[gmx-users] Re.Importance of -rcon and -dd options when
On Wed, Mar 14, 2012 at 7:40 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Importance of -rcon and -dd options when using mdrun with mpi. (Mark Abraham) 2. clashes (Dariush Mohammadyani) 3. Re: clashes (Justin A. Lemkul) -- Message: 1 Date: Wed, 14 Mar 2012 23:21:34 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Importance of -rcon and -dd options when using mdrun with mpi. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f608d4e.10...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am running mdrun on single node with 8 CPU and getting following error Fatal error:- D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are connected via constraints from the neighbouring cells. This probably means your constraint length are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs order. The .log file has a detailed analysis of how DD is setting things up. You need to make sure that this output is sensible for your system. You should also desist from using P-R pressure coupling during equilibration (i.e. with velocity generation), as warned in the manual section on pressure coupling. Perhaps your system is blowing up. Mark Dear Mark, Thanks for the reply. I have successfully done the equilibration run ,while doing production run I am gettiing above error (almost after 10 ns run). Also It would be worth working if you explain the importance -rcon value and other things that I have asked . Regards, Pavan For solving this problem following are the attempts by me. *1] Decreasing grid cell size:-* As per the suggestion in error, I tried to decrease the grid cells by option -dd from 8 1 1 to 6 1 1 , it has thrown following error.. Fatal error:-The size of the DD grid (6) does not match the number of nodes(8). Can you please suggest any better way to overcome this for decreasing grid cell size. *2] -rcon option:* What is the correlation between the -rcon value with DD cell size(Directly or inversely proportional ) , for the problem entitled above what should be the strategy (to decrease or to increase rcon value). If one changes the -rcon value will it affect the lincs accuracy, or in other words the run will hold the same continuation or any change in it. For changing the -rcon value the reference of previous log file i.e. Estimated maximum distance required for p-lincs say 0.877, so one can increase than what has been estimated. *3] lincs_order and lincs_iter :* ** If we don't want to deteriorate the lincs accuracy (1+ lincs_iter)*lincs_order has to remain constant , In my case With lincs_order = 4 and lincs_iter =1 I got above error. So I decreased lincs _order (2) and increased lincs_iter(3) proportionally. What I am following is right or I have misunderstood it. If so please correct it. Can this value be fraction? Values which I have tried are relevant or very bad?** Please explain it. If the same problem can be solved by any other methodology please explain it. *Please see the mdp file details.* integrator= md nsteps = 1000 dt = 0.002 ; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout = 1000; xtc compressed trajectory output every 2 ps nstenergy = 1000; save energies every 2 ps nstlog = 1000; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb=
Re: [gmx-users] Re.Importance of -rcon and -dd options when
On 15/03/2012 5:36 PM, PAVAN PAYGHAN wrote: On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am running mdrun on single node with 8 CPU and getting following error Fatal error:- D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are connected via constraints from the neighbouring cells. This probably means your constraint length are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs order. The .log file has a detailed analysis of how DD is setting things up. You need to make sure that this output is sensible for your system. You should also desist from using P-R pressure coupling during equilibration (i.e. with velocity generation), as warned in the manual section on pressure coupling. Perhaps your system is blowing up. Mark Dear Mark, Thanks for the reply. I have successfully done the equilibration run ,while doing production run I am gettiing above error (almost after 10 ns run). Also It would be worth working if you explain the importance -rcon value and other things that I have asked . A description of your system, GROMACS version and objective are important to solving the problem. I don't think we've seen those. Nobody wants to spend time talking about DD options if you are trying to run a system with 1000 atoms on 8 processors. By not describing fully, you make it easy for people to not be bothered. Regards, Pavan For solving this problem following are the attempts by me. *1] Decreasing grid cell size:-* As per the suggestion in error, I tried to decrease the grid cells by option -dd from 8 1 1 to 6 1 1 , it has thrown following error.. Fatal error:-The size of the DD grid (6) does not match the number of nodes(8). Can you please suggest any better way to overcome this for decreasing grid cell size. You can't decrease the number of DD cells since you need one per processor. Maybe you are trying to parallelize a system that is too small for this number of processors, which brings us back to needing a description of your system. *2] -rcon option:* What is the correlation between the -rcon value with DD cell size(Directly or inversely proportional ) , for the problem entitled above what should be the strategy (to decrease or to increase rcon value). If one changes the -rcon value will it affect the lincs accuracy, or in other words the run will hold the same continuation or any change in it. For changing the -rcon value the reference of previous log file i.e. Estimated maximum distance required for p-lincs say 0.877, so one can increase than what has been estimated. You need to read mdrun -h about -rcon. You need to be trying to increase the ratio of cell size to constraint length, per the error message. *3] lincs_order and lincs_iter :* ** If we don't want to deteriorate the lincs accuracy (1+ lincs_iter)*lincs_order has to remain constant , In my case With lincs_order = 4 and lincs_iter =1 I got above error. So I decreased lincs _order (2) and increased lincs_iter(3) proportionally. What I am following is right or I have misunderstood it. If so please correct it. Can this value be fraction? The values must be integers. Values which I have tried are relevant or very bad?** That is a correct approach for maintaining LINCS accuracy and trying to decrease the required constraint length, however it may not help solve the underlying problem. Mark Please explain it. If the same problem can be solved by any other methodology please explain it. *Please see the mdp file details.* integrator= md nsteps = 1000 dt = 0.002 ; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout = 1000; xtc compressed trajectory output every 2 ps nstenergy = 1000; save energies every 2 ps nstlog = 1000; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) lincs_iter = 1 ; accuracy of LINCS
[gmx-users] Problems with simulation on multi-nodes cluster
Dear Gromacs Users! I have some problems with running my simulation on multi-modes station wich use open_MPI I've launch my jobs by means of that script. The below example of running work on 1 node ( 12 cpu). #!/bin/sh #PBS -N gromacs #PBS -l nodes=1:red:ppn=12 #PBS -V #PBS -o gromacs.out #PBS -e gromacs.err cd /globaltmp/xz/job_name grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on that cluster I have no problems with running of my jobs but when I try to use more than one nodes I've obtain error ( the example is attached in the gromacs.err file as well as mmd.mdp of that system). Another outcome of such multi-node simulation is that my job has been started but no calculation were done ( the name_of_my_job.log file was empty and no update of .trr file was seen ). Commonly this error occurs when I uses many nodes (8-10) Finally sometimes I've obtain some errors with the PME order ( this time I've used 3 nodes). The exactly error differs when I varry the number of nodes. Could you tell me whats wrong could be with my cluster? Thanks for help James gromacs.err Description: Binary data md.mdp Description: Binary data -- 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] Problems with simulation on multi-nodes cluster
On 15/03/2012 6:04 PM, James Starlight wrote: Dear Gromacs Users! I have some problems with running my simulation on multi-modes station wich use open_MPI I've launch my jobs by means of that script. The below example of running work on 1 node ( 12 cpu). #!/bin/sh #PBS -N gromacs #PBS -l nodes=1:red:ppn=12 #PBS -V #PBS -o gromacs.out #PBS -e gromacs.err cd /globaltmp/xz/job_name grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on that cluster I have no problems with running of my jobs but when I try to use more than one nodes I've obtain error ( the example is attached in the gromacs.err file as well as mmd.mdp of that system). Another outcome of such multi-node simulation is that my job has been started but no calculation were done ( the name_of_my_job.log file was empty and no update of .trr file was seen ). Commonly this error occurs when I uses many nodes (8-10) Finally sometimes I've obtain some errors with the PME order ( this time I've used 3 nodes). The exactly error differs when I varry the number of nodes. Could you tell me whats wrong could be with my cluster? The error message is quite explicit and is clearly nothing to do with GROMACS. Your invocation of mpiexec is malformed. You need to consult your local documentation. 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
Re: [gmx-users] Problems with simulation on multi-nodes cluster
Try separating your grompp run from your mpirun: You should not really be having the scheduler execute the grompp. Run your grompp step to generate a .tpr either on the head node or on your local machine (then copy it over to the cluster). (The -p that the scheduler is complaining about only appears in the grompp step, so don't have the scheduler run it). On 2012-03-15 10:04:49AM +0300, James Starlight wrote: Dear Gromacs Users! I have some problems with running my simulation on multi-modes station wich use open_MPI I've launch my jobs by means of that script. The below example of running work on 1 node ( 12 cpu). #!/bin/sh #PBS -N gromacs #PBS -l nodes=1:red:ppn=12 #PBS -V #PBS -o gromacs.out #PBS -e gromacs.err cd /globaltmp/xz/job_name grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on that cluster I have no problems with running of my jobs but when I try to use more than one nodes I've obtain error ( the example is attached in the gromacs.err file as well as mmd.mdp of that system). Another outcome of such multi-node simulation is that my job has been started but no calculation were done ( the name_of_my_job.log file was empty and no update of .trr file was seen ). Commonly this error occurs when I uses many nodes (8-10) Finally sometimes I've obtain some errors with the PME order ( this time I've used 3 nodes). The exactly error differs when I varry the number of nodes. Could you tell me whats wrong could be with my cluster? Thanks for help James -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Problems with simulation on multi-nodes cluster
On 15/03/2012 6:13 PM, Peter C. Lai wrote: Try separating your grompp run from your mpirun: You should not really be having the scheduler execute the grompp. Run your grompp step to generate a .tpr either on the head node or on your local machine (then copy it over to the cluster). Good advice. (The -p that the scheduler is complaining about only appears in the grompp step, so don't have the scheduler run it). grompp is running successfully, as you can see from the output I think mpiexec -np 12 is being interpreted as mpiexec -n 12 -p, and the process of separating the grompp stage from the mdrun stage would help make that clear - read documentation first, however. Mark On 2012-03-15 10:04:49AM +0300, James Starlight wrote: Dear Gromacs Users! I have some problems with running my simulation on multi-modes station wich use open_MPI I've launch my jobs by means of that script. The below example of running work on 1 node ( 12 cpu). #!/bin/sh #PBS -N gromacs #PBS -l nodes=1:red:ppn=12 #PBS -V #PBS -o gromacs.out #PBS -e gromacs.err cd /globaltmp/xz/job_name grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on that cluster I have no problems with running of my jobs but when I try to use more than one nodes I've obtain error ( the example is attached in the gromacs.err file as well as mmd.mdp of that system). Another outcome of such multi-node simulation is that my job has been started but no calculation were done ( the name_of_my_job.log file was empty and no update of .trr file was seen ). Commonly this error occurs when I uses many nodes (8-10) Finally sometimes I've obtain some errors with the PME order ( this time I've used 3 nodes). The exactly error differs when I varry the number of nodes. Could you tell me whats wrong could be with my cluster? Thanks for help James -- 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] Generation of the Distance Restraints
Mark, thanks again for explanation The force is the negative of the derivative of the potential with respect to the distance. So the force is also zero between r_0 and r_1. So if you want a distance to be restrained between 1 and 2 nm, set r_0=1 and r_1=2. That way the force is zero if the distance is satisfactory, and non-zero when it is not. I'm not quite understood the restrains definition in that case :( So in the above example the distance between 1 and 2 nm would be restrained and in accordance to the graph the forces will be zero. But in the range below 1 and 2 nm the forces would be increased in quadratic progression. So if I understood correctly only when atoms are not in the desired distance range forces will occur that must bring atoms to the desired distance. This is the opposite to the position restrains where the forses are constant to prevent movement of the atoms. Does it correct? I leave the choice of r_2 to you as an exercise So as I understood the forces occured after r_2 threshold must be extremely hight in comparison to gradually parabolic rise in the two others thresholds. In what exacly cases this rapid increase must be usefull in comparison to the gradually parabolic manner? Thanks again James Mark I must define R1=1 and R2=2 values from my example 1Rij2 to obtain quadratic restrain forces done in my distance range ( from 1 to 2 angstr). In other words this would restrains the i and j atom to the desired distance by the force wich would increased by the quadratic progresion upon distance will increased up to 2. Does it correct ? So the value R0 ( no forces= no restraints) must correspond to the values above and below my range. How the same range value for R0 could be defined ? JAmes 14 марта 2012 г. 3:42 пользователь Mark Abraham mark.abra...@anu.edu.auнаписал: I can't think of a clearer way to explain the functional form of the distance restraint than the given equation with an example graph of it nearby. You have some distance range that you want to see happen based on some external information. You need to choose the distance constants for that functional form to reproduce that in a way that you judge will work, given your initial distance. The linear regime above r_2 is useful for not having forces that are massively large (from a quadratic potential) far from the region of zero potential. Whether this is important depends on your starting configuration. I already answered this. http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html I've found only theoretical explanation of such possibility ( gradually increasing force constant during simulation). But I intresting in practical implementation. Could I do it in scope of single MDrun by some options in mdm fle or should I do step-by-step series of simulation with gradually changing forces appplied on the disres in each MDrun? Only step by step. Something like simulated annealing is only available for temperature variation. Mark James -- 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
[gmx-users] re: Unreadable trajectory [solved]
Writing 100,000 or 100.000 for 10 is prone to misinterpretation. Get out of the habit of using a thousands separator in scientific contexts :-) Thanks for the advice. 2. Remove contraints and repeat steps a-h. The problem I'm having is that I cannot visualize the trajectories from step 2.e) onwards with VMD simply segfaulting. While it may well be a VMD issue but I can't visualize the trajectory using ngmx (blank screen) either, so it's an issue either with my inputs or Gromacs. Your .mdp file is not writing any trajectory frames. Thanks for pointing that out! It was writing only information on velocities. I'm still getting used to the GROMACS way of doing things. One input (i.e. MDP file) for each run and all that. Mark I tried to use trjconv tool to adjust the centering or remove the PBC or save just the polymer residues but the utility always fails with: WARNING no output, last frame read at t=200. Checking the run log file did not reveal any errors. Checking the EDR file revealed no jumps in any of the enery terms. What's most surprising, is that I can visualize the GRO file that is generated at the end of the simulation. The relevant files are on the following links: - MDP: http://dl.dropbox.com/u/5761806/md-nvt-2-nofix.mdp - LOG: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.log - TPR: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.tpr I use GROMACS 4.5.5, the system is electrically neutral. To prepare a new TPR file a use the GRO file from the previous run. Don't, you're losing precision and introducing perturbations. grompp -t old.cpt is your friend. Mark Using that. Many many thanks! Thanks for the help, Jernej Zidar -- 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] Generation of the Distance Restraints
On 15/03/2012 7:06 PM, James Starlight wrote: Mark, thanks again for explanation The force is the negative of the derivative of the potential with respect to the distance. So the force is also zero between r_0 and r_1. So if you want a distance to be restrained between 1 and 2 nm, set r_0=1 and r_1=2. That way the force is zero if the distance is satisfactory, and non-zero when it is not. I'm not quite understood the restrains definition in that case :( So in the above example the distance between 1 and 2 nm would be restrained and in accordance to the graph the forces will be zero. The word restrained is ambiguous. Being in the region of zero force can be said to have been restrained, but being outside the region where force is action can be said to be being restrained. But in the range below 1 and 2 nm the forces would be increased in quadratic progression. Below 1nm and above 2nm. So if I understood correctly only when atoms are not in the desired distance range forces will occur that must bring atoms to the desired distance. This is the opposite to the position restrains where the forses are constant to prevent movement of the atoms. Does it correct? The forces in PR are not constant. See manual 4.3.1. The forces act in each case to return the distance/displacement to the region/point of zero force. A GROMACS position restraint is exactly like a GROMACS distance restraint to the original position with r_0==r_1 and r_2 infinite. I leave the choice of r_2 to you as an exercise So as I understood the forces occured after r_2 threshold must be extremely hight in comparison to gradually parabolic rise in the two others thresholds. In what exacly cases this rapid increase must be usefull in comparison to the gradually parabolic manner? A linear rise of the potential above r_2 is *more* gradual than a parabolic rise in the limit of large r, which is the important part, as Fig 4.13 makes clear... You still might be confusing potential and force in your mind. Get that clear :-) Mark Thanks again James Mark I must define R1=1 and R2=2 values from my example 1Rij2 to obtain quadratic restrain forces done in my distance range ( from 1 to 2 angstr). In other words this would restrains the i and j atom to the desired distance by the force wich would increased by the quadratic progresion upon distance will increased up to 2. Does it correct ? So the value R0 ( no forces= no restraints) must correspond to the values above and below my range. How the same range value for R0 could be defined ? JAmes 14 ? 2012 ?. 3:42 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au ???: I can't think of a clearer way to explain the functional form of the distance restraint than the given equation with an example graph of it nearby. You have some distance range that you want to see happen based on some external information. You need to choose the distance constants for that functional form to reproduce that in a way that you judge will work, given your initial distance. The linear regime above r_2 is useful for not having forces that are massively large (from a quadratic potential) far from the region of zero potential. Whether this is important depends on your starting configuration. I already answered this. http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html I've found only theoretical explanation of such possibility ( gradually increasing force constant during simulation). But I intresting in practical implementation. Could I do it in scope of single MDrun by some options in mdm fle or should I do step-by-step series of simulation with gradually changing forces appplied on the disres in each MDrun? Only step by step. Something like simulated annealing is only available for temperature variation. Mark James -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto: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
[gmx-users] 4.6 development version
Dear Gromacs user, since a few days we try to get the heterogeneous parallelization on a Dell blade server with Tesla M2090 GPUs to work using the worksheet on the page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization we only get the OpenMM pure GPU version with mdrun-gpu running. Actually is the heterogeneous parallelization already working in the development version you can download using the link on the page: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 and how can we get it running? Just adding the CMake variable GMX_GPU=ON when compiling mdrun did not enable the heterogeneous parallelization. We want to use the heterogeneous parallelization used in the 4.6 version to find out which is the optimal GPU/CPU ratio for our studied systems, since we soon have to buy machines for the upgrade of our cluster. Thanks a lot yours Sebastian -- 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] Umbrella_pull_simulation
I have added some new windows in mutant umbrella sampling which removes the sampling gap around 4 nm. Also I sampled more windows in the initial COM distance in the hope that I get energy minimum of profile well defined. I also did boot strapping for error estimates. The files can be assessed at http://www.freefilehosting.net/umbrellamut On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: The attached profile.xvg and histo.xvg are here. sorry for sending earlier mail without attachments Shahid Nayeem On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem msnay...@gmail.commailto: msnay...@gmail.com wrote: As suggested by you I added some new window and extended some simulation and I got the attached profile and histo file. Please see these files. Experimentally it is known that wt protein-protein interaction is stronger than the mutants. But I get here is reverse. what could be the possible reason for it. My profile.xvg and histo.xvg are right or they need more improvement. I wouldn't base any conclusions off of them. You have a sampling gap at just over 4 nm in the mutant simulations. More importantly, you do not have a defined energy minimum in the mutant windows so it is impossible to calculate a reliable value for DeltaG. Moreover, in the absence of any error estimates, you can't make any conclusions about these data. g_wham can generate error bars for you; I'd suggest you do it. -Justin Shahid Nayeem On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value is converged or not. If not then I should extend the simulation. I've already made numerous suggestions. The value in pullf.xvg is a consequence of the nature of the system. Looking at the interactions between your proteins, the stability of those proteins, etc. is far more informative, like you would for any simulation (even those that do not make use of the pull code). -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
[gmx-users] Re:g_energy g_enemat
-Does anyone off hand know the code (or line numbers ) for the actual energy calculations in either g_energy or g_enemat? Basically, it says it does not implement this yes (the error) or just does not print something out. Basically, I wanted to look at the code but didnt want to sit there for a week just trying to figure out what is what...all though I know thats a tall order. Basically, I can just use g_energy to extract the components for everything in my index files, and then do a spreadsheet based thing such as e^(file 33-file42)-(File 56-file77)= times a few hundred if I want to say look at dozens of amino acids over the trajectory plus total energy contributions. This however would yield the same results as if I had g_enemat working for the energy analysis thus... , has anyone gotten g_enemat to work for energy calculations (not just extraction of particular groups components). I searched the mailing list and found a dozen or so odd questions and answeres but no one mentiones the above. Although runing this over spread sheets generates a nice curve, so If anyone does have g_enemat running nicely, is the output simple a single figure or a .xvg file with the entire results based on a reference structure/energy? Sincerely, Stephan Lloyd Watkins -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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] 4.6 development version
You guys should hit up UniZurich, the have a series of 1024 CPUs in combination with several hundred GPU's in a cluster system. You could then test out some things, including scalability etc... Sincerely, Stephan Lloyd Watkins Original-Nachricht Datum: Thu, 15 Mar 2012 10:33:11 +0100 Von: SebastianWaltz sebastian.wa...@physik.uni-freiburg.de An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] 4.6 development version Dear Gromacs user, since a few days we try to get the heterogeneous parallelization on a Dell blade server with Tesla M2090 GPUs to work using the worksheet on the page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization we only get the OpenMM pure GPU version with mdrun-gpu running. Actually is the heterogeneous parallelization already working in the development version you can download using the link on the page: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 and how can we get it running? Just adding the CMake variable GMX_GPU=ON when compiling mdrun did not enable the heterogeneous parallelization. We want to use the heterogeneous parallelization used in the 4.6 version to find out which is the optimal GPU/CPU ratio for our studied systems, since we soon have to buy machines for the upgrade of our cluster. Thanks a lot yours Sebastian -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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] Umbrella_pull_simulation
The similar files for wt can be assesed at http://www.freefilehosting.net/umbrellawt I expected wild type binding energy to be less than mutant The command used for g_wham is g_wham_mpi_4.5.4 -it tpr-files.dat -if pullf-files.dat -o profile_mut.xvg -hist histo_mut.xvg -unit kCal -b 500 -nBootstrap 200 -bsres bsResult_mut.xvg -bsprof bsprofile_mut.xvg -ac I get the values exactly opposite to my expectation and unable to find out where I am wrong please suggest. Shahid Nayeem On Thu, Mar 15, 2012 at 3:31 PM, shahid nayeem msnay...@gmail.com wrote: I have added some new windows in mutant umbrella sampling which removes the sampling gap around 4 nm. Also I sampled more windows in the initial COM distance in the hope that I get energy minimum of profile well defined. I also did boot strapping for error estimates. The files can be assessed at http://www.freefilehosting.net/umbrellamut On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: The attached profile.xvg and histo.xvg are here. sorry for sending earlier mail without attachments Shahid Nayeem On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem msnay...@gmail.commailto: msnay...@gmail.com wrote: As suggested by you I added some new window and extended some simulation and I got the attached profile and histo file. Please see these files. Experimentally it is known that wt protein-protein interaction is stronger than the mutants. But I get here is reverse. what could be the possible reason for it. My profile.xvg and histo.xvg are right or they need more improvement. I wouldn't base any conclusions off of them. You have a sampling gap at just over 4 nm in the mutant simulations. More importantly, you do not have a defined energy minimum in the mutant windows so it is impossible to calculate a reliable value for DeltaG. Moreover, in the absence of any error estimates, you can't make any conclusions about these data. g_wham can generate error bars for you; I'd suggest you do it. -Justin Shahid Nayeem On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value is converged or not. If not then I should extend the simulation. I've already made numerous suggestions. The value in pullf.xvg is a consequence of the nature of the system. Looking at the interactions between your proteins, the stability of those proteins, etc. is far more informative, like you would for any simulation (even those that do not make use of the pull code). -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
[gmx-users] center the system on specific atoms type
Dear all, I am running a simulation in of a fullerene in different solvents. I would like to keep the fullerene somehow centred in the box, so I changed co comm_grps = System to mm_grps = FUL. If I do this the following error pop up: There are: 395 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... NOTE 1 [file short1.mdp]: 4728 atoms are not part of any of the VCM groups WARNING 1 [file short1.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. I am not sure if it is possible to tackle this Any suggestion would be welcomed. Best regards: R -- 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] center the system on specific atoms type
Hey :) Why would you want to keep it constant? It's asking for trouble. The fluctuations in a small part of the system like a fullerene molecule can be pretty large. If you try to correct the VCM of that bit only, you make it constantly bump into your solvent molecules. Especially if you have nstcomm = 10 or so, the shift may be considerable, and you may cause overlaps and crash your system. And that while it's so easy to center on the fullerene afterwards! Cheers, Tsjerk On Thu, Mar 15, 2012 at 11:16 AM, R.Perez Garcia r.perez.gar...@student.rug.nl wrote: Dear all, I am running a simulation in of a fullerene in different solvents. I would like to keep the fullerene somehow centred in the box, so I changed co comm_grps = System to mm_grps = FUL. If I do this the following error pop up: There are: 395 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... NOTE 1 [file short1.mdp]: 4728 atoms are not part of any of the VCM groups WARNING 1 [file short1.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. I am not sure if it is possible to tackle this Any suggestion would be welcomed. Best regards: R -- 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 -- 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
Re: [gmx-users] center the system on specific atoms type
Dear Tsjerk, Thank you for your answer! I dont like trouble, so, Ii will leave comm_grps = System... But, could you spare some comments how to center it afterwards? I dont know why but the fullerene like to spend a lot of time in the boundary (i.e. divided in two, where it is difficult to see). Best regards: R On 15-03-12, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) Why would you want to keep it constant? It's asking for trouble. The fluctuations in a small part of the system like a fullerene molecule can be pretty large. If you try to correct the VCM of that bit only, you make it constantly bump into your solvent molecules. Especially if you have nstcomm = 10 or so, the shift may be considerable, and you may cause overlaps and crash your system. And that while it's so easy to center on the fullerene afterwards! Cheers, Tsjerk On Thu, Mar 15, 2012 at 11:16 AM, R.Perez Garcia r.perez.gar...@student.rug.nl wrote: Dear all, I am running a simulation in of a fullerene in different solvents. I would like to keep the fullerene somehow centred in the box, so I changed co comm_grps = System to mm_grps = FUL. If I do this the following error pop up: There are: 395 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... NOTE 1 [file short1.mdp]: 4728 atoms are not part of any of the VCM groups WARNING 1 [file short1.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. I am not sure if it is possible to tackle this Any suggestion would be welcomed. Best regards: R -- 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 -- 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 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
Re: [gmx-users] center the system on specific atoms type
Hey :) There's a suggested trjconv workflow at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cheers, T. On Thu, Mar 15, 2012 at 11:41 AM, R.Perez Garcia r.perez.gar...@student.rug.nl wrote: Dear Tsjerk, Thank you for your answer! I dont like trouble, so, Ii will leave comm_grps = System... But, could you spare some comments how to center it afterwards? I dont know why but the fullerene like to spend a lot of time in the boundary (i.e. divided in two, where it is difficult to see). Best regards: R On 15-03-12, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) Why would you want to keep it constant? It's asking for trouble. The fluctuations in a small part of the system like a fullerene molecule can be pretty large. If you try to correct the VCM of that bit only, you make it constantly bump into your solvent molecules. Especially if you have nstcomm = 10 or so, the shift may be considerable, and you may cause overlaps and crash your system. And that while it's so easy to center on the fullerene afterwards! Cheers, Tsjerk On Thu, Mar 15, 2012 at 11:16 AM, R.Perez Garcia r.perez.gar...@student.rug.nl wrote: Dear all, I am running a simulation in of a fullerene in different solvents. I would like to keep the fullerene somehow centred in the box, so I changed co comm_grps = System to mm_grps = FUL. If I do this the following error pop up: There are: 395 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... NOTE 1 [file short1.mdp]: 4728 atoms are not part of any of the VCM groups WARNING 1 [file short1.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. I am not sure if it is possible to tackle this Any suggestion would be welcomed. Best regards: R -- 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 -- 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 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 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 -- 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] question about replica exchange
Dear gmx user If I may I have a specific question about replica exchange. I want to define different Hamiltonians for the different temperatures. It seems that the replica exchange can handle it. I wanted to ask if it's implemented in a general way so different Hamiltonians can be used for different temperatures? Thanks a lot, Best regards, Asaf -- 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] Problems with simulation on multi-nodes cluster
Mark, Peter, I've tried to do .tpr file on my local CPU and launch only mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm MD_100 on the cluster with 2 nodes. I see my job as working but when I've checking the MD_100.log (attached) file there are no any information about simulation steps in that file ( when I use just one node I see in that file step-by-step progression of my simulation like below wich was find in the same log file for ONE NODE simulation ): Started mdrun on node 0 Thu Mar 15 11:22:35 2012 Step Time Lambda 00.00.0 Grid: 12 x 9 x 12 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.32179e+043.27485e+032.53267e+034.06443e+026.15315e+04 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip. 4.12152e+04 -5.51788e+03 -1.70930e+03 -4.54886e+05 -1.46292e+05 Dis. Rest. D.R.Viol. (nm) Dih. Rest. PotentialKinetic En. 2.14240e-023.46794e+001.33793e+03 -4.84889e+059.88771e+04 Total Energy Conserved En.Temperature Pres. DC (bar) Pressure (bar) -3.86012e+05 -3.86012e+053.11520e+02 -1.14114e+023.67861e+02 Constr. rmsd 3.75854e-05 Step Time Lambda 20004.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.31741e+043.25280e+032.58442e+033.51371e+026.15913e+04 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip. 4.16349e+04 -5.53474e+03 -1.70930e+03 -4.56561e+05 -1.46485e+05 Dis. Rest. D.R.Viol. (nm) Dih. Rest. PotentialKinetic En. 4.78276e+013.38844e+009.82735e+00 -4.87644e+059.83280e+04 Total Energy Conserved En.Temperature Pres. DC (bar) Pressure (bar) -3.89316e+05 -3.87063e+053.09790e+02 -1.14114e+027.25905e+02 Constr. rmsd 1.88008e-05 end etc... What's wrong can be with multi-node computations? James 15 марта 2012 г. 11:25 пользователь Mark Abraham mark.abra...@anu.edu.auнаписал: On 15/03/2012 6:13 PM, Peter C. Lai wrote: Try separating your grompp run from your mpirun: You should not really be having the scheduler execute the grompp. Run your grompp step to generate a .tpr either on the head node or on your local machine (then copy it over to the cluster). Good advice. (The -p that the scheduler is complaining about only appears in the grompp step, so don't have the scheduler run it). grompp is running successfully, as you can see from the output I think mpiexec -np 12 is being interpreted as mpiexec -n 12 -p, and the process of separating the grompp stage from the mdrun stage would help make that clear - read documentation first, however. Mark On 2012-03-15 10:04:49AM +0300, James Starlight wrote: Dear Gromacs Users! I have some problems with running my simulation on multi-modes station wich use open_MPI I've launch my jobs by means of that script. The below example of running work on 1 node ( 12 cpu). #!/bin/sh #PBS -N gromacs #PBS -l nodes=1:red:ppn=12 #PBS -V #PBS -o gromacs.out #PBS -e gromacs.err cd /globaltmp/xz/job_name grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on that cluster I have no problems with running of my jobs but when I try to use more than one nodes I've obtain error ( the example is attached in the gromacs.err file as well as mmd.mdp of that system). Another outcome of such multi-node simulation is that my job has been started but no calculation were done ( the name_of_my_job.log file was empty and no update of .trr file was seen ). Commonly this error occurs when I uses many nodes (8-10) Finally sometimes I've obtain some errors with the PME order ( this time I've used 3 nodes). The exactly error differs when I varry the number of nodes. Could you tell me whats wrong could be with my cluster? Thanks for help James -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**
Re: [gmx-users] Umbrella_pull_simulation
shahid nayeem wrote: The similar files for wt can be assesed at http://www.freefilehosting.net/umbrellawt I expected wild type binding energy to be less than mutant The command used for g_wham is g_wham_mpi_4.5.4 -it tpr-files.dat -if pullf-files.dat -o profile_mut.xvg -hist histo_mut.xvg -unit kCal -b 500 -nBootstrap 200 -bsres bsResult_mut.xvg -bsprof bsprofile_mut.xvg -ac I get the values exactly opposite to my expectation and unable to find out where I am wrong please suggest. Determining flaws in one's model or improved ways of doing things is the hardest part about being a scientist. From the data presented, Gromacs has done its job and the results are reasonable. The fact that they don't align with expectations is something you will have to reconcile and only you are equipped to deal with it. No one on this list really knows enough about what you're doing to do your thinking for you, nor should they. The principal function of this list is to troubleshoot problems with Gromacs, of which there are none here. Good luck. -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
Re: [gmx-users] using MPI
If you are to run on a single node, then there's no need for mpi nowadays. mdrun uses all cores it can find anyway. If you need to split your calculation over many machines, however, you will need mpi. Best, Erik 15 mar 2012 kl. 04.50 skrev cuong nguyen: Dear Gromacs users, I prepare to run my simulations on the supercomputer on single node with 64 CPUs. Although I have seen on Gromacs Mannual suggesting to use MPI to parellel, I still haven't understood how to use this application and which commands I have to use. Please help me to deal with this? Many thanks and regards, Cuong -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Announcement: Large biomolecule benchmark report
Dear all, we proudly announce our third benchmarking report on (large) biomolecular systems carried out on various HPC platforms. We have expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS, LAMMPS and NAMD) and to five protein and protein-membrane systems ranging from 20 thousand to 3 million atoms. Please find the report on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx where we also offer the raw runtime data. We also plan to release the complete joint benchmark suite at a later date (as soon as we have access to a web server with sufficient storage space). We are open to any questions or comments related to our reports. Kind regards, Hannes Loeffler STFC Daresbury -- Scanned by iCritical. -- 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] Information on .mdp files
Lara Bunte wrote: Hello I want to learn how to create a .mdp file and learn what I can write in such a file and learn what the entries in this file are meaning. I did not find this in the manual. Could you please give me link or some source where I can find this information? The entirety of Chapter 7 in the manual is devoted to this information. There is an online manual (linked from the PDF manual), but it contains the same information and is present mostly for convenience. -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
AW: [gmx-users] Information on .mdp files
Hey. Well, it's always good to check the online documentation for such things. http://www.gromacs.org/Documentation/File_Formats/.mdp_File There you should find all information you need. Including examples and all usable keywords sorted by topic/task. Good luck, Felix -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Lara Bunte Gesendet: Donnerstag, 15. März 2012 16:24 An: gmx-users@gromacs.org Betreff: [gmx-users] Information on .mdp files Hello I want to learn how to create a .mdp file and learn what I can write in such a file and learn what the entries in this file are meaning. I did not find this in the manual. Could you please give me link or some source where I can find this information? Thanks and best greetings Lara -- 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] g_sas
Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In this way I can obtain Area per residue from res_area file and area per atom from atom_area file. How to get area per residue with data of area per atom from atom_area file? When I average on area per atoms for a selected residue, it doesn't correspond with area per residue for a selected residue from res_area. How to correlate area per residue for a selected residue with area per atoms for a selected residue? Thanks in advance, Afsaneh -- 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_sas
afsaneh maleki wrote: Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In this way I can obtain Area per residue from res_area file and area per atom from atom_area file. How to get area per residue with data of area per atom from atom_area file? When I average on area per atoms for a selected residue, it doesn't correspond with area per residue for a selected residue from res_area. It shouldn't. Averaging the areas per atom should not produce anything related to the constituent residue(s). The sum of the atom areas should yield the residue area. A quick look through the code seems to indicate that this is true, that is, the two quantities are not produced independently; residue area arises from atom area. -Justin How to correlate area per residue for a selected residue with area per atoms for a selected residue? Thanks in advance, Afsaneh -- 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] bug in g_msd
Hi all Is there a bug with g_msd when using the -mol flag. I have my own program that calculates the MSD. If I compare it with the gromacs utility for one system the curves are the exact same, however when I compare with another system th curves are very different. Someone else mentioned something similar a few days ago, so I was just wondering if this was the case. Cheers Gavin -- 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] [Fwd: bug in g_msd]
---BeginMessage--- Hi all Is there a bug with g_msd when using the -mol flag. I have my own program that calculates the MSD. If I compare it with the gromacs utility for one system the curves are the exact same, however when I compare with another system th curves are very different. Someone else mentioned something similar a few days ago, so I was just wondering if this was the case. Cheers Gavin ---End Message--- -- 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] bug in g_msd
Gavin Melaugh wrote: Hi all Is there a bug with g_msd when using the -mol flag. I have my own program that calculates the MSD. If I compare it with the gromacs utility for one system the curves are the exact same, however when I compare with another system th curves are very different. Someone else mentioned something similar a few days ago, so I was just wondering if this was the case. Sounds like this is a known issue: http://redmine.gromacs.org/issues/774 -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] Structural features for LINCS application
Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Thank you, Francesco -- 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] Announcement: Large biomolecule benchmark report
On 2012-03-15 14:37, Hannes Loeffler wrote: Dear all, we proudly announce our third benchmarking report on (large) biomolecular systems carried out on various HPC platforms. We have expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS, LAMMPS and NAMD) and to five protein and protein-membrane systems ranging from 20 thousand to 3 million atoms. Please find the report on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx where we also offer the raw runtime data. We also plan to release the complete joint benchmark suite at a later date (as soon as we have access to a web server with sufficient storage space). We are open to any questions or comments related to our reports. It looks very interesting, and having benchmarks done by independent researchers is the best way to avoid bias. The differences are quite revealing, but it's also good that you point to problems compiling gromacs. Is this going to be submitted for publication somewhere too? Thanks for doing this, it must have been quite a job! Kind regards, Hannes Loeffler STFC Daresbury -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] ***Extended deadline: March 26*** COMETS 2012 - 3rd International Track on Collaborative Modeling and Simulation - Call for Papers
* Deadline Extended to March 26, 2012 *** (Please accept our apologies if you receive multiple copies of this message) # IEEE WETICE 2012 3rd IEEE Track on Collaborative Modeling and Simulation (Comets 2012) in cooperation with AFIS (INCOSE France Chapter) MIMOS (Italian Association for MS) CALL FOR PAPERS # June 25-27, 2012, Toulouse (France) http://www.sel.uniroma2.it/comets12 # # Papers Due: March 26, 2012 Extended Deadline # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. # Modeling and Simulation (MS) is increasingly becoming a central activity in the design of new systems and in the analysis of existing systems because it enables designers and researchers to investigate systems behavior through virtual representations. For this reason, MS is gaining a primary role in many industrial and research fields, such as space, critical infrastructures, manufacturing, emergency management, biomedical systems and sustainable future. However, as the complexity of the investigated systems increases and the types of investigations widens, the cost of MS activities increases for the more complex models and for the communications among a wider number and variety of MS stakeholders (e.g., sub-domain experts, simulator users, simulator engineers, and final system users). To address the increasing costs of MS activities, collaborative technologies must be introduced to support these activities by fostering the sharing and reuse of models, by facilitating the communications among MS stakeholders, and more generally by integrating processes, tools and platforms. Aside from seeking applications of collaborative technologies to MS activities, the track seeks innovative contributions that deal with the application of MS practices to the design of collaborative environments. These environments are continuously becoming more complex, and therefore their design requires systematic approaches to meet the required quality of collaboration. This is important for two reasons: to reduce rework activities on the actual collaborative environment, and to maximize the productivity and the quality of the process the collaborative environment supports. MS offers the methodologies and tools for such investigations and therefore it can be used to improve the quality of collaborative environments. A non–exhaustive list of topics of interest includes: * collaborative environments for MS * collaborative Systems of Systems MS * workflow modelling for collaborative environments and processes * agent-based MS * collaborative distributed simulation * collaborative component-based MS * net-centric MS * web-based MS * model sharing and reuse * model building and evaluation * modeling and simulation of business processes * modeling for collaboration * simulation-based performance evaluation of collaborative networks * model-driven simulation engineering * domain specific languages for the simulation of collaborative environments * domain specific languages for collaborative MS * databases and repositories for MS * distributed virtual environments * virtual research environment for MS * collaborative DEVS MS To stimulate creativity, however, the track maintains a wider scope and invites interested researchers to present contributions that offer original perspectives on collaboration and MS. +++ On-Line Submissions and Publication +++ CoMetS'12 intends to bring together researchers and practitioners to discuss key issues, approaches, open problems, innovative applications and trends in the track research area. This year, we will accept submissions in two forms: (1) papers (2) poster and industrial presentations (1) Papers should contain original contributions not published or submitted elsewhere. Papers up to six pages (including figures, tables and references) can be submitted. Papers should follow the IEEE format, which is single spaced, two columns, 10 pt Times/Roman font. All submissions should be electronic (in PDF) and will be peer-reviewed by at least three program committee members. Accepted full papers will be included in the proceedings and published by the IEEE Computer Society Press (IEEE approval pending). Please note that at least one author for each accepted paper should register to attend WETICE 2012 (http://www.wetice.org) to have the paper published in the proceedings. (2) Posters should describe a practical, on-the-field, experience in any domain area using collaborative
[gmx-users] Re: on the RAM capacity needed for GROMACS
Dear All, Suppose I need to install the GROMACS in my laptop. Will you please tell me the requirement on the capacity of RAM? I still did not invent a system that would not run on my 8GB RAM laptop. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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: Energy exclusions for freeze groups, and the pressure
Hi, I am so sorry to bother you. If you have time, do you have any ideas or advice about my trouble below about implementing energy group exclusions to avoid spurious contribution to the pressure and virial due to frozen atoms? Thank you so very much! Andrew DeYoung Carnegie Mellon University Hi, I have a system containing two graphene sheets (with residue names GR1 and GR2, respectively) plus some liquid. I would like to hold the two graphene sheets fixed in space and observe the dynamics of the liquid around it. To hold the graphene sheets fixed in space, I used freeze groups: freezegrps = GR1 GR2 freezedim = Y Y Y Y Y Y ; freeze x, y z directions This indeed holds the sheets fixed in space, just as I want. However, the pressure increases dramatically, from about 10^3 bar with no frozen atoms to about 10^29 bar when the graphene sheets are frozen. I noticed that the manual says (http://manual.gromacs.org/current/online/mdp_opt.html#neq): To avoid spurious contibrutions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that frozen coordinates are not subject to pressure scaling. So, it seems that to avoid spurious contribution to the pressure, I need to exclude interactions between completely frozen atoms. I used the following directives in my .mdp file: energygrps = GR1 GR2 freezegrps = GR1 GR2 freezedim = Y Y Y Y Y Y ; freeze x, y z directions energygrp_excl = GR1 GR1 GR2 GR2 GR1 GR2 This series of directives, I think, should tell Gromacs to exclude the nonbonded interactions between atoms within GR1, between atoms within GR2, and between atoms in GR1 and in GR2. However, when I run g_energy to extract the (average) pressure (selecting Pressure from the menu in g_energy), it turns out that the pressure is the same with or without the energy group exclusion defined by my directive energygrp_excl above; the average pressure in each case is a whopping 6.91498*10^29 bar (and the RMSDs are the same, too). So it seems that the spurious contribution to the pressure described in the manual is not actually being removed by my energy exclusions. Can you please help me think what I may be doing wrong, or how I can otheriwse remove the spurious contribution to the pressure in the case of freeze groups? Or, is the key sentence in the manual actually Note that frozen coordinates are not subject to pressure scaling.? What does it mean that frozen coordinates are not subject to pressure scaling? Does this mean that the pressure is not computed for freeze groups? Thank you so very much for your time! I truly appreciate it. Andrew DeYoung Carnegie Mellon University -- 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] Announcement: Large biomolecule benchmark report
I fully agree with David, it's great to have independent benchmarks! In fact, already the the previous version of the report has been of great use for us, we have referred to the results in a few occasions. -- Szilárd On Thu, Mar 15, 2012 at 2:37 PM, Hannes Loeffler hannes.loeff...@stfc.ac.uk wrote: Dear all, we proudly announce our third benchmarking report on (large) biomolecular systems carried out on various HPC platforms. We have expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS, LAMMPS and NAMD) and to five protein and protein-membrane systems ranging from 20 thousand to 3 million atoms. Please find the report on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx where we also offer the raw runtime data. We also plan to release the complete joint benchmark suite at a later date (as soon as we have access to a web server with sufficient storage space). We are open to any questions or comments related to our reports. Kind regards, Hannes Loeffler STFC Daresbury -- Scanned by iCritical. -- 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
Re: [gmx-users] Structural features for LINCS application
On 16/03/2012 6:02 AM, Francesco Oteri wrote: Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Coupled constraints, such as you might have in a cluster, can be delicate. Equilibrating with a quite small time step can be necessary. 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
