[gmx-users] Reg. thread MPI errror with gromacs-2016.4
Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on GPU.I run the production simulation using job file and it terminated with the fatal error: setting the number of thread-MPI ranks is only supported with thread-MPI and Gromacs was compiled without thread-MPI. Please guide me in setting the gromacs-GPU related option to run simulation without an error. #!/bin/sh#SBATCH --job-name=test#SBATCH --partition=dual_v100_node#SBATCH --nodes=2#SBATCH --ntask=20#SBATCH --time=24:00:00#SBATCH --nodelist=tesla[21-22]#SBATCH --gres=gpu:2srun /applic/applications/gromacs/2016.4/bin/gmx_mpi mdrun -deffnm step7_production -ntmpi 4 -ntomp 10 -pin onRegards,ChangdevDr. Changdev G. GadhePost-Doc Researcher,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia,Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850Email: f07...@kist.re.kr -- 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] Reg. thread MPI errror with gromacs-2016.4
Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on GPU.I run the production simulation using job file and it terminated with the fatal error: setting the number of thread-MPI ranks is only supported with thread-MPI and Gromacs was compiled without thread-MPI. Please guide me in setting the gromacs-GPU related option to run simulation without an error. #!/bin/sh#SBATCH --job-name=test#SBATCH --partition=dual_v100_node#SBATCH --nodes=2#SBATCH --ntask=20#SBATCH --time=24:00:00#SBATCH --nodelist=tesla[21-22]#SBATCH --gres=gpu:2srun /applic/applications/gromacs/2016.4/bin/gmx_mpi mdrun -deffnm step7_production -ntmpi 4 -ntomp 10 -pin onRegards,ChangdevDr. Changdev G. GadhePost-Doc Researcher,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia,Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850Email: f07...@kist.re.kr -- 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] Reg. mdrun error: not all ion group molecules consist of 3 atoms
Hello,I am performing computational Electrophysiology gromacs tutorial. I successfully pass the grompp for the compEL but failed with a Fatal error at mdrun step, not all ion group molecules consist of 3 atoms.my command for grompp was gmx_mpi_d grompp -f step7-prod.mdp -o step7-prod.tpr -c step6.6-double-box-in-Z.gro -n index-for-twin.ndx -p topol.top -maxwarn -1 , it runs successfully but when I tried with gmx_mpi_d mdrun -deffnm step7_prod it terminated with a fatal error.I did create an index group for TIP3|SOD|CLA together and named as SOL_ions and put inside step7_prod.mdp These are my .mdp file options tcoupl = Nose-Hoover, tc_groups = PROA PROB DMPC SOL_ions, tau_t = 1.0 1.0 1.0 1.0 , ref_t = 320.15 320.15 320.15 320.15, comm_grps = PROA PROB DMPC SOL_ions, rest of the parameters are default as like normal mdp file. Inside CompEL, swap-group = SOD, solvent-group = TIP3,Do I need to separate the coupling group SOL_ions, as TIP3, SOD, CLA because in compEL I am going to swap between SOD and TIP3.Looking forward to hearing from you.Regards,ChangdevDr. Changdev G. GadhePost-Doc Researcher,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia,Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850Email: f07...@kist.re.kr -- 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] Reg. mdrun error: not all ion group molecules consist of 3 atoms
Hello,I am performing computational Electrophysiology gromacs tutorial. I successfully pass the grompp for the compEL but failed with a Fatal error at mdrun step, not all ion group molecules consist of 3 atoms.my command for grompp was gmx_mpi_d grompp -f step7-prod.mdp -o step7-prod.tpr -c step6.6-double-box-in-Z.gro -n index-for-twin.ndx -p topol.top -maxwarn -1 , it runs successfully but when I tried with gmx_mpi_d mdrun -deffnm step7_prod it terminated with a fatal error.I did create an index group for TIP3|SOD|CLA together and named as SOL_ions and put inside step7_prod.mdp These are my .mdp file options tcoupl = Nose-Hoover, tc_groups = PROA PROB DMPC SOL_ions, tau_t = 1.0 1.0 1.0 1.0 , ref_t = 320.15 320.15 320.15 320.15, comm_grps = PROA PROB DMPC SOL_ions, rest of the parameters are default as like normal mdp file. Inside CompEL, swap-group = SOD, solvent-group = TIP3,Do I need to separate the coupling group SOL_ions, as TIP3, SOD, CLA because in compEL I am going to swap between SOD and TIP3.Looking forward to hearing from you.Regards,ChangdevDr. Changdev G. GadhePost-Doc Researcher,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia,Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850Email: f07...@kist.re.kr -- 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] Error while running perl distances.pl
Hello Vytautas,
I changed the script file to
gmx_mpi_d distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'
rest is same
but it showed the same error as previous one.
Error
readline() on closed filehandle IN at distances.pl line 16
Use of uminitialized value $distance in concatanation (.) or string at
distances.pl line 30.
Could you help me out to solve this issue.
Dr. Changdev G. Gadhe
Post-Doc Researcher,
Convergence Research Center for Diagnosis, Treatment and Care System of
Dementia,
Korea Institute of Science and Technology,
Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850
Email: f07...@kist.re.kr
---Original message---
From: "Vytautas Rakeviius "
To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장데부
고라크스나트
Cc.: gadhe.chang...@gmail.com
Sent date: 2017-09-04 15:36:29 GMT +0900 (Asia/Seoul)
Title: Re: [gmx-users] Error while running perl distances.pl
Script assumes that variable $distance is the second row separated by space in
the file dist{number}.xvg which appears after execution of system call
gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg
-select \'com of group \"lig\" plus com of group \"protein\"\'
I just think that dist{number}.xvg creation fails for you in first place
because "gmx distance" in the script is not adjusted according to your system.
You use _mpi_d in your post.
On Monday, September 4, 2017, 5:48:43 AM GMT+3, 가디 장데부 고라크스나트
wrote:
Hello Gmx user,
I would like to transport solute molecule from the ion channel (intracellular
to extracellular site) using steered MD and umbrella sampling method to
calculate the energy.
I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but
in distance.pl it shows some errors.
I used the distance of pulling along the Z-axis but still it do not work. I
found when I use distance as a pull-geometry, solute moves away from the
channel rather transporting through channel. Then I tried direction as a
pull-geoetry, then solute transported from the chanel,and generated pullf.xvg
but not pullx.xvg file.
I separated the trajectory using trjconv command
gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o conf.gro -sep
It generated conformations.
Now I would like to calculate the COM distance between ion channel (protein)
and solute (lig) using perl distance.pl but I received following error.
Error
readline() on closed filehandle IN at distances.pl line 16
Use of uminitialized value $distance in concatanation (.) or string at
distances.pl line 30.
Here is the distance.pl file which I used for this purpose which was downloaded
from Dr. Lemkul's tutorial file.
-
#!/usr/bin/perl -w
use strict;
# loop g_dist command - measure distance in each frame, write to a file
for (my $i=0; $i<=800; $i++) {
print "Processing configuration $i...\n";
system("gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'
&>/dev/null");
}
# write output to single file
open(OUT, ">>summary_distances.dat");
for (my $j=0; $j<=800; $j++) {
open(IN, ";
my $distance;
foreach $_ (@array) {
if ($_ =~ /[#@]/) {
# do nothing, it's a comment or formatting line
} else {
my @line = split(" ", $_);
$distance = $line[1];
}
}
close(IN);
print OUT "$j\t$distance\n";
}
close(OUT);
# clean up
print "Cleaning up...\n";
for (my $k=0; $k<=800; $k++) {
unlink "dist${k}.xvg";
}
exit;
-
this generated the summary_distances.dat with only frame numbers but there is
no distance column in the file.
Please help me to solve this issue
Regards,
Dr. Changdev G. Gadhe
Post-Doc Researcher,
Convergence Research Center for Diagnosis, Treatment and Care System of
Dementia,
Korea Institute of Science and Technology,
Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850
Email: f07...@kist.re.kr
--
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.o
[gmx-users] Error while running perl distances.pl
Hello Gmx user,
I would like to transport solute molecule from the ion channel (intracellular
to extracellular site) using steered MD and umbrella sampling method to
calculate the energy.
I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but
in distance.pl it shows some errors.
I used the distance of pulling along the Z-axis but still it do not work. I
found when I use distance as a pull-geometry, solute moves away from the
channel rather transporting through channel. Then I tried direction as a
pull-geoetry, then solute transported from the chanel,and generated pullf.xvg
but not pullx.xvg file.
I separated the trajectory using trjconv command
gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o conf.gro -sep
It generated conformations.
Now I would like to calculate the COM distance between ion channel (protein)
and solute (lig) using perl distance.pl but I received following error.
Error
readline() on closed filehandle IN at distances.pl line 16
Use of uminitialized value $distance in concatanation (.) or string at
distances.pl line 30.
Here is the distance.pl file which I used for this purpose which was downloaded
from Dr. Lemkul's tutorial file.
-
#!/usr/bin/perl -w
use strict;
# loop g_dist command - measure distance in each frame, write to a file
for (my $i=0; $i<=800; $i++) {
print "Processing configuration $i...\n";
system("gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'
&>/dev/null");
}
# write output to single file
open(OUT, ">>summary_distances.dat");
for (my $j=0; $j<=800; $j++) {
open(IN, ";
my $distance;
foreach $_ (@array) {
if ($_ =~ /[#@]/) {
# do nothing, it's a comment or formatting line
} else {
my @line = split(" ", $_);
$distance = $line[1];
}
}
close(IN);
print OUT "$j\t$distance\n";
}
close(OUT);
# clean up
print "Cleaning up...\n";
for (my $k=0; $k<=800; $k++) {
unlink "dist${k}.xvg";
}
exit;
-
this generated the summary_distances.dat with only frame numbers but there is
no distance column in the file.
Please help me to solve this issue
Regards,
Dr. Changdev G. Gadhe
Post-Doc Researcher,
Convergence Research Center for Diagnosis, Treatment and Care System of
Dementia,
Korea Institute of Science and Technology,
Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850
Email: f07...@kist.re.kr
--
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] Error while running perl distances.pl
Hello Gmx user,
I would like to transport solute molecule from the ion channel (intracellular
to extracellular site) using steered MD and umbrella sampling method to
calculate the energy.
I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but
in distance.pl it shows some errors.
I used the distance of pulling along the Z-axis but still it do not work. I
found when I use distance as a pull-geometry, solute moves away from the
channel rather transporting through channel. Then I tried direction as a
pull-geoetry, then solute transported from the chanel,and generated pullf.xvg
but not pullx.xvg file.
I separated the trajectory using trjconv command
gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o conf.gro -sep
It generated conformations.
Now I would like to calculate the COM distance between ion channel (protein)
and solute (lig) using perl distance.pl but I received following error.
Error
readline() on closed filehandle IN at distances.pl line 16
Use of uminitialized value $distance in concatanation (.) or string at
distances.pl line 30.
Here is the distance.pl file which I used for this purpose which was downloaded
from Dr. Lemkul's tutorial file.
-
#!/usr/bin/perl -w
use strict;
# loop g_dist command - measure distance in each frame, write to a file
for (my $i=0; $i<=800; $i++) {
print "Processing configuration $i...\n";
system("gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'
&>/dev/null");
}
# write output to single file
open(OUT, ">>summary_distances.dat");
for (my $j=0; $j<=800; $j++) {
open(IN, ";
my $distance;
foreach $_ (@array) {
if ($_ =~ /[#@]/) {
# do nothing, it's a comment or formatting line
} else {
my @line = split(" ", $_);
$distance = $line[1];
}
}
close(IN);
print OUT "$j\t$distance\n";
}
close(OUT);
# clean up
print "Cleaning up...\n";
for (my $k=0; $k<=800; $k++) {
unlink "dist${k}.xvg";
}
exit;
-
this generated the summary_distances.dat with only frame numbers but there is
no distance column in the file.
Please help me to solve this issue
Regards,
Dr. Changdev G. Gadhe
Post-Doc Researcher,
Convergence Research Center for Diagnosis, Treatment and Care System of
Dementia,
Korea Institute of Science and Technology,
Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850
Email: f07...@kist.re.kr
--
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] InflateGRO script
Hello there, This is Changdev and I am facing problem in InflateGRO script. I am working on membrane protein and would like to embed the protein into 512 DPPC lipids. I used the command from Dr. Justin's tutorial. perl inflategro.pl system.gro 4 DPPC 14 sys_infl.gro 5 area.dat after running this command it shows following error. However, it did generate the sys_infl.gro but when I checked using VMD, there is nothing visible in this file. So, please help me in this regard to solve this problem. Regards, Dr. Changdev G. Gadhe Post-Doc Researcher, Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850 Email: f07...@kist.re.kr -- 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] Reg. Umbrella sampling problem with direction
Hello Everyone, I am novice in umbrella sampling. I did followed Dr. Justin's tutorial and it works fine for me. However, I would like to transport solute (along z-axis) from an ion channel (intracellular to extracellular site) so I made the system (Protein+solute+DPPC+Sol+ion) and came upto the Step 5 of tutorial successfully. Now I wanted to get the distances among frames using perl distance.pl but I just get the frame number. So, I seek your advice and suggestion on the input parameter of Pull-code. Here is the pull-code I used for the simulation. ; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name= Protein pull_group2_name= DRG pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = direction pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_vec= 0 0 1 pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k= 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Please guide in making correct input parameter for pull-code I get this output in pullx.xvg file @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Position (nm)" @TYPE xy 0. -2.51551 0.1000 -2.50136 0.2000 -2.49201 0.3000 -2.49526 0.4000 -2.47566 0.5000 -2.4618 0.6000 -2.47792 0.7000 -2.47152 0.8000 -2.48659 0.9000 -2.49259 1. -2.53279 1.1000 -2.53133 1.2000 -2.51926 1.3000 -2.51488 Or how can I use this output to calculate the distance among the frames and further use for g_wham program. Looking forward to interact with you. Regards, Changdev -- 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] Reg. Umbrella sampling problem with direction
Hello Everyone, I am novice in umbrella sampling. I did followed Dr. Justin's tutorial and it works fine for me. However, I would like to transport solute (along z-axis) from an ion channel (intracellular to extracellular site) so I made the system (Protein+solute+DPPC+Sol+ion) and came upto the Step 5 of tutorial successfully. Now I wanted to get the distances among frames using perl distance.pl but I just get the frame number. So, I seek your advice and suggestion on the input parameter of Pull-code. Here is the pull-code I used for the simulation. ; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name= Protein pull_group2_name= DRG pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = direction pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_vec= 0 0 1 pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k= 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Please guide in making correct input parameter for pull-code I get this output in pullx.xvg file @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Position (nm)" @TYPE xy 0. -2.51551 0.1000 -2.50136 0.2000 -2.49201 0.3000 -2.49526 0.4000 -2.47566 0.5000 -2.4618 0.6000 -2.47792 0.7000 -2.47152 0.8000 -2.48659 0.9000 -2.49259 1. -2.53279 1.1000 -2.53133 1.2000 -2.51926 1.3000 -2.51488 Or how can I use this output to calculate the distance among the frames and further use for g_wham program. Looking forward to interact with you. Regards, Changdev -- 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.
