[gmx-users] Error- Atom not found in residue seq nr while adding atom
Hi Users, I did the following step= pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top and received an error= Atom ND1 not found in residue seq.nr. 7 while adding atom. I dont understand how do i rectify this. -- Aiswarya -- 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- Atom not found in residue seq nr while adding atom
Hi Javier, I did tried using the swisspdb for adding missing atoms still am receiving the same error. On Wed, Apr 18, 2012 at 3:44 PM, Javier Cerezo j...@um.es wrote: Your PDB structure have probably some missing atoms. Check if this is the case for residue nr. 7. To solve it you can use an external tool to process your PDB file adding the missing atoms. I've used SwissPDB and worked fine. Javier El 18/04/12 11:24, aiswarya pawar escribió: Hi Users, I did the following step= pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top and received an error= Atom ND1 not found in residue seq.nr. 7 while adding atom. I dont understand how do i rectify this. -- Aiswarya -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] using more processors for g_mindist
Mark, i want to know which water atoms stay within a cut off to protein atom. ie i need the duration at which a water resides on the protein atoms. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 6:01 PM, aiswarya pawar wrote: Mark, Right now am computing distance between each protein atom against all water atoms, That's expensive. mdrun goes to great lengths to speed up computing billions of distances. which is taking too long for 5ns run. i cant reduce the frames Yes you can. Even if you think you need data from every frame, you probably don't because they're correlated with each other, and at the very least you can do a pilot study on a frame every 100ps or every nanosecond before committing to one on all the frames. either the number of water atoms. So is there any alternate. You are not likely to get a better solution if you only describe your attempt, rather than describe the objective. Asking how do I hammer harder? if you're hammering a screw makes it impossible to get the correct solution Use a screwdriver. Mark Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjconv), or the number of atoms (also trjconv), or some such. Mark and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] using more processors for g_mindist
Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist 5.00e+02 518 42680 5.01e+02 518 20942 5.02e+02 518 67844 5.03e+02 518 5984 5.04e+02 518 67844 5.05e+02 518 5984 5.06e+02 518 30116 5.07e+02 518 67844 5.08e+02 518 32957 5.09e+02 518 67844 5.10e+02 518 19610 5.11e+02 518 19610 5.12e+02 518 22895 5.13e+02 518 30116 5.14e+02 518 19610 5.15e+02 518 22895 5.16e+02 518 13628 5.17e+02 518 5984 2nd column is the protein atom and the 3rd column the water atom. if iam doing g_dist how is it possible to know the which water molecule has to be considered for the distance calculations ie should i compute the distance between one protein atom against all the water within the cut off individually? Thanks On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein atoms. ... and identity of the atoms is needed for measuring duration of contact. g_dist does something like this, and reading g_mindist -h should have prompted you to find this out. Otherwise, you will have to construct an index group for each water molecule, and script a loop to examine each water molecule separately using some tool that observes what you really want to measure. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. You also need to be clear about whether you care about continuous contact. Does a water molecule that oscillates at a distance around the cutoff reside about 50% of the time? You still don't need high time resolution for testing whether this analysis might give you the information you want. The water molecules that are in contact for more than 50% of the time (continuous or not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 6:01 PM, aiswarya pawar wrote: Mark, Right now am computing distance between each protein atom against all water atoms, That's expensive. mdrun goes to great lengths to speed up computing billions of distances. which is taking too long for 5ns run. i cant reduce the frames Yes you can. Even if you think you need data from every frame, you probably don't because they're correlated with each other, and at the very least you can do a pilot study on a frame every 100ps or every nanosecond before committing to one on all the frames. either the number of water atoms. So is there any alternate. You are not likely to get a better solution if you only describe your attempt, rather than describe the objective. Asking how do I hammer harder? if you're hammering a screw makes it impossible to get the correct solution Use a screwdriver. Mark Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjconv), or the number of atoms (also trjconv), or some such. Mark and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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
[gmx-users] using more processors for g_mindist
Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- 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] using more processors for g_mindist
Mark, Right now am computing distance between each protein atom against all water atoms, which is taking too long for 5ns run. i cant reduce the frames either the number of water atoms. So is there any alternate. Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjconv), or the number of atoms (also trjconv), or some such. Mark and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] Error energy minimization on protein with implicit water
Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 5000; Maximum number of (minimization) steps to perform nstenergy= 1; Write energies to disk every nstenergy steps energygrps= System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type= simple ; Method to determine neighbor list (simple, grid) coulombtype= cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.0; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) I get a note as = System has non-zero total charge: -4.96e+00 then i tried using genion step as= genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log then again the grompp step and mdrun . but while doing mdrun i get an error as= Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 but here i have given nsteps as 5000 so why does it stop. -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] Error energy minimization on protein with implicit water
Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 5000; Maximum number of (minimization) steps to perform nstenergy= 1; Write energies to disk every nstenergy steps energygrps= System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type= simple ; Method to determine neighbor list (simple, grid) coulombtype= cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.0; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) I get a note as = System has non-zero total charge: -4.96e+00 then i tried using genion step as= genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log then again the grompp step and mdrun . but while doing mdrun i get an error as= Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 but here i have given nsteps as 5000 so why does it stop. -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 energy minimization on protein with implicit water
By setting the emtol to 1.0, didnt work. Anyother way i could figure out. On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1.0 emtol = 1.0 If mdrun could not converge to 1000, setting a target of 1 will not solve anything. The OP should refer to: http://www.gromacs.org/**Documentation/Errors#Stepsize_** too_small.2c_or_no_change_in_**energy._Converged_to_machine_** precision.2c_but_not_to_the_**requested_precisionhttp://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] g_analyze doubt
Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. Thanks -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] g_analyze doubt
Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203 3.0000.64633530.16900010.5680003 -0.257 4.0000.68088910.2630.605 -0.1669998 5.0000.68835610.3090.592 -0.1670003 6.0000.62016600.27699970.513 -0.2090001 7.0000.68320050.29100010.580 -0.211 8.0000.64729990.29600020.533 -0.2150002 9.0000.65426920.1880.540 -0.3180003 10.0000.67256020.32300020.5780001 -0.118 11.0000.61387120.34700010.4769998 -0.171 12.0000.69996450.2860.6150002 -0.172 13.0000.65045930.1210.6160002 -0.171 14.0000.64471600.2110.586 -0.1629996 15.0000.66456100.2040.5710001 -0.2720003 16.0000.64812760.23300030.5560002 -0.237 17.0000.6530.22400020.560 -0.243 18.0000.71192580.26500010.6220002 -0.223 19.0000.66535630.0920.6170001 -0.230 20.0000.68816380.25200010.6070004 -0.204 21.0000.71619440.20900010.6220002 -0.2870002 22.0000.65877780.1410.6020002 -0.2279997 23.0000.57986310.01700020.5160003 -0.263 24.0000.58625640.0390.5239997 -0.258 25.0000.6923014 -0.12400010.552 -0.3990002 26.0000.5787479 -0.0870.5050001 -0.2680001 27.0000.5776323 -0.25899980.473 -0.2070003 28.0000.5910018 -0.16300010.5250001 -0.217 29.0000.4448786 -0.15700010.402 -0.1079998 30.0000.4806164 -0.21600010.401 -0.1560001 31.0000.5405830 -0.1710.473 -0.198 32.0000.5614526 -0.10800030.493 -0.2459998 33.0000.4994450 -0.0730.453 -0.204 34.0000.5323368 -0.14200020.4830003 -0.1730003 From this the first column is the time and the second is the water protein atom distance. so when am using the g_analyze i would use the 1st and 2nd column for the input? More over now this distances are below 0.8 nm . what would i do if my data in between shows distance more than 0.8nm. Thanks On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, if necessary. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] g_analyze doubt
If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm) t: 1473 5369 SOL 20624 OW 0.763485 (nm) t: 1474 5369 SOL 20624 OW 0.767805 (nm) t: 1475 5369 SOL 20624 OW 0.736003 (nm) t: 1476 5369 SOL 20624 OW 0.707953 (nm) t: 1477 5369 SOL 20624 OW 0.713135 (nm) t: 1478 5369 SOL 20624 OW 0.694042 (nm) t: 1480 5369 SOL 20624 OW 0.733907 (nm) t: 1481 5369 SOL 20624 OW 0.705245 (nm) t: 1482 5369 SOL 20624 OW 0.678473 (nm) t: 1483 5369 SOL 20624 OW 0.6288 (nm) t: 1492 5369 SOL 20624 OW 0.794252 (nm) t: 1496 5369 SOL 20624 OW 0.753049 (nm) t: 1497 5369 SOL 20624 OW 0.782796 (nm) t: 1498 5369 SOL 20624 OW 0.799607 (nm) t: 1499 5369 SOL 20624 OW 0.69987 (nm) t: 1500 5369 SOL 20624 OW 0.763511 (nm) t: 1501 5369 SOL 20624 OW 0.764072 (nm) t: 1502 5369 SOL 20624 OW 0.739181 (nm) t: 1503 5369 SOL 20624 OW 0.70336 (nm) In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this? On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, if necessary. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: [gmx-users] mdrun-gpu error
Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
Re: [gmx-users] mdrun-gpu error
when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels// bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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
Re: [gmx-users] mdrun-gpu error
Szilárd, I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right. Thanks On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: That's a generic GPU kernel launch failure which can mean anything, from faulty hardware to bad driver to messed up installation. Does the memory test run? Try to compile/install again and see if it works. -- Szilárd On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels// bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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] mdrun-gpu error
Justin, Sorry for not giving the correct information. Gromacs version 4.5.5 Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor) Cuda version 3.1 CMake 2.8 I installed the OpenMM from the source using commands= ccmake -i . make make test make install everything went fine and set the paths export OPENMM_ROOT_DIR=path_to_custom_openmm_installation cmake -DGMX_OPENMM=ON then make make install The submission script used is= #!/bin/csh #PBS -l gpu=1 #PBS -l ncpus=1 #PBS -o /global/utemp/cuda-out2.out #PBS -e /global/utemp/cuda-err2.out /home/staff/software/gromacs_gpu_t/bin/mdrun-gpu -device OpenMM:platform=Cuda,DeviceID=0,Memtest=15,**,force-device=yes -v -deffnm /global/utemp/md for this i receive an error such as Cuda error in file '/home/staff/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Szilárd, I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right. You're trying to solve multiple problems at once. You told Mark that the normal mdrun executable (which works independently of any GPU components) also hangs, so either your filesystem is faulty or your installation procedure produced nonfunctional executables. You're posting bits and pieces of information, which makes it incredibly hard for anyone to help you. Let's recap and try again. Please provide: 1. The Gromacs version you're using 2. Description of the hardware (GPU and non-GPU components) 3. Installation procedure for Gromacs and any of the prerequisite software and libraries that were required, including versions 4. The exact command(s) you're issuing, including the full script that is causing a problem -Justin Thanks On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll szilard.p...@cbr.su.semailto: szilard.p...@cbr.su.se** wrote: That's a generic GPU kernel launch failure which can mean anything, from faulty hardware to bad driver to messed up installation. Does the memory test run? Try to compile/install again and see if it works. -- Szilárd On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pawar@gmail.**comaiswarya.pa...@gmail.com wrote: when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/**software/openmm_tesla/** platforms/cuda/./src/kernels//**bbsort.cu http://bbsort.cu http://bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pawar@gmail.**comaiswarya.pa...@gmail.com wrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se** wrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.**aumark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.**aumark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com mailto:aiswarya.pawar@gmail.**com aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerryŽ on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se** Sender: gmx-users-boun...@gromacs.org
[gmx-users] mdrun-gpu error
Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] mdrun-gpu error
Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing list gmx-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 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] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values
Hi users, Am trying to run the grimaces gpu version. I receive an error while doing the nvt step . my nvt.mdp file goes like this= ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, volume and temperature) cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 1250 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1; Write every step to the log nstenergy= 5; Write energies at every step nstxtcout= 0; Do not write a compressed trajectory energygrps = System ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 epsilon_rf = 54 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling tcoupl = Berendsen tc-grps = System tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = hbonds i get an error as Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values please tell me whats wrong. Thanks -- 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] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values
Yes it worked. Thanks :) On Tue, Jan 17, 2012 at 10:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, Am trying to run the grimaces gpu version. I receive an error while doing the nvt step . my nvt.mdp file goes like this= ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, volume and temperature) cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 1250 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1; Write every step to the log nstenergy= 5; Write energies at every step nstxtcout= 0; Do not write a compressed trajectory energygrps = System ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 epsilon_rf = 54 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling tcoupl = Berendsen tc-grps = System tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDSconstraints = hbonds i get an error as Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values please tell me whats wrong. Precisely what it says. You specify one group to be coupled (System), but then provide coupling information for two groups. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: [gmx-users] Regarding trajectory file
You can write this on VMD forum. Anyways you can try by doing this in the Tcl console- set sel [atomselect top solvent] $sel get {x y z} This would give you the coordinates of the solvent, for your purpose you got to iterate so as to get for each time step. Aiswarya SERC Dept, IISc Bangalore On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote: Dear All, I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I want to get the coordinates of solvent and solute at different time steps from the trajectory file (*.xtc). Can anybody tell me how to extract the details using VMD or any other viewer. You're unlikely to get help for non-GROMACS software on this mailing list. Check out manual section 7.4 for clues on what GROMACS tools might help, and then section 8 and appendix D for more details. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] no output in atm-pair.out
Dear Users, Am running a shell script for the command g_mindist= #!/bin/bash groups=`grep ^\[ -o index.ndx | wc -l` for ((i=0; i$groups; i++)) do echo $((i++)) 3393 | g_mindist -f md.xtc -s md.tpr -od $i.xvg -o atm-pair$i.out -d 0.8 -e 5000 -n index.ndx done here the index file has 3393 groups, the script reads each group against the final group ie 3393 (1-3393,2-3393,3-3393etc), the .xvg file has been created successfully but the .out file is empty. Please tell me why its so. Thanks, Aiswarya -- 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] Re: LINCS error
I did few changes ie decreased the time step/ increased the equilibration steps/ omitted the generation of velocity in production run / did 2 steps of equilibration / checked the starting structure for steric clashes. I don't understand what else should I try to fix the lincs warnings. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Wed, 21 Dec 2011 00:15:15 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Re: LINCS error -- 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] Re: LINCS error
i went through the mailing list, but i dont understand when i run the same protein on my computer it runs correctly without any LINCS warning. On the cluster with 64 processors the job runs but crashes in between and shows the LINCS warning. Please anyone tell me what could be the reason. Is anything wrong with my protein. On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- 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] LINCS error
I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.00.4449 0.2622 0.1000 2031 2030 90.00.1949 0.1264 0.1000 Wrote pdb files with previous and current coordinates Step 43231, time 86.462 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.066301, max 3.173023 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.00.2622 0.4173 0.1000 2031 2030 89.90.1264 0.1675 0.1000 --- Program mdrun, VERSION 4.5.3 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (1001) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and my md.mdp file i altered goes like this= ; VARIOUS PREPROCESSING OPTIONS title= Production Simulation cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 250; Make it 10 ns ; OUTPUT CONTROL OPTIONS nstxout = 500 ; Writing full precision coordinates every nanosecond nstvout = 500 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 2500 ; Writing to the log file every step nstenergy= 2500 ; Writing out energy information every step nstxtcout= 500 ; Writing coordinates every 5 ps energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 how should i rectify this. Please help On Sun, Dec 18, 2011 at 8:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/12/2011 1:05 AM, aiswarya pawar wrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulationfor general advice. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic
[gmx-users] LINCS error
Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- 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] compatible gromacs
I did the openmpi installation on IBM cluster, when i try to run the md.tpr is read but gets abort and leaves and error saying= p4_error: interrupt SIGx:4 Anyone knows the solution to this. Thanks, Aiswarya On Fri, Dec 16, 2011 at 2:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/12/2011 4:55 PM, aiswarya pawar wrote: Hi users, i would like to know which version of gromacs would be compatible with the cluster architecture = Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005 ppc64 ppc64 ppc64 GNU/Linux Any. And which gromacs version would be compatible with the mpi version = mpich-1.2.7 Don't know - use of MPICH is discouraged because of some historical problems. Knowledge that a particular version works well with modern version of GROMACS would be a useful addition to the installation guide. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
Fw: [gmx-users] Re: submission error
Lina, I used the same script for mpi ie other than usr/bin/poe I have given usr/bin/mpirun I still receive the same errorOn 15/12/2011 4:51 PM, aiswarya pawar wrote: Hi, When i tried running mdrun without mip i received the same error ie when i gave mdrun -deffnm md i got= Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file md.tpr, VERSION 4.5.4 (single precision) Loaded with Money p0_23443: p4_error: interrupt SIGx: 4 The job you ran below with poe did not have the MPI suffix, so I am not convinced you are doing appropriate things with appropriate executables. Above, a p4_error is consistent with an MPI-enabled executable. Get an MPI hello world program and get it running before worrying about GROMACS. Follow the user guide for your cluster. Get your MPI-enabled mdrun suffixed with _mpi like the installation guides recommend. Mark Thanks, Aiswarya On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Please anyone can help with this error. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Thu, 15 Dec 2011 17:03:12 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Re: submission error -- 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] compatible gromacs
Hi users, i would like to know which version of gromacs would be compatible with the cluster architecture = Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005 ppc64 ppc64 ppc64 GNU/Linux And which gromacs version would be compatible with the mpi version = mpich-1.2.7 Thanks, Aiswarya -- 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] submission error
Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Please anyone can help with this error. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] submission error
Mark, I still the same error. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Wed, 14 Dec 2011 23:03:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] submission error On 14/12/2011 10:30 PM, aiswarya pawar wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Looks like a problem with file writing privileges or maybe disk quota. Either make a new run directory or clean up before using this job script, and see how you go. 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: [gmx-users] submission error
Am using mipch2-1.2.7. Is this the problem? Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: aiswarya.pa...@gmail.com Date: Wed, 14 Dec 2011 13:09:19 To: Gromacs mailgmx-users@gromacs.org Reply-To: aiswarya.pa...@gmail.com Subject: Re: [gmx-users] submission error Mark, I still the same error. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Wed, 14 Dec 2011 23:03:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] submission error On 14/12/2011 10:30 PM, aiswarya pawar wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Looks like a problem with file writing privileges or maybe disk quota. Either make a new run directory or clean up before using this job script, and see how you go. 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] Re: submission error
Hi, When i tried running mdrun without mip i received the same error ie when i gave mdrun -deffnm md i got= Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file md.tpr, VERSION 4.5.4 (single precision) Loaded with Money p0_23443: p4_error: interrupt SIGx: 4 Thanks, Aiswarya On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Please anyone can help with this error. Thanks -- 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] Gromacs Installation error
Hi gromacs users, Iam trying to install gromacs on IBM cluster. I have successfully installed installed fftw-3.3 version with commands= ./configure --enable-threads --enable-float make make install the set the enviroment= setenv CPPFLAGS -I/home/fftw/include setenv LDFLAGS -L/home/fftw/lib Then the gromacs installation= ./configure --prefix=/home/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC=mpCC CC=xlC_r -q64 CFLAGS=-O3 -qarch=ppc64 -qtune=auto CXX=xlC_r -q64 CXXFLAGS=-O3 -qarch=ppc64 -qtune=auto F77=mpixlf_r FFLAGS=-O3 -qarch=ppc64 -qtune=auto the configure did well but while doing make mdrun i started getting error such as= source='vmdio.c' object='vmdio.lo' libtool=yes \ DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \ /bin/sh ../../libtool --tag=CC --mode=compile mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include -O3 -qarch=ppc64 -qtune=auto -c -o vmdio.lo vmdio.c mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include -O3 -qarch=ppc64 -qtune=auto -c vmdio.c -o vmdio.o 1506-503 (W) Option -qlongdouble / -qldbl128 is not supported for LINUX for Power. /usr/include/glob.h, line 166.34: 1506-276 (S) Syntax error: possible missing identifier? /usr/include/glob.h, line 166.12: 1506-033 (S) Function __REDIRECT_NTH is not valid. Function cannot return a function. /usr/include/glob.h, line 166.12: 1506-282 (S) The type of the parameters must be specified in a prototype. /usr/include/glob.h, line 169.35: 1506-334 (S) Identifier glob_t has already been defined on line 113 of /usr/include/glob.h. /usr/include/glob.h, line 169.42: 1506-277 (S) Syntax error: possible missing ';' or ','? /usr/include/glob.h, line 171.39: 1506-276 (S) Syntax error: possible missing identifier? /usr/include/glob.h, line 171.13: 1506-282 (S) The type of the parameters must be specified in a prototype. /usr/include/glob.h, line 171.13: 1506-343 (S) Redeclaration of __REDIRECT_NTH differs from previous declaration on line 166 of /usr/include/glob.h. /usr/include/glob.h, line 171.13: 1506-050 (I) Return type void in redeclaration is not compatible with the previous return type int(const char*,int). /usr/include/glob.h, line 171.58: 1506-160 (S) Object globfree64 cannot be declared as type void. /usr/include/glob.h, line 175.12: 1506-343 (S) Redeclaration of glob64 differs from previous declaration on line 169 of /usr/include/glob.h. /usr/include/glob.h, line 175.12: 1506-382 (I) The type int(const char* restrict,int,int(*)(const char*,int),struct {...}* restrict) of identifier glob64 differs from previous type int. make[2]: *** [vmdio.lo] Error 1 make[2]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib' (cd ./src/mdlib make ; exit 0) make[1]: Entering directory `/home/gromacs-4.5.5/src/mdlib' make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `libmd_mpi.la'. Stop. make[1]: Leaving directory `/home/gromacs-4.5.5/src/mdlib' (cd ./src/kernel make mdrun ; exit 0) make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel' /bin/sh ../../libtool --tag=CC --mode=link mpCC -O3 -qarch=ppc64 -qtune=auto -no-undefined -version-info 6:0:0 -L/home/staff/sec/secdpal/soft/lib -o libgmxpreprocess_mpi.la -rpath /home/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 make[1]: Leaving directory `/home/gromacs-4.5.5/src/kernel' please help! Aiswarya -- 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] mdrun_mpi error
i used the option still i get the error as= /bin/sh ../../libtool --tag=CC --mode=compile mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\/home/staff/sec/secdpal/soft/gromacs/share/top\ -I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5 -c -o vmdio.lo vmdio.c mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\/home/staff/sec/secdpal/soft/gromacs/share/top\ -I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5 -c vmdio.c -o vmdio.o 1506-503 (W) Option -qlongdouble / -qldbl128 is not supported for LINUX for Power. /usr/include/glob.h, line 166.34: 1506-276 (S) Syntax error: possible missing identifier? /usr/include/glob.h, line 166.12: 1506-033 (S) Function __REDIRECT_NTH is not valid. Function cannot return a function. /usr/include/glob.h, line 166.12: 1506-282 (S) The type of the parameters must be specified in a prototype. /usr/include/glob.h, line 169.35: 1506-334 (S) Identifier glob_t has already been defined on line 113 of /usr/include/glob.h. /usr/include/glob.h, line 169.42: 1506-277 (S) Syntax error: possible missing ';' or ','? /usr/include/glob.h, line 171.39: 1506-276 (S) Syntax error: possible missing identifier? /usr/include/glob.h, line 171.13: 1506-282 (S) The type of the parameters must be specified in a prototype. /usr/include/glob.h, line 171.13: 1506-343 (S) Redeclaration of __REDIRECT_NTH differs from previous declaration on line 166 of /usr/include/glob.h. /usr/include/glob.h, line 171.13: 1506-050 (I) Return type void in redeclaration is not compatible with the previous return type int(const char*,int). /usr/include/glob.h, line 171.58: 1506-160 (S) Object globfree64 cannot be declared as type void. /usr/include/glob.h, line 175.12: 1506-343 (S) Redeclaration of glob64 differs from previous declaration on line 169 of /usr/include/glob.h. /usr/include/glob.h, line 175.12: 1506-382 (I) The type int(const char* restrict,int,int(*)(const char*,int),struct {...}* restrict) of identifier glob64 differs from previous type int. make[2]: *** [vmdio.lo] Error 1 make[2]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib' (cd ./src/mdlib make ; exit 0) make[1]: Entering directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib' make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the future make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` libmd_mpi.la'. Stop. make[1]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib' (cd ./src/kernel make mdrun ; exit 0) make[1]: Entering directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel' make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the future /bin/sh ../../libtool --tag=CC --mode=link mpCC -O3 -qarch=ppc64 -qtune=pwr5 -no-undefined -version-info 6:0:0 -L/home/staff/sec/secdpal/soft/lib -o libgmxpreprocess_mpi.la -rpath /home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 make[1]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel' make: warning: Clock skew detected. Your build may be incomplete. On Sat, Dec 10, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/12/2011 6:31 PM, aiswarya pawar wrote: Hi, I tried giving this- ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d -qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450 and the configure process ran well. but when i gave make mdrun, i get an error which says= make[2]: *** [vmdio.lo] Error 1 The first error happened above this line, so we can't tell what is wrong. As a wild guess, use --without-dlopen with configure. Mark make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/ gmxlib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' (cd ./src/mdlib make ; exit 0) make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib' make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the future make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` libmd_mpi.la'. Stop. make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib' (cd ./src/kernel make mdrun ; exit 0) make[1]: Entering directory `/home/gromacs
Re: [gmx-users] mdrun_mpi error
Hi, I tried giving this- ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d -qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450 and the configure process ran well. but when i gave make mdrun, i get an error which says= make[2]: *** [vmdio.lo] Error 1 make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' (cd ./src/mdlib make ; exit 0) make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib' make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the future make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` libmd_mpi.la'. Stop. make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib' (cd ./src/kernel make mdrun ; exit 0) make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel' make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the future /bin/sh ../../libtool --tag=CC --mode=link mpcc -O3 -qarch=450d -qtune=450 -no-undefined -version-info 6:0:0 -L/home/staff/sec/secdpal/soft/lib -o libgmxpreprocess_mpi.la -rpath /home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/12/2011 6:35 PM, aiswarya pawar wrote: Hi users, Am running the mdrun_mpi on cluster with the md.mdp parameters as- ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The grompp runs fine. but when i run the mdrun_mpi i get an error such as- Child exited abnormally! Killing remote processes...DONE There's no information here upon which one can diagnose anything. Look at the stderr, stdout and .log files and consult the errors page on the GROMACS website for clues. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: [gmx-users] mdrun_mpi error
Hi, I tried giving this- ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d -qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450 and the configure process ran well. but when i gave make mdrun, i get an error which says= make[2]: *** [vmdio.lo] Error 1 make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/ gmxlib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' (cd ./src/mdlib make ; exit 0) make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib' make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the future make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` libmd_mpi.la'. Stop. make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib' (cd ./src/kernel make mdrun ; exit 0) make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel' make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the future /bin/sh ../../libtool --tag=CC --mode=link mpcc -O3 -qarch=450d -qtune=450 -no-undefined -version-info 6:0:0 -L/home/soft/lib -o libgmxpreprocess_mpi.la -rpath /home/soft/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 On Sat, Dec 10, 2011 at 1:01 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi, I tried giving this- ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d -qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450 and the configure process ran well. but when i gave make mdrun, i get an error which says= make[2]: *** [vmdio.lo] Error 1 make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' (cd ./src/mdlib make ; exit 0) make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib' make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the future make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` libmd_mpi.la'. Stop. make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib' (cd ./src/kernel make mdrun ; exit 0) make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel' make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the future /bin/sh ../../libtool --tag=CC --mode=link mpcc -O3 -qarch=450d -qtune=450 -no-undefined -version-info 6:0:0 -L/home/staff/sec/secdpal/soft/lib -o libgmxpreprocess_mpi.la -rpath /home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/12/2011 6:35 PM, aiswarya pawar wrote: Hi users, Am running the mdrun_mpi on cluster with the md.mdp parameters as- ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The grompp runs fine. but when i run the mdrun_mpi i get an error such as- Child exited abnormally! Killing remote processes...DONE There's no information here upon which one can diagnose anything. Look at the stderr, stdout and .log files and consult the errors page
Re: [gmx-users] gromacs installation error
when i gave following command for gromacs= ./configure --with-fft=fftw3 --enable-float --disable-threads it installed gromacs successfully, but i require a mpi mdrun. when i give enable mpi it gives me same error as fftw3 library not found. Thanks On Wed, Dec 7, 2011 at 2:21 PM, Javier Cerezo j...@um.es wrote: You mean that $ ls /home/fftw gives you the content of the installed fftw library (i.e. bin/ include/ lib/ share/)? El 06/12/11 16:21, aiswarya.pa...@gmail.com escribió: Hi, Thanks for the reply, I check the path and everything still I get this error. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezo j...@um.es j...@um.es Sender: gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org gmx-users@gromacs.org Subject: Re: [gmx-users] gromacs installation error -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- 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] mdrun_mpi error
Hi users, Am running the mdrun_mpi on cluster with the md.mdp parameters as- ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The grompp runs fine. but when i run the mdrun_mpi i get an error such as- Child exited abnormally! Killing remote processes...DONE Aiswarya -- 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] gromacs installation error
Hi Gromacs users, Am trying to install gromacs-4.5.5 version on IBM cluster with Linux platform and am getting an error such as configure: error: Cannot find fftw3f library. The steps i followed- Installed fftw-3.3 version ./configure --enable-threads --enable-float make make install setenv CPPFLAGS -I/home/fftw/include setenv LDFLAGS -L/home/fftw/lib In gromacs-4.5.5 directory ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3 in this i got the error. please help. Thanks, Aiswarya -- 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] gromacs installation error
Hi, Thanks for the reply, I check the path and everything still I get this error. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezo j...@um.es Sender: gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] gromacs installation error -- 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] increase the time frame
Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. Thanks, Aiswarya -- 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] increase the time frame
After running this minimization when i did gmxcheck i got this output trn version: GMX_trn_file (single precision) Reading frame 0 time9.000 # Atoms 4113 Reading frame 3 time 57.000 Timesteps at t=31 don't match (12, 26) Reading frame 4 time 69.000 Timesteps at t=57 don't match (26, 12) Reading frame 14 time 192.000 Timesteps at t=184 don't match (13, 8) Last frame 14 time 192.000 Item#frames Step15 Time15 Lambda 15 Coords 15 Velocities 0 Forces 0 Box 15 why is it saying that Timesteps at t=31 don't match (12, 26). On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 21/10/2011 5:09 PM, aiswarya pawar wrote: Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. This will write every frame of the EM, but if it only has two steps... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Minimization error
Hi Users, I performed a simple minimization for a protein complex in vacuum. Didn't get any error while performing the minimization but when visualised the pdb file after the minimization the chains of the protein complex separated. What could be the reason. Thanks, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Minimization error
Hi, All the parameters are ok, still i get the complex separated. On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya.pa...@gmail.com wrote: Hi Users, I performed a simple minimization for a protein complex in vacuum. Didn't get any error while performing the minimization but when visualised the pdb file after the minimization the chains of the protein complex separated. What could be the reason. Please see FAQ #3 under the heading: http://www.gromacs.org/**Documentation/FAQs#Analysis_**and_Visualizationhttp://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization -Justin Thanks, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] non interactive command
Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? Thanks -- 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] non interactive command
justin, if i use echo command then i need to run again and again for each selection right? how can i run as whole bunch. Thanks On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? You should only provide the chosen number(s), otherwise the program will try to read all of them. In the case where you have many different programs to run, it is vastly easier to run, for instance: echo x y | g_program -flags -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: [gmx-users] non interactive command
i have N number of selection ie it should run as a batch. like its should select group1: 0 and select group2: 32, this is 1st run then after this next run should be select group1: 1 and select group2: 32 and so on. On Wed, Sep 28, 2011 at 10:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: justin, if i use echo command then i need to run again and again for each selection right? how can i run as whole bunch. I don't understand your question. You can write a trivial shell script for all of your analysis, e.g.: #!/bin/bash echo 4 4 | g_rms -f traj.xtc -s topol.tpr echo 1 | g_gyrate -f traj.xtc -s topol.tpr (etc) -Justin Thanks On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? You should only provide the chosen number(s), otherwise the program will try to read all of them. In the case where you have many different programs to run, it is vastly easier to run, for instance: echo x y | g_program -flags -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] g_analyze doubt
Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. Thanks -- 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] g_analyze doubt
HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Thanks, On Mon, Sep 26, 2011 at 12:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/09/2011 4:51 PM, aiswarya pawar wrote: Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. I don't understand your question. Your first sentence implies you know what quantity you want to autocorrelate, and the second implies you don't. g_analyze needs a time series in an .xvg file of some data to compute an autocorrelation. Usually, an .xvg file written by a GROMACS tool is already prepared for such further analysis. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: [gmx-users] g_analyze doubt
Mark, i read the help but i still didnt understand how do i compute the time series for this data, should i use this data as such for the input? Thanks, On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/09/2011 5:10 PM, aiswarya pawar wrote: HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Have you read g_analyze -h and tried it out? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] g_analyze
Hi users, I have got a data from g_mindist ie water and protein atom distance in each time frame. Now I have to find the auto correlation function using g_analyze but my output file from g_mindist has the time frame,water molecule number. How do I compute the ACF. In ACF data set the x axis is for time and what data provided in y axis. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] g_mindist doubt
Hi users, The g_mindist gives the minimum distance between the atoms other than the actual distance. Thanks -- 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] g_mindist doubt
Hi Tsjerk, i used the command in format- g_mindist -f md.xtc -s md.tpr -n 13.ndx -od 13.xvg -on 13.xvg -o 13.out -b 500 -e 1500 -d 0.5 so here i obtain the output- atmpair.out- 0.00e+0013 21161 1.00e+0013 21161 2.00e+0013 21161 3.00e+0013 21161 4.00e+0013 21161 5.00e+0013 21161 6.00e+0013 21161 7.00e+0013 21161 8.00e+0013 21161 9.00e+0013 21161 1.00e+0113 21161 1.10e+0113 21161 1.20e+0113 21161 1.30e+0113 21161 1.40e+0113 21161 1.50e+0113 18698 1.60e+0113 21161 1.70e+0113 18698 1.80e+0113 18698 1.90e+0113 18698 2.00e+0113 18698 2.10e+0113 21455 2.20e+0113 7142 2.30e+0113 7142 and distance output- 0.00e+00 1.360443e+00 1.00e+00 1.246777e+00 2.00e+00 1.386871e+00 3.00e+00 1.250959e+00 4.00e+00 1.314306e+00 5.00e+00 1.273990e+00 6.00e+00 1.175991e+00 7.00e+00 1.154678e+00 8.00e+00 1.249905e+00 9.00e+00 1.110049e+00 1.00e+01 1.023204e+00 1.10e+01 1.004968e+00 1.20e+01 1.214452e+00 1.30e+01 1.297469e+00 1.40e+01 1.307791e+00 1.50e+01 1.276168e+00 1.60e+01 1.552775e+00 1.70e+01 1.668275e+00 1.80e+01 1.786125e+00 1.90e+01 1.733398e+00 2.00e+01 1.656987e+00 2.10e+01 1.715875e+00 2.20e+01 1.848419e+00 2.30e+01 1.932844e+00 Now my doubt is the whether these distances shown are the exact distance ie actual or the minimum distance measured between the two atoms. Thanks On Thu, Sep 22, 2011 at 12:13 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Aiswarya, What did you do, what did you get, what did you expect and what is your hunch regarding the difference between your result and your expectation? Tsjerk On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, The g_mindist gives the minimum distance between the atoms other than the actual distance. Thanks -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] surface atoms
Hi users, what are options for obtaining the surface atoms exposed to solvent, i need the list of these atoms. Thanks -- 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] Running the batch command
Hi users, Am using g_mindist to calculate the distances. Now I have to calculate for each atom ie around 1000atoms. If I try running this command in a shell script, how would designate the index file, ie my index file has protein atoms and water atoms, and have to find distance between one protein atom to all the water atoms. How would be the flow of the script. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] residue numbering different
Hi Users, When i list the residues in a index file it shows a numbering of residues and when open the same protein in VMD and check the residue numbering its different. i want to visualise the protein in VMD and select a residue number from VMD and use in gromacs ie want to make an index file in gromacs so how would go about. Thanks -- 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] g_dist error
Mark, the command line goes like this- g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 the index file has group1- a_1322 ( this is just a single atom from a protein. its in sidechain) group2- a_OW ( this is water atoms) now as per the utility it should give me and output as- t:1 1322 a 54119 OW 0.389 but am getting something different On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 3:40 PM, aiswarya pawar wrote: Hi Mark, The -dist option says- print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1. That means it should give me the distance from OW to protein atom. If you choose correct groups that are correctly defined with respect to your trajectory and use a large enough distance cutoff. And when am already specifying only one atom from protein ie say 1322. why do i get this kind of output- We can't tell. We don't know what your command line is, what's in your simulation system, the contents of your index groups, or which groups you've selected for which role. Clearly something is not working properly, and our time constraints mean that we're going to assume you've done something wrong, in the absence of evidence to the contrary. Mark t: 275 20230 SOL 62618 OW 0.341434 (nm) t: 275 22019 SOL 67985 OW 0.171584 (nm) t: 276 10768 SOL 34232 OW 0.303328 (nm) t: 276 20230 SOL 62618 OW 0.325176 (nm) t: 276 22019 SOL 67985 OW 0.187259 (nm) t: 277 10768 SOL 34232 OW 0.306008 (nm) t: 277 20230 SOL 62618 OW 0.326195 (nm) t: 277 22019 SOL 67985 OW 0.181089 (nm) t: 278 10768 SOL 34232 OW 0.274507 (nm) t: 278 22019 SOL 67985 OW 0.292652 (nm) t: 279 10618 SOL 33782 OW 0.319922 (nm) t: 280 10618 SOL 33782 OW 0.330082 (nm) t: 280 22019 SOL 67985 OW 0.330203 (nm) t: 281 8273 SOL 26747 OW 0.278731 (nm) t: 281 10618 SOL 33782 OW 0.325434 (nm) t: 281 11535 SOL 36533 OW 0.200327 (nm) t: 281 17036 SOL 53036 OW 0.343946 (nm) t: 282 8273 SOL 26747 OW 0.256558 (nm) t: 282 11535 SOL 36533 OW 0.327147 (nm) t: 283 8273 SOL 26747 OW 0.165061 (nm) t: 283 10618 SOL 33782 OW 0.306578 (nm) t: 283 17191 SOL 53501 OW 0.333075 (nm) t: 284 8273 SOL 26747 OW 0.19427 (nm) t: 284 10618 SOL 33782 OW 0.321927 (nm) t: 284 17191 SOL 53501 OW 0.30832 (nm) On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote: Iam -dist option because I need the distance between two groups That is not what g_dist -dist does. Please read g_dist -h. excluding -dist gives me X,Y,Z output which I don't want. And other output which you do, but you have to use -o to get it. Read g_dist -h. And am not specifying an -o. You need to specify -o to achieve your purpose. However, as I said quite a while ago, there is no value in measuring the distance between a protein phase and a water phase if they are in contact... Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Date: Mon, 12 Sep 2011 22:35:28 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but not together. -Justin Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Sender: gmx-users-boun...@gromacs.org Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org gmx-users@gromacs.org Subject: Re: [gmx-users] g_dist error aiswarya pawar wrote: hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. The printed distance indicates that there is a certain water molecule that is just over 2 hydrogen bonding lengths away from your protein's backbone. Sounds normal to me. -Justin Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu jalem...@vt.edu wrote: aiswarya pawar wrote
Re: [gmx-users] g_dist error
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it takes the default index file, so there isnt any wrong in selecting the atoms. On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 4:14 PM, aiswarya pawar wrote: Mark, the command line goes like this- g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 This command line is not using an index file. The index groups defined for the grompp that produced the .tpr are being used (which may be the default ones, depending what you did). Please copy and show the interactive input you made to g_dist after it showed the groups it knew about. the index file has group1- a_1322 ( this is just a single atom from a protein. its in sidechain) group2- a_OW ( this is water atoms) Your output is listing the time of the frame, and the residue number, residue name, atom number, and atom name of the matching atom. Apparently a water molecule can sometimes be closer than 0.2nm, and sometimes not. Mark now as per the utility it should give me and output as- t:1 1322 a 54119 OW 0.389 but am getting something different On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 3:40 PM, aiswarya pawar wrote: Hi Mark, The -dist option says- print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1. That means it should give me the distance from OW to protein atom. If you choose correct groups that are correctly defined with respect to your trajectory and use a large enough distance cutoff. And when am already specifying only one atom from protein ie say 1322. why do i get this kind of output- We can't tell. We don't know what your command line is, what's in your simulation system, the contents of your index groups, or which groups you've selected for which role. Clearly something is not working properly, and our time constraints mean that we're going to assume you've done something wrong, in the absence of evidence to the contrary. Mark t: 275 20230 SOL 62618 OW 0.341434 (nm) t: 275 22019 SOL 67985 OW 0.171584 (nm) t: 276 10768 SOL 34232 OW 0.303328 (nm) t: 276 20230 SOL 62618 OW 0.325176 (nm) t: 276 22019 SOL 67985 OW 0.187259 (nm) t: 277 10768 SOL 34232 OW 0.306008 (nm) t: 277 20230 SOL 62618 OW 0.326195 (nm) t: 277 22019 SOL 67985 OW 0.181089 (nm) t: 278 10768 SOL 34232 OW 0.274507 (nm) t: 278 22019 SOL 67985 OW 0.292652 (nm) t: 279 10618 SOL 33782 OW 0.319922 (nm) t: 280 10618 SOL 33782 OW 0.330082 (nm) t: 280 22019 SOL 67985 OW 0.330203 (nm) t: 281 8273 SOL 26747 OW 0.278731 (nm) t: 281 10618 SOL 33782 OW 0.325434 (nm) t: 281 11535 SOL 36533 OW 0.200327 (nm) t: 281 17036 SOL 53036 OW 0.343946 (nm) t: 282 8273 SOL 26747 OW 0.256558 (nm) t: 282 11535 SOL 36533 OW 0.327147 (nm) t: 283 8273 SOL 26747 OW 0.165061 (nm) t: 283 10618 SOL 33782 OW 0.306578 (nm) t: 283 17191 SOL 53501 OW 0.333075 (nm) t: 284 8273 SOL 26747 OW 0.19427 (nm) t: 284 10618 SOL 33782 OW 0.321927 (nm) t: 284 17191 SOL 53501 OW 0.30832 (nm) On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote: Iam -dist option because I need the distance between two groups That is not what g_dist -dist does. Please read g_dist -h. excluding -dist gives me X,Y,Z output which I don't want. And other output which you do, but you have to use -o to get it. Read g_dist -h. And am not specifying an -o. You need to specify -o to achieve your purpose. However, as I said quite a while ago, there is no value in measuring the distance between a protein phase and a water phase if they are in contact... Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Date: Mon, 12 Sep 2011 22:35:28 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but not together. -Justin Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Sender: gmx-users-boun
[gmx-users] Re: no output in g_dist
Hi everyone, when am doing this g_dist between the protein and water am getting the distance between water-water. why it is so?? and is there a way i can find distance in each time frame. Thanks On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi users, To get the distance between water and protein i did - g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 from this i should obtain an output file as distance.xvg which i dont get. and my output is printed on the terminal as- t: 1 136 SOL 2336 OW 0.772373 (nm) t: 1 136 SOL 2337 HW1 0.706358 (nm) t: 1 136 SOL 2338 HW2 0.807787 (nm) t: 1 139 SOL 2345 OW 0.821094 (nm) t: 1 139 SOL 2346 HW1 0.810919 (nm) t: 1 139 SOL 2347 HW2 0.771526 (nm) t: 1 7237 SOL 23640 HW1 0.997056 (nm) t: 1 11793 SOL 37307 OW 0.868929 (nm) t: 1 11793 SOL 37308 HW1 0.927205 (nm) t: 1 11793 SOL 37309 HW2 0.776699 (nm) t: 2 125 SOL 2303 OW 0.940527 (nm) In this t: 1 136 SOL 2336 OW 0.772373 (nm) does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them. Thanks -- 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] g_dist error
Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) Thanks -- 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] g_dist output error
Hi gromacs Users, Am using g_dist to find the distance between water and protein. for that i made a index file such as- a CA(protein atoms) a OW(water atoms) i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35 instead of getting the result for protein-SOL distance . my output shows SOL-OW distance as seen below- t: 1 136 SOL 2336 OW 0.772373 (nm) can anyone tell me whats wrong with this. Thanks -- 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] g_dist error
Hi Justin, Am using g_dist to find the distance between water and protein. for that i made a index file such as- a CA(protein atoms) a OW(water atoms) i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35 instead of getting the result for protein-SOL distance . my output shows SOL-OW distance as seen below- t: 1 136 SOL 2336 OW 0.772373 (nm) even after specifying am getting an wrong output. Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) This is not a water-water distance, it is the output of the -dist option telling you that water molecule 136 has its OW atom at 0.7723273 nm from whatever your reference group is. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: [gmx-users] g_dist error
hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) This is not a water-water distance, it is the output of the -dist option telling you that water molecule 136 has its OW atom at 0.7723273 nm from whatever your reference group is. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: [gmx-users] g_dist output error
hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. Thanks On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Hi gromacs Users, Am using g_dist to find the distance between water and protein. for that i made a index file such as- a CA(protein atoms) a OW(water atoms) i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35 instead of getting the result for protein-SOL distance . my output shows SOL-OW distance as seen below- t: 1 136 SOL 2336 OW 0.772373 (nm) can anyone tell me whats wrong with this. Please see my previous message. This is not a SOL-water distance. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: [gmx-users] g_dist error
Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu Sender: gmx-users-boun...@gromacs.org Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] g_dist error aiswarya pawar wrote: hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. The printed distance indicates that there is a certain water molecule that is just over 2 hydrogen bonding lengths away from your protein's backbone. Sounds normal to me. -Justin Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: aiswarya pawar wrote: Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) This is not a water-water distance, it is the output of the -dist option telling you that water molecule 136 has its OW atom at 0.7723273 nm from whatever your reference group is. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: [gmx-users] g_dist error
Iam -dist option because I need the distance between two groups, excluding -dist gives me X,Y,Z output which I don't want. And am not specifying an -o. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu Date: Mon, 12 Sep 2011 22:35:28 To: aiswarya.pa...@gmail.com; Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but not together. -Justin Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu Sender: gmx-users-boun...@gromacs.org Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] g_dist error aiswarya pawar wrote: hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. The printed distance indicates that there is a certain water molecule that is just over 2 hydrogen bonding lengths away from your protein's backbone. Sounds normal to me. -Justin Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: aiswarya pawar wrote: Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) This is not a water-water distance, it is the output of the -dist option telling you that water molecule 136 has its OW atom at 0.7723273 nm from whatever your reference group is. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] g_dist error
Hi Mark, The -dist option says- print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1. That means it should give me the distance from OW to protein atom. And when am already specifying only one atom from protein ie say 1322. why do i get this kind of output- t: 275 20230 SOL 62618 OW 0.341434 (nm) t: 275 22019 SOL 67985 OW 0.171584 (nm) t: 276 10768 SOL 34232 OW 0.303328 (nm) t: 276 20230 SOL 62618 OW 0.325176 (nm) t: 276 22019 SOL 67985 OW 0.187259 (nm) t: 277 10768 SOL 34232 OW 0.306008 (nm) t: 277 20230 SOL 62618 OW 0.326195 (nm) t: 277 22019 SOL 67985 OW 0.181089 (nm) t: 278 10768 SOL 34232 OW 0.274507 (nm) t: 278 22019 SOL 67985 OW 0.292652 (nm) t: 279 10618 SOL 33782 OW 0.319922 (nm) t: 280 10618 SOL 33782 OW 0.330082 (nm) t: 280 22019 SOL 67985 OW 0.330203 (nm) t: 281 8273 SOL 26747 OW 0.278731 (nm) t: 281 10618 SOL 33782 OW 0.325434 (nm) t: 281 11535 SOL 36533 OW 0.200327 (nm) t: 281 17036 SOL 53036 OW 0.343946 (nm) t: 282 8273 SOL 26747 OW 0.256558 (nm) t: 282 11535 SOL 36533 OW 0.327147 (nm) t: 283 8273 SOL 26747 OW 0.165061 (nm) t: 283 10618 SOL 33782 OW 0.306578 (nm) t: 283 17191 SOL 53501 OW 0.333075 (nm) t: 284 8273 SOL 26747 OW 0.19427 (nm) t: 284 10618 SOL 33782 OW 0.321927 (nm) t: 284 17191 SOL 53501 OW 0.30832 (nm) On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote: Iam -dist option because I need the distance between two groups That is not what g_dist -dist does. Please read g_dist -h. excluding -dist gives me X,Y,Z output which I don't want. And other output which you do, but you have to use -o to get it. Read g_dist -h. And am not specifying an -o. You need to specify -o to achieve your purpose. However, as I said quite a while ago, there is no value in measuring the distance between a protein phase and a water phase if they are in contact... Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Date: Mon, 12 Sep 2011 22:35:28 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but not together. -Justin Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Sender: gmx-users-boun...@gromacs.org Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org gmx-users@gromacs.org Subject: Re: [gmx-users] g_dist error aiswarya pawar wrote: hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. The printed distance indicates that there is a certain water molecule that is just over 2 hydrogen bonding lengths away from your protein's backbone. Sounds normal to me. -Justin Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu jalem...@vt.edu wrote: aiswarya pawar wrote: Hi Users, Am using g_dist to find the distance between water and protein. but my output has the values of SOL-water distance. t: 1 136 SOL 2336 OW 0.772373 (nm) This is not a water-water distance, it is the output of the -dist option telling you that water molecule 136 has its OW atom at 0.7723273 nm from whatever your reference group is. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org
[gmx-users] gridcount
Hi all, am facing an error while installing gridcount- make[1]: *** [g_ri3Dc.o] Error 1 make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src' make: *** [all] Error 2 This error is while giving the make command. Thanks -- 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] conversion of gromacs topology format
Hi gromacs users, Is there a way to convert gromacs topology format to Amber. Thanks, Aiswarya -- 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] no output in g_dist
Hi users, To get the distance between water and protein i did - g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 from this i should obtain an output file as distance.xvg which i dont get. and my output is printed on the terminal as- t: 1 136 SOL 2336 OW 0.772373 (nm) t: 1 136 SOL 2337 HW1 0.706358 (nm) t: 1 136 SOL 2338 HW2 0.807787 (nm) t: 1 139 SOL 2345 OW 0.821094 (nm) t: 1 139 SOL 2346 HW1 0.810919 (nm) t: 1 139 SOL 2347 HW2 0.771526 (nm) t: 1 7237 SOL 23640 HW1 0.997056 (nm) t: 1 11793 SOL 37307 OW 0.868929 (nm) t: 1 11793 SOL 37308 HW1 0.927205 (nm) t: 1 11793 SOL 37309 HW2 0.776699 (nm) t: 2 125 SOL 2303 OW 0.940527 (nm) In this t: 1 136 SOL 2336 OW 0.772373 (nm) does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them. Thanks -- 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] Re: no output in g_dist
Thanks Lina and Justin. Is this data good for finding the distance of protein and water as function of time. On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi users, To get the distance between water and protein i did - g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 from this i should obtain an output file as distance.xvg which i dont get. and my output is printed on the terminal as- t: 1 136 SOL 2336 OW 0.772373 (nm) t: 1 136 SOL 2337 HW1 0.706358 (nm) t: 1 136 SOL 2338 HW2 0.807787 (nm) t: 1 139 SOL 2345 OW 0.821094 (nm) t: 1 139 SOL 2346 HW1 0.810919 (nm) t: 1 139 SOL 2347 HW2 0.771526 (nm) t: 1 7237 SOL 23640 HW1 0.997056 (nm) t: 1 11793 SOL 37307 OW 0.868929 (nm) t: 1 11793 SOL 37308 HW1 0.927205 (nm) t: 1 11793 SOL 37309 HW2 0.776699 (nm) t: 2 125 SOL 2303 OW 0.940527 (nm) In this t: 1 136 SOL 2336 OW 0.772373 (nm) does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them. Thanks -- 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] No addition of ions
Hi Gromacs users, Am running a MD simulation over a protein complex and before adding the ions. we run a grompp option then we get result as model net charge as some integer ie if +2.00. so we got to add 2 CL ions. But when i ran my protein for grompp it didnt give me any net charge so am not able to add any ions. is this correct?? Thanks, Aiswarya -- 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] Hydrogen existence time
Emanuel, Am trying out the procedure u have mentioned but on the other hand i found out a article which mentions does the same. https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html The article states- use the g_hbond program to analyse hydrogen bonds. First select protein twice, to get the intramolecular hydrogen bonds, then select protein and water to get the protein-water h-bonds. Compare the numbers, and their fluctuations. Is there a trend in the graphs, or a correlation between them? You can also compute the residence time of the water molecules on the different functional groups of the protein., e.g. the Ala sidechain. For this we will have to make an index file first: % make_ndx -f after_em_sol EOF a OW q EOF % g_hbond -contact -n index -ac -r 0.6 -b 200 In the g_hbond command select Sidechain and OW. The -c option computes the autocorrelation function of the contact time between Cβ and OW. View the file hbac.xvg using xmgrace. Use xmgrace to integrate the ACF, this will give you the correlation time. Is it higher or lower than you expected? Why? Now do the same analysis for interactions between Carbonyl groups and Amide groups and water oxygens. For these analyses you should put the distance to 0.35, the largest hydrogen bonding distance. Compare the residence times with that on the hydrophobic sidechain. as it mentioned the -contact wouldnt include any H bonds between the groups. but i didnt understand what does OW states cause already there is an option for water. does this procedure be good for an residence time. -Aiswarya On Thu, Aug 25, 2011 at 5:18 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/08/2011 12:00 AM, aiswarya.pa...@gmail.com wrote: Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. So that's the autocorrelation of the existence function. Now you need a geometric criterion for existence. Note that g_hbond with well-constructed groups will calculate the autocorrelation of the existence function for an H-bond. See g_hbond -h. g_dist, some scripting and g_analyse might be necessary for other criteria. Mark Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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: Re: Antw: Re: [gmx-users] Hydrogen existence time
Dear Emanuel, Thank you so much for the pseudo-code, it made me understand the flow. from your code it shows that, your using distance and angle as an criteria to select a water molecule in just one one time frame. right?? i didnt get how to calculate the time of the frame. what programming should be applied and what for. Thanks, Aiswarya On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de wrote: Hello Aiswarya, Your program should look like this, in pseudo-code: pseudo-code: do n_frames_of_your_trajectory g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent (second-group)).ndx -o atm-pair.out -d your-distance-value -b (one frame of your trajectory) -e (the same frame) processing the atm-pair.out list and write them into an index file : 1.ndx, with each water in one group take just these atoms and residues, which are at your specific distance at your 'location' do measure the angle in relation to your protein for this frame for each specified water g_angle -f traj.trr -s .tpr -n 1.ndx -b (one frame of your trajectory) -e (the same frame) enddo read the angles from the output take just the one water with specific angle out of your list. (By using g_mindist -d , and g_angle you specify one specific point in relation to your protein) (By using -b and -e you specify one specific time) save the residue number of this water and your frame calculate the time of this frame enddo now you have an array of residue numbers at this particular location for each time analyse this array, then you know the maximum frame-time of one water-molecule at this specific location. You will not get any information about one particular time - just an average. This must be your residence time. Your application needs some little programming. ** 24.08.11 18.14 Uhr Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- *From: * aiswarya.pa...@gmail.com *Date: *Wed, 24 Aug 2011 16:13:05 + *To: *Gromacs mailgmx-users@gromacs.org *ReplyTo: * aiswarya.pa...@gmail.com *Subject: *Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- *From: * Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de *Date: *Wed, 24 Aug 2011 16:16:37 +0200 *To: *aiswarya.pa...@gmail.com; gmx-users@gromacs.org *Subject: *Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. -- means : The residence time is low. Small diffusion-coeff. -- means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. aiswarya.pa...@gmail.com 24.08.11 16.01 Uhr Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!** -- 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] Conversion of gromacs trajectory file
Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Conversion of gromacs trajectory file
Hi Justin, Thank for the quick response. I would try out your script for the conversion. Best, Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Discussion list for GROMACS users ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Conversion of gromacs trajectory file Sent: 24 Aug 2011 5:35 PM aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does the opposite (mdcrd to .xtc) linked from my site: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It's a bit awkward, but does the job. Perhaps you can reverse-engineer it for your purpose. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Hydrogen existence time
Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Hydrogen existence time
Dear Justin, So what does the hydrogen bond existence state? Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Hydrogen existence time
Any idea how can I calculate the residence time of water. Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:58 PM aiswarya.pa...@gmail.com wrote: Dear Justin, So what does the hydrogen bond existence state? The length of time for which a given hydrogen bond exists (i.e. satisfies the geometrical criteria in the context of some particular partner group). -Justin Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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: Antw: Re: [gmx-users] Hydrogen existence time
Dear Emanuel, Iam following what you have mentioned earlier. But as you said hydrogen bond correlation time gives the average hydrogen bond existence time. So I confused understanding whether an H Bond existence time would give me the residence time. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Sender: gmx-users-boun...@gromacs.org Date: Wed, 24 Aug 2011 15:42:11 To: gmx-users@gromacs.org; jalem...@vt.edu Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] Hydrogen existence time -- 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: [gmx-users] Hydrogen existence time
Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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: Antw: Re: [gmx-users] Hydrogen existence time
Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Date: Wed, 24 Aug 2011 16:16:37 To: aiswarya.pa...@gmail.com; gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. -- means : The residence time is low. Small diffusion-coeff. -- means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. 24.08.11 16.01 Uhr Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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: Antw: Re: [gmx-users] Hydrogen existence time
Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 To: Gromacs mailgmx-users@gromacs.org Reply-To: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Date: Wed, 24 Aug 2011 16:16:37 To: aiswarya.pa...@gmail.com; gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. -- means : The residence time is low. Small diffusion-coeff. -- means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. 24.08.11 16.01 Uhr Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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: Antw: Re: [gmx-users] calculate residence time for a protein complex
Mark, Sorry for the trouble. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Sender: gmx-users-boun...@gromacs.org Date: Mon, 22 Aug 2011 12:36:02 To: gmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] calculate residence time for a protein complex -- 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: Antw: Re: [gmx-users] calculate residence time for a protein complex
Dear Emanuel, Thank you so much for the response. I did the H bond count using the g_hbond. After this these H bond are correlated against time right?? I just want to make sure I got it right. And more over I should give a distance constrain so as to give me the existence of water at a time. I just want to be more clear on the correlation function of H bonding. Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Sender: gmx-users-boun...@gromacs.org Date: Mon, 22 Aug 2011 12:36:02 To: gmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] calculate residence time for a protein complex -- 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] calculate residence time for a protein complex
Hi, I have simulated a protein complex and now i would like to know the residing water molecules between the protein complex. g_hbond and trjorder helps in giving the number of hydrogen bonds and distance. but is this the residence time calculation. please help me with this. there few posts given in the archives regarding the residence time which is not very clear to me. but will the residence time calculation same for single protein and complex Thank you, Aiswarya -- 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] calculate residence time for a protein complex
Hi, I have simulated a protein complex and now i would like to know the residing water molecules between the protein complex. g_hbond and trjorder helps in giving the number of hydrogen bonds and distance. but is this the residence time calculation. please help me with this. there few posts given in the archives regarding the residence time which is not very clear to me. but will the residence time calculation same for single protein and complex Thank you, Aiswarya -- 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