Re: [gmx-users] rotacf error
How I can remove the prolines, I have 6 in the protein... Em dom., 15 de dez. de 2019 às 03:10, David van der Spoel < sp...@xray.bmc.uu.se> escreveu: > Den 2019-12-15 kl. 04:13, skrev Mario Andres Rodriguez Pineda: > > Hi all > > I want to calculate the order parameter of the NH vector for each amino > > acids of a protein in a gromacs trajectory for compare with NMR > > experimental data. > > I found that it can be calculated using rotacf to calculate the > correlation > > time, when trying to run the program I get an error. In the attached > file I > > show more details about the error andhow I created the index. Could you > > help me to correct the index for calculate the correlation time and in > turn > > the order parameter S2? > > Thanks for your help. > > > > > you likely have Proline residues in your protein which do not have a H. > More tricky, if you have two prolines you get an even number of atoms > again but it can be completely wrong. Solution is to remove prolines in > make_ndx before you select a group of NH. > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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.
[gmx-users] rotacf error
Hi all I want to calculate the order parameter of the NH vector for each amino acids of a protein in a gromacs trajectory for compare with NMR experimental data. I found that it can be calculated using rotacf to calculate the correlation time, when trying to run the program I get an error. In the attached file I show more details about the error andhow I created the index. Could you help me to correct the index for calculate the correlation time and in turn the order parameter S2? 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* gmx_mpi make_ndx -f protein_md.tpr -o nh.ndx << EOF > a N | a H > r 590 | r 645 | r 649 | r 655 | r 664 | r 680 > 10 & !11 > name 12 NH > del 0-11 > q > EOF > name 12 NH > del 0-11 > q > EOF Reading structure file Reading file cbd212_md.tpr, VERSION 2018.6 (single precision) Reading file cbd212_md.tpr, VERSION 2018.6 (single precision) Going to read 0 old index file(s) Analysing residue names: There are: 146Protein residues There are: 23993 Water residues There are: 196Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 74517 atoms 1 Protein : 2342 atoms 2 Protein-H : 1186 atoms 3 C-alpha : 146 atoms 4 Backbone: 438 atoms 5 MainChain : 585 atoms 6 MainChain+Cb: 723 atoms 7 MainChain+H : 727 atoms 8 SideChain : 1615 atoms 9 SideChain-H : 601 atoms 10 Prot-Masses : 2342 atoms 11 non-Protein : 72175 atoms 12 Water : 71979 atoms 13 SOL : 71979 atoms 14 non-Water : 2538 atoms 15 Ion : 196 atoms 16 NA : 103 atoms 17 CL :93 atoms 18 Water_and_ions : 72175 atoms nr : group '!': not 'name' nr name 'splitch' nrEnter: list groups 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 't': atom type '|': or 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > Found 146 atoms with name N Found 139 atoms with name H Merged two groups with OR: 146 139 -> 285 19 N_H : 285 atoms > Merged two groups with OR: 14 14 -> 28 Merged two groups with OR: 28 14 -> 42 Merged two groups with OR: 42 14 -> 56 Merged two groups with OR: 56 14 -> 70 Merged two groups with OR: 70 14 -> 84 20 r_590_r_645_r_649_r_655_r_664_r_680:84 atoms > Copied index group 10 'Prot-Masses' Copied index group 11 'non-Protein' Complemented group: 2342 atoms Merged two groups with AND: 2342 2342 -> 2342 21 Prot-Masses_&_!non-Protein: 2342 atoms > > Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'non-Protein' > gmx_mpi rotacf -s protein_md.tpr -f protein_nopbc.xtc -P 2 -d -n nh.ndx -o protein_rotacf.xvg -dt 1000 Group 0 ( NH) has 71979 elements Group 1 (SOL) has 71979 elements Group 2 ( non-Water) has 2538 elements Group 3 (Ion) has 196 elements Group 4 ( NA) has 103 elements Group 5 ( CL) has93 elements Group 6 ( Water_and_ions) has 72175 elements Group 7 (N_H) has 285 elements Group 8 (r_590_r_645_r_649_r_655_r_664_r_680) has84 elements Group 9 (Prot-Masses_&_!non-Protein) has 2342 elements Select a group: 7 Selected 7: 'N_H' --- Program: gmx rotacf, version 2018.6 Source file: src/gromacs/gmxana/gmx_rotacf.cpp (line 140) Fatal error: number of index elements not multiple of 2, these can not be atom doublets For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. -- 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
Re: [gmx-users] distance analysis error
Thanks a lot Dr. Dallas... Em qua, 16 de out de 2019 às 19:44, Dallas Warren escreveu: > Have a read of the instructions for using the script: > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html > > That, and the error printed, state that you need to use a pair of > positions, not a single one. > > So your index group should be: > > [ F519-S678 ] > 1450 3976 > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On Thu, 17 Oct 2019 at 09:28, Mario Andres Rodriguez Pineda < > mand...@iq.usp.br> wrote: > > > Hi everbody > > I'm trying to analyse an preotein simulation made in Gromacs 2018, but > when > > i send the command this returened to me this error: > > > > Inconsistency in user input: > > Selection 'F519' does not evaluate into an even number of positions > (there > > are > > 1 positions) > > > > I made this index of both CB atoms that i want measure the distance in > all > > MD trajectory: > > [ F519 ] > > 1450 > > [ S678 ] > > 3976 > > > > Can someone help me? > > Thanks > > -- > > *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. > -- > 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.
[gmx-users] distance analysis error
Hi everbody I'm trying to analyse an preotein simulation made in Gromacs 2018, but when i send the command this returened to me this error: Inconsistency in user input: Selection 'F519' does not evaluate into an even number of positions (there are 1 positions) I made this index of both CB atoms that i want measure the distance in all MD trajectory: [ F519 ] 1450 [ S678 ] 3976 Can someone help me? Thanks -- *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
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
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.
[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.
[gmx-users] gpu cpu use
Hi everybody I have acces to one computer with 2 GPU and 2 CPU. Can i use both GPU and both CPU in a simulation? Each cCPU have 10 cores and 20 threads I'm trying whith this command: mpirun -np 4 gmx mdrun -ntomp 6 -gpu_id 00 but i don't undesrtand these numbers and i can use it 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] gromacs error in vacuum preparation simulation
Thanks, for your help. Em seg, 11 de mar de 2019 às 19:31, Justin Lemkul escreveu: > > > On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote: > > If i don't use -maxwarn option they send me the same error. > > Omitting -maxwarn won't fix problems, but it is a very bad habit to > casually use -maxwarn as it overrides critical problems with your input. > > > I see also this: > > WARNING 1 [file topol.top, line 23986]: > >You are using Ewald electrostatics in a system with net charge. This > can > >lead to severe artifacts, such as ions moving into regions with low > >dielectric, due to the uniform background charge. We suggest to > >neutralize your system with counter ions, possibly in combination > with a > >physiological salt concentration. > > Cheking the archive toppol.top this line is empty > > > > I'm try to minimize the energy of my protein in vacum, whithout ions or > > solvent > > As the message says, you shouldn't be using PME for this system. In > vacuum, you should be using plain cutoff electrostatics with infinite > cutoffs (rlist=rcoulomb=rvdw=0). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- *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] gromacs error in vacuum preparation simulation
If i don't use -maxwarn option they send me the same error. I see also this: WARNING 1 [file topol.top, line 23986]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. Cheking the archive toppol.top this line is empty I'm try to minimize the energy of my protein in vacum, whithout ions or solvent Em seg, 11 de mar de 2019 às 17:12, Justin Lemkul escreveu: > > > On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote: > > Hi everybody > > I want to do one dynamic simulation of one protein > > i'm try to minimize the protein in vacum before the simulation runing but > > gromacs send me this error: > > --- > > Program: gmx grompp, version 2018.6 > > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991) > > > > Fatal error: > > There was 1 error in input file(s) > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > -- > > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > with errorcode 1. > > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > You may or may not see output from other processes, depending on > > exactly when Open MPI kills them. > > > -- > > this is the command that i use for minimization in vacum. > > gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o > > cbd212_vac.tpr -maxwarn 1 > > Run grompp interactively if you want to see the actual error. It may > also be printed to a log file from your queuing system. Also, never use > -maxwarn. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- *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.
[gmx-users] gromacs error in vacuum preparation simulation
Hi everybody I want to do one dynamic simulation of one protein i'm try to minimize the protein in vacum before the simulation runing but gromacs send me this error: --- Program: gmx grompp, version 2018.6 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991) Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- this is the command that i use for minimization in vacum. gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o cbd212_vac.tpr -maxwarn 1 I can't find the solution for this problem. 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] doubt regarding order parameter calculated by gmx chi S2max and S2min
Good afternon. How can i calculate th S2 order parameters??? Thanks. Em qua, 19 de dez de 2018 às 11:51, Dr Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> escreveu: > Hi Everyone, > > Is the S2max and S2min produced by gmx chi is same as Ss (slow order > parameter)and Sf (fast order parameter) respectively. If not may anybody > please explain what are those (S2max and S2min). > > Thanks a lot. > Sincerely > Tushar > -- > 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 * -- 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] Recovery simulation error (Bratin Kumar Das)
Thank you very much to all. Your indications helped me to continue and not lose the work done Em dom, 18 de nov de 2018 às 14:00, Edjan Silva escreveu: > to the end of the command you typed add: -deffnm cbd211_md > > > Em sáb, 17 de nov de 2018 às 08:00, > sys.kth.se> escreveu: > > > 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: Recovery simulation error (Bratin Kumar Das) > > > > > > -- > > > > Message: 1 > > Date: Sat, 17 Nov 2018 09:33:24 +0530 > > From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Recovery simulation error > > Message-ID: > > < > > cam7tw5tjyoudjqapcgeb6odi58vh-2q_-ymstzoteng_asp...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Use the following command... > > Gmx mdrun -v -s cbd211_md.tpr -cpi cbd211_md.cpt -append -deffnm > cbd211_md > > > > On Sat, Nov 17, 2018, 9:26 AM Bratin Kumar Das < > > 177cy500.bra...@nitk.edu.in> > > wrote: > > > > > Use -deffnm flag and specify the name ..same as the previous output > > > file...do not forget to give the -append flag > > > > > > On Sat, Nov 17, 2018, 3:09 AM Mario Andres Rodriguez Pineda < > > > mand...@iq.usp.br> wrote: > > > > > >> Hi Gromacs Users. > > >> I has been a simulation with gromacs 2016 but my simulation stopped by > > an > > >> energy break. i try to restar in the last checkpoint but this does > work > > >> and > > >> send me this error: > > >> Expected output files not present or named differently: > > >> cbd211_md.log > > >> cbd211_md.xtc > > >> cbd211_md.trr > > >> cbd211_md.edr > > >> Fatal error: > > >> File appending requested, but 4 of the 4 output files are not present > or > > >> are > > >> named differently. For safety reasons, GROMACS-2016 and later only > > allows > > >> file > > >> appending to be used when all files have the same names as they had in > > the > > >> original run. Checkpointing is merely intended for plain continuation > of > > >> runs. > > >> For safety reasons you must specify all file names (e.g. with > -deffnm), > > >> and > > >> all these files must match the names used in the run prior to > > >> checkpointing > > >> since we will append to them by default. If the files are not > available, > > >> you > > >> can add the -noappend flag to mdrun and write separate new parts. For > > mere > > >> concatenation of files, you should use the gmx trjcat tool instead. > > >> > > >> I used this command: > > >> gmx mdrun -s cbd211_md.tpr -cpi cbd211_md.cpt -v > > >> > > >> All the archives ar in the directory > > >> > > >> Can you help me? Thanks > > >> > > >> > > >> > > >> -- > > >> *MSc. MARIO ANDR?S RODR?GUEZ PINEDA* > > >> *Estudiante Doctorado en Biotecnolog?a* > > >> *UNAL- MEDELL?N * > > >> -- > > >> 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] Recovery simulation error
Hi Gromacs Users. I has been a simulation with gromacs 2016 but my simulation stopped by an energy break. i try to restar in the last checkpoint but this does work and send me this error: Expected output files not present or named differently: cbd211_md.log cbd211_md.xtc cbd211_md.trr cbd211_md.edr Fatal error: File appending requested, but 4 of the 4 output files are not present or are named differently. For safety reasons, GROMACS-2016 and later only allows file appending to be used when all files have the same names as they had in the original run. Checkpointing is merely intended for plain continuation of runs. For safety reasons you must specify all file names (e.g. with -deffnm), and all these files must match the names used in the run prior to checkpointing since we will append to them by default. If the files are not available, you can add the -noappend flag to mdrun and write separate new parts. For mere concatenation of files, you should use the gmx trjcat tool instead. I used this command: gmx mdrun -s cbd211_md.tpr -cpi cbd211_md.cpt -v All the archives ar in the directory Can you help me? Thanks -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN * -- 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] GPU ERROR RUNING A SIMULATION
Hi again every body. I'm tryin running a simulation of a protein in water using Gromacs 2018.3. When i try to minimize the energy in NVT equilibration this send me this error during mdrun: Reading file cbd12_nvt.tpr, VERSION 2018.3 (single precision) Multiple energy groups is not implemented for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file. Can you help me please? I don't know what to do in this case and the simulations is very slow... -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN * -- 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] simulation error
when i try to run mdrun they start showing this: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= -2.46652e+06 Fmax= 6.62812e+05, atom= 2881 Step=1, Dmax= 1.0e-02 nm, Epot= -2.48761e+06 Fmax= 6.51531e+05, atom= 2881 Step=2, Dmax= 1.2e-02 nm, Epot= -2.51019e+06 Fmax= 6.38455e+05, atom= 2881 Step=3, Dmax= 1.4e-02 nm, Epot= -2.53494e+06 Fmax= 6.23418e+05, atom= 2881 Step=4, Dmax= 1.7e-02 nm, Epot= -2.56238e+06 Fmax= 6.06180e+05, atom= 2881 Step=5, Dmax= 2.1e-02 nm, Epot= -2.59295e+06 Fmax= 5.86164e+05, atom= 2881 Step=6, Dmax= 2.5e-02 nm, Epot= -2.62704e+06 Fmax= 5.62063e+05, atom= 2881 Step=7, Dmax= 3.0e-02 nm, Epot= -2.66494e+06 Fmax= 5.31531e+05, atom= 2881 Step=8, Dmax= 3.6e-02 nm, Epot= -2.70684e+06 Fmax= 4.91124e+05, atom= 2881 Step=9, Dmax= 4.3e-02 nm, Epot= -2.75366e+06 Fmax= 4.36752e+05, atom= 2881 Step= 10, Dmax= 5.2e-02 nm, Epot= -2.80104e+06 Fmax= 3.67647e+05, atom= 2881 Step= 11, Dmax= 6.2e-02 nm, Epot= -2.84787e+06 Fmax= 4.16988e+05, atom= 2883 Step= 12, Dmax= 7.4e-02 nm, Epot= -2.86654e+06 Fmax= 2.20175e+06, atom= 2903 Step= 13, Dmax= 8.9e-02 nm, Epot= -2.88894e+06 Fmax= 2.80767e+05, atom= 2883 Step= 14, Dmax= 1.1e-01 nm, Epot= -2.95328e+06 Fmax= 1.33061e+05, atom= 2883 Step= 15, Dmax= 1.3e-01 nm, Epot= -3.03044e+06 Fmax= 2.52114e+05, atom= 2881 step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) I don't understand what happend. Please can you help me? How i can reduce timestep? Em ter, 18 de set de 2018 às 08:36, Justin Lemkul escreveu: > > > On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote: > > These were the errors until the moment of executing the minimization: > > > > After adding ions grompp: > > NOTE 1 [file topol.top, line 37566]: > >System has non-zero total charge: -18.99 > >Total charge should normally be an integer. See > >http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > >for discussion on how close it should be to an integer. > > > > minimization mdrun > > step 16: One or more water molecules can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > tMPI error: Receive buffer size too small for transmission (in valid > comm) > > Abort (core dumped) > > > > In attach send you the mdp archive for minimization run. > > The mailing list does not allow attachments. > > Use the -v flag of mdrun to track the energy and forces at every step > until the crash to see what's going on and where the maximum force is > acting. There's probably a bad contact somewhere that can't be relaxed > and you need to investigate why that's happening. > > -Justin > > > Thanks for your help > > > > Em seg, 17 de set de 2018 às 19:56, Justin Lemkul > > escreveu: > > > >> > >> On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: > >>> Hi everyone. > >>> I'm trying simulate a protein in water followin lysozyme tutorial using > >>> gromacs 2016.3. When triying minimize the system after make the box and > >>> insert a salt concentration the minimization has been stoped sendingme > >> the > >>> following error: > >>> > >>> step 16: One or more water molecules can not be settled. > >>> Check for bad contacts and/or reduce the timestep if appropriate. > >>> Wrote pdb files with previous and current coordinates > >>> tMPI error: Receive buffer size too small for transmission (in valid > >> comm) > >>> Abort (core dumped) > >> Water SETTLE problems are not unusual in energy minimization and are > >> often resolved. If, however, such a message immediately precedes a > >> failure, then you have a serious problem with either the coordinates or > >> topology. mdrun prints out which atom is experiencing the maximum force, > >> so start by looking there, as well as reviewing your notes about what > >> warnings pdb2gmx or grompp may have issued (but surely you wouldn't have > >> ignored any, right? :). > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Virginia Tech Department of Biochemistry > >> > >> 303 Engel Hall > >> 340 West C
Re: [gmx-users] simulation error
These were the errors until the moment of executing the minimization: After adding ions grompp: NOTE 1 [file topol.top, line 37566]: System has non-zero total charge: -18.99 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. minimization mdrun step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) In attach send you the mdp archive for minimization run. Thanks for your help Em seg, 17 de set de 2018 às 19:56, Justin Lemkul escreveu: > > > On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: > > Hi everyone. > > I'm trying simulate a protein in water followin lysozyme tutorial using > > gromacs 2016.3. When triying minimize the system after make the box and > > insert a salt concentration the minimization has been stoped sendingme > the > > following error: > > > > step 16: One or more water molecules can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > tMPI error: Receive buffer size too small for transmission (in valid > comm) > > Abort (core dumped) > > Water SETTLE problems are not unusual in energy minimization and are > often resolved. If, however, such a message immediately precedes a > failure, then you have a serious problem with either the coordinates or > topology. mdrun prints out which atom is experiencing the maximum force, > so start by looking there, as well as reviewing your notes about what > warnings pdb2gmx or grompp may have issued (but surely you wouldn't have > ignored any, right? :). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN * -- 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] simulation error
Hi everyone. I'm trying simulate a protein in water followin lysozyme tutorial using gromacs 2016.3. When triying minimize the system after make the box and insert a salt concentration the minimization has been stoped sendingme the following error: step 16: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) How i can fix it? Thanks for your help. -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN * -- 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.
