Re: Sv: Re: [gmx-users] double and single precision
Hi GMX-users! If someone else get the same problem. I will present how I could recover the edr files: 1. Calculate the number of bytes for header consisted of in single and double precision, respectively. run some short test runs to calculate this 2. Calculate the number of bytes for each frame. The first frame took apparently less space than the others. I guess it is due to the average and sum data, that one can see from gmxdump -e 3. Calculate the number of frames in the first simulation with gmxcheck -e 3. I used head, tail and cat to cut and paste in the files. #bytes of corrupted file# - #bytes of header DP# - "#bytes per frame# * #frames in first run# head -c #bytes of header SP# singleprec.edr > headerSP tail -c corruptedr.edr | cat headerSP - > newedr.edr check the new file with gmxcheck -e I got these byte numbers (NPT-simulation): Single precision: Header: 964b, 1st frame: 240b, then 576 b/frame Double precision: Header+1st frame: 1376, then 1084 b/frame Thanks to Berk Hess who helped me a lot! /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS 033- 435 45 37 edvin.erdt...@hb.se D424 >>> 2012-02-20 kl. 09:38, skrev Mark Abraham : > On 20/02/2012 7:29 PM, Edvin Erdtman wrote: > > Hi > > > > So the best I can do now is to recreate the first part, and rerun "new" > > the simulations? > > > > If you have a full frame (positions+velocities+maybe energies, or a > checkpoint file) then I expect so. Save your crossbreed files in case > someone has a better idea. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Sv: Re: [gmx-users] double and single precision
Hi again How do I "set the env.var. GMX_ENX_NO_FATAL"? I have tried in bash with: GMX_ENX_NO_FATAL=1 and then eneconv -e But I still get fatal error. /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS >>> 2012-02-20 kl. 09:38, skrev Mark Abraham : > On 20/02/2012 7:29 PM, Edvin Erdtman wrote: > > Hi > > > > So the best I can do now is to recreate the first part, and rerun "new" > > the simulations? > > > > If you have a full frame (positions+velocities+maybe energies, or a > checkpoint file) then I expect so. Save your crossbreed files in case > someone has a better idea. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Sv: Re: [gmx-users] double and single precision
Hi So the best I can do now is to recreate the first part, and rerun "new" the simulations? /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS >>> 2012-02-20 kl. 09:26, skrev Mark Abraham : > On 20/02/2012 7:19 PM, Edvin Erdtman wrote: > > Hi > > > > I have been running GMX in double precision and by mistake an extension > > of a run in single precision was written to the same files. > > > > When I run for example gmxcheck or g_energy I get the following error > > after the program has scanned through the double part: > > > > Fatal error: > > Energy header magic number mismatch, this is not a GROMACS edr file > > If you want to use the correct frames before the corrupted frame and > > avoid this fatal error set the env.var. GMX_ENX_NO_FATAL > > For more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > Can I do something to divide the file into a double and a single part? > > We should probably put in a check to prevent this occurring (and an > environment variable to override it?). > > I expect you can get the first part back through using eneconv -e and > the above environment variable. > > I can't think of a way to access the second (and subsequent) parts > without writing new code - but perhaps that code should exist anyway, > emitting a warning that a change of precision was detected. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] double and single precision
Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic number mismatch, this is not a GROMACS edr file If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can I do something to divide the file into a double and a single part? /Edvin Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] double and single precision
Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic number mismatch, this is not a GROMACS edr file If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can I do something to divide the file into a double and a single part? /Edvin Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Sv: Re: [gmx-users] Add bridging residue
> "Justin A. Lemkul" wrote: > Please see the following: > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > Yes. I know all that! But my question was if there is a possibility to build a new residue which has a cross-link bond to another residue. How can I define the bond between the residues? pdb2gmx do that automatically for CYS-CYS, right? but not for my new residue. /EE -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Add bridging residue
Hi To the Amber force field I want to add a new residue, which is connected covalently to another residue in a protein (similar to a CYS-CYS bridge). Can I define this bond somewhere in the force field files (rtp, atp...) so that the inter-residue bond can be generated by pdb2gmx? Or do I have to do it manually in the top-file? /Edvin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with equilibration of DPPC membrane with protein
Hi We have tried with no cutoff, as I have written in former emails, but that was when we got trouble with LINCS warnings. We then thought that we could try to continue remove lipids in the compression-steps to get rid of that LINCS warnings, and to have a stable system! Is it maybe the protein that is the problem - need to be more minimized? /Edvin Justin A. Lemkul wrote: Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), and position restraints on the protein, I have also merged Cl and SOL in the same temp group, but it does not seem to work anyway. We still get the LINCS warnings. Why are you using a cutoff during the compression phase? You will continue to delete lipids! I have never had a problem if I scale up by a factor of 4, with a 1.4-nm cutoff, then compress by a factor of 0.95 (with no cutoff). Maybe that will make a difference? -Justin begin:vcard fn:Edvin Erdtman n:Erdtman;Edvin org;quoted-printable:=C3=96rebro University;Biophysical Chemistry, School of Science and Technology adr;quoted-printable:;;;=C3=96rebro;;701 82 ;Sweden email;internet:edvin.erdt...@oru.se title:Fil. Lic. tel;work:019-30 13 81 tel;fax:019-30 35 66 x-mozilla-html:TRUE url:http://www.oru.se/nat/Edvin_Erdtman version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error with equilibration of DPPC membrane with protein
Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), and position restraints on the protein, I have also merged Cl and SOL in the same temp group, but it does not seem to work anyway. We still get the LINCS warnings. Thankful for all help! /Edvin Edvin Erdtman wrote: Hi again an Thank you for comments! Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used position restraints for the protein as mentioned in Methods 41 (2007) 475-488. We have tried with a scaling factor of 0,95 and 0,97, and a cut-off value of 14 to expand the box and 0 to reduce the box (is that ok???). perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5 em2/area.dat with scaling factor 0.95 23 steps were needed, and with 0,97 39 steps were followed. This seems reasonable. When we have not used position restraints for the protein, and used a cutoff value of 4 Å, the simulation were performed well even without annealing. 4 A cutoff? For what? That is far too short for a lipid bilayer simulation. Or am I misunderstanding where you are applying this 4 A? Is it part of InflateGRO? Yes that is a cut-off for the InflateGRO. cutoff of distance between alpha-carbon of protein and phosphorus atoms in DPPC (0 in the upper example of running the perl script). If the distance are within this value, then that DPPC will be removed. I thought that this parameter was used only in the diverging step with Inflategro, not when compressing the system. Therefore we tried to run calculations with that parameter set to 0 instead (above). We have tried to energy minimize the system with steepest descent method in each step of decreasing the box. Do each of these minimizations complete satisfactorily? Most of them converged to Fmax < 1000. After water soaking, we have tried with both cg and steep energy minimizations. The problems we are facing: - All the energy minimizations are not reaching Fmax < 1000 How close to Fmax are you getting? If it's still on the order of 10^3 you may be OK; if it's a lot larger then you have other problems to deal with. The highest force we got (using scaling factor = 0.97) at step 33: "Maximum force = 2.6218958e+03 on atom 4591" tcoupl = Nose-hoover tc-grps = DPPC Cl SOL Protein tau_t= 0.1 0.1 0.1 0.1 ref_t= 100 100 100 100 Here is a potential problem. Never couple solvent and ions separately. Make an index group of these two merged species. See here: http://wiki.gromacs.org/index.php/thermostats Thank you for that advice, I will do that. But really I don't think that is our main problem. We tried also without chlorine (system total charge of +2), but we got the same error. Another bit of general advice. I had a very mysterious problem once where during equilibration of a DPPC bilayer my lipids were blowing apart for no apparent reason. Upon very close inspection of the trajectory (setting nstxout = 1) I identified the initial location of the explosion. A Cl- ion was immediately next to a phosphate oxygen (very hard to see!), and it was causing a huge force that was ripping my lipid apart. Just an idea, if the InflateGRO minimizations are working OK, but the solvated system with ions is not working. -Justin Thankful for all help we can get! /Edvin and Sujith /Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Edvin Erdtman n:Erdtman;Edvin org;quoted-printable:=C3=96rebro University;Biophysical Chemistry, School of Science and Technology adr;quoted-printable:;;;=C3=96rebro;;701 82 ;Sweden email;internet:edvin.erdt...@oru.se title:Fil. Lic. tel;work:019-30 13 81 tel;fax:019-30 35 66 x-mozilla-html:TRUE url:http://www.oru.se/nat/Edvin_Erdtman version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.
Re: [gmx-users] Error with equilibration of DPPC membrane with protein
Hi again an Thank you for comments! Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used position restraints for the protein as mentioned in Methods 41 (2007) 475-488. We have tried with a scaling factor of 0,95 and 0,97, and a cut-off value of 14 to expand the box and 0 to reduce the box (is that ok???). perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5 em2/area.dat with scaling factor 0.95 23 steps were needed, and with 0,97 39 steps were followed. This seems reasonable. When we have not used position restraints for the protein, and used a cutoff value of 4 Å, the simulation were performed well even without annealing. 4 A cutoff? For what? That is far too short for a lipid bilayer simulation. Or am I misunderstanding where you are applying this 4 A? Is it part of InflateGRO? Yes that is a cut-off for the InflateGRO. cutoff of distance between alpha-carbon of protein and phosphorus atoms in DPPC (0 in the upper example of running the perl script). If the distance are within this value, then that DPPC will be removed. I thought that this parameter was used only in the diverging step with Inflategro, not when compressing the system. Therefore we tried to run calculations with that parameter set to 0 instead (above). We have tried to energy minimize the system with steepest descent method in each step of decreasing the box. Do each of these minimizations complete satisfactorily? Most of them converged to Fmax < 1000. After water soaking, we have tried with both cg and steep energy minimizations. The problems we are facing: - All the energy minimizations are not reaching Fmax < 1000 How close to Fmax are you getting? If it's still on the order of 10^3 you may be OK; if it's a lot larger then you have other problems to deal with. The highest force we got (using scaling factor = 0.97) at step 33: "Maximum force = 2.6218958e+03 on atom 4591" tcoupl = Nose-hoover tc-grps = DPPC Cl SOL Protein tau_t= 0.1 0.1 0.1 0.1 ref_t= 100 100 100 100 Here is a potential problem. Never couple solvent and ions separately. Make an index group of these two merged species. See here: http://wiki.gromacs.org/index.php/thermostats Thank you for that advice, I will do that. But really I don't think that is our main problem. We tried also without chlorine (system total charge of +2), but we got the same error. Another bit of general advice. I had a very mysterious problem once where during equilibration of a DPPC bilayer my lipids were blowing apart for no apparent reason. Upon very close inspection of the trajectory (setting nstxout = 1) I identified the initial location of the explosion. A Cl- ion was immediately next to a phosphate oxygen (very hard to see!), and it was causing a huge force that was ripping my lipid apart. Just an idea, if the InflateGRO minimizations are working OK, but the solvated system with ions is not working. -Justin Thankful for all help we can get! /Edvin and Sujith /Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error with equilibration of DPPC membrane with protein
Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We used position restraints for the protein as mentioned in Methods 41 (2007) 475-488. We have tried with a scaling factor of 0,95 and 0,97, and a cut-off value of 14 to expand the box and 0 to reduce the box (is that ok???). perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5 em2/area.dat with scaling factor 0.95 23 steps were needed, and with 0,97 39 steps were followed. When we have not used position restraints for the protein, and used a cutoff value of 4 Å, the simulation were performed well even without annealing. We have tried to energy minimize the system with steepest descent method in each step of decreasing the box. After water soaking, we have tried with both cg and steep energy minimizations. The problems we are facing: - All the energy minimizations are not reaching Fmax < 1000 - When running md, the system explodes, like this: relative constraint deviation after LINCS: rms 0.024475, max 1.283027 (between atoms 2654 and 2656) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4615 4616 57.90.0896 0.1057 0.1080 ... These are our inputs: em.mdp for the decrease-box-steps and after water soak: cpp = /lib/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 800 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no -- grompp.mdp for md simlulations: cpp = /lib/cpp include = define = -DPOSRES integrator = md dt = 0.002 nsteps = 300 ;6000 ps nstlog = 5000 nstenergy= 100 nstxout = 5 nstxtcout= 250 nstvout = 5 nstfout = 0 xtc_grps = DPPC Cl SOL Protein energygrps = DPPC Cl SOL Protein nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 tcoupl = Nose-hoover tc-grps = DPPC Cl SOL Protein tau_t= 0.1 0.1 0.1 0.1 ref_t= 100 100 100 100 Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 gen_vel = yes gen_temp = 100 gen_seed = 173529 constraints = all-bonds annealing= single single single single annealing_npoints= 2 2 2 2 annealing_time = 0 500 0 500 0 500 0 500 annealing_temp = 100 323 100 323 100 323 100 323 pbc = xyz optimize_fft = yes unconstrained_start = no - Thankful for all help we can get! /Edvin and Sujith -- Fil. Lic. Edvin Erdtman, PhD. student in Biophysical Chemistry School of Science and Technology Modeling and Simulation Center and Örebro Life Science Center Örebro University 701 82 Örebro, Sweden E-mail: edvin.erdt...@oru.se Phone:+46 (0)19 30 13 81 Fax: +46 (0)19 30 35 66 Personal web: http://www.oru.se/nt/Edvin_Erdtman Office: B2313 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Cuted trr file not readable
Hi I have made a mistake... I have deleted the trr file while computing. The system continue saving to the same filename, but the first 950 ps is lost. that is ok I don't need it, but now I want to enlong the simulation by using tpbconv. The file is not readable since it can not determine the precision of the file (that is the error I got, "can not determine precision of trn file"). Is it in any manner possible to restore, so the trr molecule can be used? /Edvin -- Edvin Erdtman Ph.D. student Department of Natural Sciences and Örebro Life Science Center Örebro University 701 82 Örebro, Sweden phone: +46 (0)19 30 36 69 fax: +46 (0)19 30 35 66 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
> >Ok (you didn't say that in the first mail...). > >Does it also happen on one processor? > > I Haven't tested in d.p. > > >After how many steps does it happen? (see Marks mail). > > after 30 steps, that is 600 ps. > > > I energy minimized the system in d.p. and it is still running after > 710 ps. > No had stopped at 710 ps... Why is it then working with single precision? -Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
>Ok (you didn't say that in the first mail...). >Does it also happen on one processor? I Haven't tested in d.p. >After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
>edvin.erdtman at nat.oru.se wrote: >> I installed both double and single precision gromacs on a new system. When >> running a membrane MD with double precision 8 processor mpi calc, this error >> appars in the error output file: > > >this usually means you have an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? ------- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1 Örebro Universitet S-701 82 Örebro, Sweden Tel: +46 19 30 36 69 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: Error on node 4, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 4 out of 8 --- Program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]), VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1335. It should have been within [ 0 .. 1296 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Thanx for Using GROMACS - Have a Nice Day Error on node 6, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 6 out of 8 gcq#10922: Thanx for Using GROMACS - Have a Nice Day * MPI-error in rank 2 Routine MPI_Abort : Terminating after call to MPI_Abort * --- mpimon --- Aborting run after process-2 terminated abnormally Childprocess 17353 exited with exitcode 2 --- gcq#10922: Thanx for Using GROMACS - Have a Nice Day Thankful for some help. Edvin --- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1 Örebro Universitet S-701 82 Örebro, Sweden Tel: +46 19 30 36 69 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist problems
Hi again! I solved it with installing gromacs again by compiling the source files instead of installing the RPM. Maybe something is wrong in the Mandriva RPM (called gromacs-3.3.1-1mdv2007.0 in the list of available packages in Mandriva drakrpm program)? Now it seems to work very well then! Edvin Edvin Erdtman wrote: $ file /usr/bin/g_dist /usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped I copied the file to another machine. And there g_dist ran with no problem! - the above command on that machine gives instead (the rest is equal): ... for GNU/Linux 2.2.5, dynamically linked (uses shared libs), not stripped It is the same version 3.3.1 but with double precision, and (as I guess) compiled for mpi usage. Can it be something that went wrong in the compilation? Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist problems
Edvin Erdtman wrote: Which compiler did you use? This maybe says more: $ file /usr/bin/g_dist /usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped I copied the file to another machine. And there g_dist ran with no problem! - the above command on that machine gives instead (the rest is equal): ... for GNU/Linux 2.2.5, dynamically linked (uses shared libs), not stripped It is the same version 3.3.1 but with double precision, and (as I guess) compiled for mpi usage. Can it be something that went wrong in the compilation? Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist problems
Which compiler did you use? This maybe says more: $ file /usr/bin/g_dist /usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped -Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist problems
David van der Spoel skrev: Edvin Erdtman wrote: Hi again... How can we tell? You haven't given us your command line, or a meaningful chunk of output. my command: g_dist -f traj.xtc -n index.ndx -s topol.tpr The output: --- Select a group: 0 Selected 0: 'DPPC' Select a group: 1 Selected 1: 'AL' Reading frame 0 time0.000 Back Off! I just backed up dist.xvg to ./#dist.xvg.1# Reading frame 400 time 200.000 -and then it stops! I need to hit ctrl-c dist.xvg ends: 216.1533.72607922.12812881.1397107 -2.8382730 216.5000 I tried to convert the trajectory using trjconv -pbc, but non of the options seems to work. I thought that it maybe would help. Someone else (who had send a message to this list Bug ? in PBC in g_dist, July 2006) had some problems with g_dist and tried to convert the trajectory. Which compiler did you use? I'm running on a Mandriva 2006 machine, installed with the rpm for mandriva. GROMACS VERSION 3.3.1 (single precision) How big is the trajectory file? 103Mb, for this (an 1ns run). Others may be up to 2Gb. Does it really stop, or did you not wait long enough? (counter output is logarithmic) Yes, I'm waiting long enough I guess. I always stops at the same spot in that trajectory. I tried to start it later, and then sometimes it gets a little bit longer, but then it stops quite soon again. Another similar trajectory doesn't stop at all, and another stops at 122.076 instead. Some just stops at : Reading frame 0 time0.000 with zero output Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dist problems
Hi again... How can we tell? You haven't given us your command line, or a meaningful chunk of output. my command: g_dist -f traj.xtc -n index.ndx -s topol.tpr The output: --- Select a group: 0 Selected 0: 'DPPC' Select a group: 1 Selected 1: 'AL' Reading frame 0 time0.000 Back Off! I just backed up dist.xvg to ./#dist.xvg.1# Reading frame 400 time 200.000 -and then it stops! I need to hit ctrl-c dist.xvg ends: 216.1533.72607922.12812881.1397107 -2.8382730 216.5000 I tried to convert the trajectory using trjconv -pbc, but non of the options seems to work. I thought that it maybe would help. Someone else (who had send a message to this list Bug ? in PBC in g_dist, July 2006) had some problems with g_dist and tried to convert the trajectory. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dist problems
Hi I am doing MD-calculations on double layer lipid membranes. When I wanted to calculate the distance between the com. of the lipids and my molecule with g_dist, the program just stops! Sometimes directly and sometimes after a couple of picoseconds. When checking the output it can end like this: 216.1533.72626512.12824731.1397220 -2.8384237 216.50001533.7 Am I doing something wrong? I tried to convert the trajectory using trjconv -pbc, but non of the options seems to work. Edvin -- Edvin Erdtman Ph.D. student Department of Natural Sciences and Örebro Life Science Center Örebro University 701 82 Örebro, Sweden phone: +46 (0)19 30 36 69 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
