG and SQD). What could be an equivalent of GLYCAM ? Thank you, Louise Lassalle -- 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.
Re: [gmx-users] dssp error
I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an executable Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao escreveu: > Have a check the installation of DSSP, > did you set the variable DSSP for do_dssp? > > > All the best, > Qinghua > > > On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote: > > gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu > ns > > -sc cbd211ssp.xvg -ver 2 > > > > Program: gmx do_dssp, version 2016.3 > > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > > > > Fatal error: > > Failed to execute command: Try specifying your dssp version with the -ver > > option. > > > > > > Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao > > > escreveu: > > > >> Hello, > >> > >> Just follow the suggestion by adding "-ver 2" to your command. > >> > >> > >> All the best, > >> Qinghua > >> > >> On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: > >>> Good afternoon. > >>> I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP > 2.0.4 > >>> for secondary structure analysis. When i try to run it i used this > >> commad: > >>> gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns > -sc > >>> protssp.xvg > >>> > >>> but gromacs send me this error: > >>> Program: gmx do_dssp, version 2016.3 > >>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > >>> > >>> Fatal error: > >>> Failed to execute command: Try specifying your dssp version with the > -ver > >>> option. > >>> > >>> Can you help me to fix this error? > >>> Thanks for your help > >>> > >>> > >> -- > >> 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 visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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.
Re: [gmx-users] dssp error
Have a check the installation of DSSP, did you set the variable DSSP for do_dssp? All the best, Qinghua On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote: gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao escreveu: Hello, Just follow the suggestion by adding "-ver 2" to your command. All the best, Qinghua On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Can you help me to fix this error? Thanks for your help -- 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 visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] dssp error
gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao escreveu: > Hello, > > Just follow the suggestion by adding "-ver 2" to your command. > > > All the best, > Qinghua > > On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: > > Good afternoon. > > I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 > > for secondary structure analysis. When i try to run it i used this > commad: > > > > gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc > > protssp.xvg > > > > but gromacs send me this error: > > Program: gmx do_dssp, version 2016.3 > > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > > > > Fatal error: > > Failed to execute command: Try specifying your dssp version with the -ver > > option. > > > > Can you help me to fix this error? > > Thanks for your help > > > > > > -- > 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. > -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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.
Re: [gmx-users] dssp error
Hello, Just follow the suggestion by adding "-ver 2" to your command. All the best, Qinghua On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Can you help me to fix this error? Thanks for your help -- 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.
[gmx-users] dssp error
Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Can you help me to fix this error? Thanks for your help -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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.
Re: [gmx-users] Freezing structure's atom
There a "gmx make_ndx" command to make .ndx group. They ahve their names. And it needs to be inserted in there. Please have a look at the .ndx file to see what it does. For any name it's just a list of atoms. On Thu, 21 Mar 2019 at 14:39, Hadi Rahmaninejad wrote: > Sorry I forgot to ask this question: did you determine "slab" group in your > .gro file? > > On Thu, Mar 21, 2019 at 10:29 AM Hadi Rahmaninejad > wrote: > > > Hello Mateusz, > > > > Thank you for your help. However, still I am a little confused. suppose > > that this is the .mdp file for minimization: > > integrator = steep ; Algorithm (steep = steepest descent > > minimization) > > emtol = 1000.0; Stop minimization when the maximum force < > > 1000.0 kJ/mol/nm > > emstep = 0.01 ; Minimization step size > > nsteps = 5 ; Maximum number of (minimization) steps to > > perform > > > > ; Parameters describing how to find the neighbors of each atom and how to > > calculate the interactions > > nstlist = 1 ; Frequency to update the neighbor list and > > long range forces > > cutoff-scheme = Verlet; Buffered neighbor searching > > ns_type = grid ; Method to determine neighbor list (simple, > > grid) > > coulombtype = PME ; Treatment of long range electrostatic > > interactions > > rcoulomb= 1.0 ; Short-range electrostatic cut-off > > rvdw= 1.0 ; Short-range Van der Waals cut-off > > pbc = xyz ; Periodic Boundary Conditions in all 3 > > dimensions" > > > > Now I need to freez some atoms that I have their index in a file like > > freez.ndx. How should I change this mdp file? In other word, which > option I > > should add to this file? > > > > Thank you once more, > > Hadi > > > > On Thu, Mar 21, 2019 at 8:42 AM Mateusz Bieniek > > wrote: > > > >> Hi Hadi, > >> > >> You can freeze atoms in any simulation, so yes in nvt.mdp or any other > >> .mdp. That is also why the freezegrps in the URL I attached is in the > >> section called mdp-options. > >> > >> When you run grompp to create the .tpr run file, it will not recognize > the > >> group "slab" so you will have to give it the index file: "gmx grompp ... > >> -n myindex". > >> > >> It might be a good idea to consider doing some tutorial with gromacs: > >> https://www.youtube.com/watch?v=kzJR2_XHkcM > >> http://www.mdtutorials.com/gmx/ > >> > >> Best, Mat > >> > >> On Thu, 21 Mar 2019 at 05:15, Hadi Rahmaninejad > >> wrote: > >> > >> > Hello Mateusz, > >> > > >> > First of all, I don’t know where should I use these these commands, > >> should > >> > I use for instance in equilibration input file like nvt. mdp file? > >> Second, > >> > in which file I should include ndx file? Could you please provide me > an > >> > example? > >> > > >> > Thank you, > >> > Hadi > >> > > >> > Sent from my iPhone > >> > > >> > > On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek > >> > wrote: > >> > > > >> > > Hi Hadi, > >> > > > >> > > To freeze atoms you have to first create the right group in your > index > >> > file > >> > > .ndx. Then, you use this: > >> > > > >> > > freezegrps = slab > >> > > freezedim= Y Y N > >> > > > >> > > Where the Ys refer to X Y Z, meaning here the slab group is frozen > in > >> X Y > >> > > dimension but not Z dimension. > >> > > > >> > > Please not that the pressure calculation breaks down when freezing > >> atoms. > >> > > In that case, they should be excluded from the pressure calculation > - > >> > > however this has not been implemented for a couple of years now in > >> Verlet > >> > > algorithm. > >> > > > >> > > For reference: > >> > > > >> > > >> > http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps > >> > > > >> > > > >> > > On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad < > >> ha.rahma...@gmail.com> > >> > > wrote: > >> > > > >> > >> Hello dear Gromacs users, > >> > >> > >> > >> I know how to restrain atoms of an structure solvated in water with > >> > force > >> > >> with option "-DPOSRES". However, for my simulation, I need to > exclude > >> > >> position changing from the simulation, in other words, I need to > >> exactly > >> > >> fixed them. I highly appreciate if any of you can help me with > this. > >> > >> > >> > >> Thank you in advance, > >> > >> Hadi > >> > >> -- > >> > >> 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 > >> >
Re: [gmx-users] Freezing structure's atom
Sorry I forgot to ask this question: did you determine "slab" group in your .gro file? On Thu, Mar 21, 2019 at 10:29 AM Hadi Rahmaninejad wrote: > Hello Mateusz, > > Thank you for your help. However, still I am a little confused. suppose > that this is the .mdp file for minimization: > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Minimization step size > nsteps = 5 ; Maximum number of (minimization) steps to > perform > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and > long range forces > cutoff-scheme = Verlet; Buffered neighbor searching > ns_type = grid ; Method to determine neighbor list (simple, > grid) > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb= 1.0 ; Short-range electrostatic cut-off > rvdw= 1.0 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions in all 3 > dimensions" > > Now I need to freez some atoms that I have their index in a file like > freez.ndx. How should I change this mdp file? In other word, which option I > should add to this file? > > Thank you once more, > Hadi > > On Thu, Mar 21, 2019 at 8:42 AM Mateusz Bieniek > wrote: > >> Hi Hadi, >> >> You can freeze atoms in any simulation, so yes in nvt.mdp or any other >> .mdp. That is also why the freezegrps in the URL I attached is in the >> section called mdp-options. >> >> When you run grompp to create the .tpr run file, it will not recognize the >> group "slab" so you will have to give it the index file: "gmx grompp ... >> -n myindex". >> >> It might be a good idea to consider doing some tutorial with gromacs: >> https://www.youtube.com/watch?v=kzJR2_XHkcM >> http://www.mdtutorials.com/gmx/ >> >> Best, Mat >> >> On Thu, 21 Mar 2019 at 05:15, Hadi Rahmaninejad >> wrote: >> >> > Hello Mateusz, >> > >> > First of all, I don’t know where should I use these these commands, >> should >> > I use for instance in equilibration input file like nvt. mdp file? >> Second, >> > in which file I should include ndx file? Could you please provide me an >> > example? >> > >> > Thank you, >> > Hadi >> > >> > Sent from my iPhone >> > >> > > On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek >> > wrote: >> > > >> > > Hi Hadi, >> > > >> > > To freeze atoms you have to first create the right group in your index >> > file >> > > .ndx. Then, you use this: >> > > >> > > freezegrps = slab >> > > freezedim= Y Y N >> > > >> > > Where the Ys refer to X Y Z, meaning here the slab group is frozen in >> X Y >> > > dimension but not Z dimension. >> > > >> > > Please not that the pressure calculation breaks down when freezing >> atoms. >> > > In that case, they should be excluded from the pressure calculation - >> > > however this has not been implemented for a couple of years now in >> Verlet >> > > algorithm. >> > > >> > > For reference: >> > > >> > >> http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps >> > > >> > > >> > > On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad < >> ha.rahma...@gmail.com> >> > > wrote: >> > > >> > >> Hello dear Gromacs users, >> > >> >> > >> I know how to restrain atoms of an structure solvated in water with >> > force >> > >> with option "-DPOSRES". However, for my simulation, I need to exclude >> > >> position changing from the simulation, in other words, I need to >> exactly >> > >> fixed them. I highly appreciate if any of you can help me with this. >> > >> >> > >> Thank you in advance, >> > >> Hadi >> > >> -- >> > >> 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 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 >> > >> > *
Re: [gmx-users] Freezing structure's atom
Hello Mateusz, Thank you for your help. However, still I am a little confused. suppose that this is the .mdp file for minimization: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions" Now I need to freez some atoms that I have their index in a file like freez.ndx. How should I change this mdp file? In other word, which option I should add to this file? Thank you once more, Hadi On Thu, Mar 21, 2019 at 8:42 AM Mateusz Bieniek wrote: > Hi Hadi, > > You can freeze atoms in any simulation, so yes in nvt.mdp or any other > .mdp. That is also why the freezegrps in the URL I attached is in the > section called mdp-options. > > When you run grompp to create the .tpr run file, it will not recognize the > group "slab" so you will have to give it the index file: "gmx grompp ... > -n myindex". > > It might be a good idea to consider doing some tutorial with gromacs: > https://www.youtube.com/watch?v=kzJR2_XHkcM > http://www.mdtutorials.com/gmx/ > > Best, Mat > > On Thu, 21 Mar 2019 at 05:15, Hadi Rahmaninejad > wrote: > > > Hello Mateusz, > > > > First of all, I don’t know where should I use these these commands, > should > > I use for instance in equilibration input file like nvt. mdp file? > Second, > > in which file I should include ndx file? Could you please provide me an > > example? > > > > Thank you, > > Hadi > > > > Sent from my iPhone > > > > > On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek > > wrote: > > > > > > Hi Hadi, > > > > > > To freeze atoms you have to first create the right group in your index > > file > > > .ndx. Then, you use this: > > > > > > freezegrps = slab > > > freezedim= Y Y N > > > > > > Where the Ys refer to X Y Z, meaning here the slab group is frozen in > X Y > > > dimension but not Z dimension. > > > > > > Please not that the pressure calculation breaks down when freezing > atoms. > > > In that case, they should be excluded from the pressure calculation - > > > however this has not been implemented for a couple of years now in > Verlet > > > algorithm. > > > > > > For reference: > > > > > > http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps > > > > > > > > > On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad > > > > wrote: > > > > > >> Hello dear Gromacs users, > > >> > > >> I know how to restrain atoms of an structure solvated in water with > > force > > >> with option "-DPOSRES". However, for my simulation, I need to exclude > > >> position changing from the simulation, in other words, I need to > exactly > > >> fixed them. I highly appreciate if any of you can help me with this. > > >> > > >> Thank you in advance, > > >> Hadi > > >> -- > > >> 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 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 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
Re: [gmx-users] Freezing structure's atom
Hi Hadi, You can freeze atoms in any simulation, so yes in nvt.mdp or any other .mdp. That is also why the freezegrps in the URL I attached is in the section called mdp-options. When you run grompp to create the .tpr run file, it will not recognize the group "slab" so you will have to give it the index file: "gmx grompp ... -n myindex". It might be a good idea to consider doing some tutorial with gromacs: https://www.youtube.com/watch?v=kzJR2_XHkcM http://www.mdtutorials.com/gmx/ Best, Mat On Thu, 21 Mar 2019 at 05:15, Hadi Rahmaninejad wrote: > Hello Mateusz, > > First of all, I don’t know where should I use these these commands, should > I use for instance in equilibration input file like nvt. mdp file? Second, > in which file I should include ndx file? Could you please provide me an > example? > > Thank you, > Hadi > > Sent from my iPhone > > > On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek > wrote: > > > > Hi Hadi, > > > > To freeze atoms you have to first create the right group in your index > file > > .ndx. Then, you use this: > > > > freezegrps = slab > > freezedim= Y Y N > > > > Where the Ys refer to X Y Z, meaning here the slab group is frozen in X Y > > dimension but not Z dimension. > > > > Please not that the pressure calculation breaks down when freezing atoms. > > In that case, they should be excluded from the pressure calculation - > > however this has not been implemented for a couple of years now in Verlet > > algorithm. > > > > For reference: > > > http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps > > > > > > On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad > > wrote: > > > >> Hello dear Gromacs users, > >> > >> I know how to restrain atoms of an structure solvated in water with > force > >> with option "-DPOSRES". However, for my simulation, I need to exclude > >> position changing from the simulation, in other words, I need to exactly > >> fixed them. I highly appreciate if any of you can help me with this. > >> > >> Thank you in advance, > >> Hadi > >> -- > >> 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 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 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 visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
