Re: [gmx-users] Removing Water from Final Simulation
... and see http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volumefor prevention cure. Mark On Mon, Jun 3, 2013 at 3:47 AM, Dallas Warren dallas.war...@monash.eduwrote: trjconv for trajectories editconf for coordinate files Along with an appropriately generated index file (using make_ndx) which contains the molecules you want in the output within a single group. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Removing Water from Final Simulation Hi GMX users! I just completed my first 30 ns simulation and would to remove all water molecules from the resulting .gro and trajectory files for the sake of my HDD. Does anyone know how to do this? Cheers, Parker -- 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] About the binary identical results by restarting from the checkpoint file
On Sun, Jun 2, 2013 at 10:37 PM, Cuiying Jian cuiying_j...@hotmail.comwrote: Hi GROMACS Users, These days, I am testing restarting simulaitions with .cpt files. I already set nlist=1 in the .mdp file. I can restart my simulations (which are stopped manually) with the following commands (version 4.0.7): mpiexec mdrun_s_mpi -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod -reprod is used to force binary identical simulaitons. During the restarted simulations, same number of processors are used as that in the simulation interrupted. The only case, in which I can get binary identical results with those from the continuous simulations (which are not stopped manually), is for SPC water molecules. Any other molecules (like -heptane), I can never get binary identical results with those from the continuous simulations. I also try to get new .tpr files by: tpbconv_s -s md.tpr -f md.trr -e md.edr -c md_c.tpr -cont and then: mpiexec mdrun_s_mpi -v -s md_c.tpr -cpt 0 -cpi md.cpt -deffnm md_c -reprod But I still cannot get binary identical results. I also test the simulations with only one processor and binary identical results are still not obtained. Using double precision does not solve the problems. I think that the above problems are caused by some information may not be stored during the running of the simulations. That seems likely. The leading candidate would be a random number generator you're using for a stochastic integrator. Your .mdp file would have been useful. On the other hand, if I run two independent simulations using the exactly same number of processors, the same commands and the same input files, i.e. mpiexec mdrun_s_mpi -v -s md.tpr -deffnm md -reprod I can always get binary identical results from these two independent simulations. I understand that MD is chaotic and if we run simulation for enough long time, simulation results should converge. Also, there are factors which may affect the reproducibility as described in the GROMACS website. But for my purpose, I am curious about whether there are certain methods through which I can get binary identical results from restarted simulations and continuous simulations. Thanks a lot. There are ways to be fully reproducible, but probably not every combination of algorithms has that property. 4.0.7 is so old no problem will be fixed, unless it can also be shown in 4.6 ;-) 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] Pressure coupling
Probably. See manual 7.3.15. Semiisotropic with some zero compressibilities is probably what you want. Mark On Sun, Jun 2, 2013 at 9:33 PM, Marcelo Vanean vanea...@gmail.com wrote: Hello everyone. I want to know if can be applied pressure coupling only in the z direction, allowing the edges x and y simulation box with fixed size. -- 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] fattyn acid parameter in OPLSAA forcefield
Please email just gmx-users, not the owner or request addresses :-) On Sun, Jun 2, 2013 at 9:37 PM, fatemeh ramezani fr_...@yahoo.com wrote: Hi all I want to simulate protein-fatty acid-AU complexs by OPLSAA force field. But OPLSAA force field, hasn't any parameter for fatty acid. Can I use CHARMM fatty acid parameters in OPLSAA force field? No. See http://www.gromacs.org/Documentation/How-tos/Parametrization Anyone has better suggestion? Read widely on similar efforts. Be prepared for a lengthy parameterization process if nobody has done this kind of system before. 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] Re: umbrella sampling for two polymer interaction
Sorry, my writing was not really excat. If you use a reference group, the force / potential acting on the pulled group is always relative to the reference group. If you use 'pull_geometry = distance' the origin potential is always in the distance 'pull_init1' along the vector from the reference group to the pulled group. (assuming the pulling velocity is zero, else there would be an additional contribution). Imagine an MD step. Both molecules have moved. 1) Calculate new origin of the umbrella potential 2) Calculate the forces 3) Let only these forces act which are allowed from 'pull_dim = X Y Z' Some cases: Y Y Y - Move the pulled group to the origin of umbrella potential Y N N - let the force act only along the X-axis N N N - let no force act 4) do next MD step and start again at (1) So if one component is N the pulled group can move freely along this axis (relative to the reference group). Just imagine the step of the pull-code as a step which happens after a MD step and remember that both step are independed from each other (ok, both use the coordinates from the previous step, but they are n that sense independend from each other as two following MD steps in a normal simulation). This means, that in the MD step, both groups can move freely, as there is now umbrella potential. But in the pull-code step, we switch the potential on. Sorry confused. In AMBER I remember I did once methane-methane interaction,just distance based umbrella sampling. But there I did not provide any direction. So should it not be N N N in Gromacs if I want to allow them freely move in xyz. With 'pull_gemoetry' you tell GROMACS how it should setup the pulling potential. With 'distance' it don't needs an explizit pull_vector, since GROMACS uses the vector connecting both groups. Am 31.05.2013 21:04, schrieb gmx-users-requ...@gromacs.org: Dear Thomas, Thanks a lot again for great reply. Please clarify this also, If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane You never want to use the pull-code and 'pull_dim = N N N' This would mean that there is no force acting between your two groups. Then one could have skipped using the pull-code... So keeping Y N N will allow free movement in yz plane. So if I want A B to move freely in xyz but just keep them separated by some distance with spring const (just like two balloons tied to each other flying in air). Sorry confused. In AMBER I remember I did once methane-methane interaction, just distance based umbrella sampling. But there I did not provide any direction. So should it not be N N N in Gromacs if I want to allow them freely move in xyz. thanks, On Fri, May 31, 2013 at 8:53 PM, Thomas Schlesierschl...@uni-mainz.dewrote: For comments to your questions see below. More general: (somewhat longer than i wanted. Hope you find some answers here) Imagine two interacting particles A and B which are alinged to the x-axis. We take A as the reference group, B as pulled group and put the origin of the umbrella potential on top of B (pull_start=yes). Simulation starts - A and B moves. Pull-code step: From A we calculate the new position of the umbrella potential, this is unequal to B, since B moved and our reference point move. Now we have a force acting on B, 'pull_dim' controls in which directions the force acts. With 'Y Y Y' B is pulled towards the origin of the umbrella potential (and with this to the position it should have relative to A). If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane. In the end one would get a structure where A and B have the right distance in the x-axis but are miles away from each other in the yz-plane. Now imagine we pull B away from A. Since MD simulations normally separete the movement of the center of mass of the system, it would look like A and B would move away from a middle point. (Interchanging A and B should give the same results). Think in your case (doing umbrella sampling) the mdp-file you suggested would be most appropiate (with 'pull_start=yes' and 'pull_ngroups=1'). This gives you a potential which fixes the distance between the two proteins. One thing you should be aware is that if you restrain the distance in 3d, you have to account for entropic effects (see also the GROMACS manual). If you restrain the system only in one direction, these don't arise. Think this is the reason why one sees some work with umbrella sampling were the restraint works only in one direction. Am 31.05.2013 17:20, schriebgmx-users-requ...@gromacs.org: Dear Thomas, Thanks a lot for your time and nice explanation. I was not able to get specially the pull_start flag but now its quite clear. I feel sorry, that should be pull_dim = N N N in my case. Also I will be much thankful if you please can help me to make understand following: STOP!!! You never want to use the pull-code and 'pull_dim = N
Re: [gmx-users] structure alignement :g_rmsdist
Hi, THanks for your answers. Just for be sure, with g_rmsdit the reference structure correspond to the frame at time 0?? Because in the manual the rmsd equation show that reference structure correspond to the time t=0 but the help doesn't confirm. THanks a lot for your help, 2013/6/2 Tsjerk Wassenaar tsje...@gmail.com Hi Nawel, g_rmsdist calculates the RMSD of distances, and distances are invariant to translation and rotation. Cheers, Tsjerk On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. I already seen the help for this command but when its write g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that* no fit is needed* like in standard RMS deviation as computed by g_rms what mean excatly no fit is needed?? Because when you compute a RMSD calculation its necessary to align the structure so I am a bit confused when its write no fit is needed. Fit is processed directly by the command? I am sorry I am little confused. THanks a lot 2013/6/2 Mark Abraham mark.j.abra...@gmail.com See g_rmsdist -h Mark On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele nawel.m...@gmail.com wrote: Hello everyone. During the calculation of the rms with g_rmsdist command , the reference and the current structure are aligned before calculating?? Regards, -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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 -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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. -- 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 -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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] structure alignement :g_rmsdist
Hi Nawel, The reference distances are computed from the reference structure provided with the option -s. Cheers, Tsjerk On Mon, Jun 3, 2013 at 12:39 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. Just for be sure, with g_rmsdit the reference structure correspond to the frame at time 0?? Because in the manual the rmsd equation show that reference structure correspond to the time t=0 but the help doesn't confirm. THanks a lot for your help, 2013/6/2 Tsjerk Wassenaar tsje...@gmail.com Hi Nawel, g_rmsdist calculates the RMSD of distances, and distances are invariant to translation and rotation. Cheers, Tsjerk On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. I already seen the help for this command but when its write g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that* no fit is needed* like in standard RMS deviation as computed by g_rms what mean excatly no fit is needed?? Because when you compute a RMSD calculation its necessary to align the structure so I am a bit confused when its write no fit is needed. Fit is processed directly by the command? I am sorry I am little confused. THanks a lot 2013/6/2 Mark Abraham mark.j.abra...@gmail.com See g_rmsdist -h Mark On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele nawel.m...@gmail.com wrote: Hello everyone. During the calculation of the rms with g_rmsdist command , the reference and the current structure are aligned before calculating?? Regards, -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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 -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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. -- 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 -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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. -- 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] structure alignement :g_rmsdist
Thanks, the tpr file using by -s option contains the starting structure of the simulation so the reference structure correspond to the first structure. Thanks a lot , 2013/6/3 Tsjerk Wassenaar tsje...@gmail.com Hi Nawel, The reference distances are computed from the reference structure provided with the option -s. Cheers, Tsjerk On Mon, Jun 3, 2013 at 12:39 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. Just for be sure, with g_rmsdit the reference structure correspond to the frame at time 0?? Because in the manual the rmsd equation show that reference structure correspond to the time t=0 but the help doesn't confirm. THanks a lot for your help, 2013/6/2 Tsjerk Wassenaar tsje...@gmail.com Hi Nawel, g_rmsdist calculates the RMSD of distances, and distances are invariant to translation and rotation. Cheers, Tsjerk On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. I already seen the help for this command but when its write g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that* no fit is needed* like in standard RMS deviation as computed by g_rms what mean excatly no fit is needed?? Because when you compute a RMSD calculation its necessary to align the structure so I am a bit confused when its write no fit is needed. Fit is processed directly by the command? I am sorry I am little confused. THanks a lot 2013/6/2 Mark Abraham mark.j.abra...@gmail.com See g_rmsdist -h Mark On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele nawel.m...@gmail.com wrote: Hello everyone. During the calculation of the rms with g_rmsdist command , the reference and the current structure are aligned before calculating?? Regards, -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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 -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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. -- 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 -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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. -- 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 -- *Mlle* Mele Nawel Master 2 In Silico Drug Design
Re: [gmx-users] Vritual Sites and simulation time-step
Mark, I've performed 50 ns simulation of water-soluble protein with and without VS. As the consequence I've observed similar behavior of both systems in case of secondfary structure conservation as well as overal degree of conformational dynamics. Also I didnt observed any fluctuation in energy and temperature (using SD as the thermostat and 2ps coupling). Is there any other Gromacs build-in tools on what I should paid more attention during investigation stability of the system with VS ? James 2013/6/2 Mark Abraham mark.j.abra...@gmail.com On Sun, Jun 2, 2013 at 4:56 PM, James Starlight jmsstarli...@gmail.com wrote: Mark, could you also provide me with some examples when usage of VS could give artifacts in simulations ? I don't know of any particular examples. This kind of thing tends to be tested ad hoc - how far can the time step be pushed and still reproduce some relevant observable? See GROMACS generalized Born paper. There is certainly some scope for people to investigate and publish such findings. See, for example, recent publications by Michael Shirts. In particular I'm interesting in usage of VS on hydrogens with membrane proteins. I really don't know anything there :-) I imagine people often use a united-atom lipid for a reason. 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] gmx 4.6.2 segementation fault (core dump)
Hi there, trying to set up gmx-4.6.2, compiled with cuda 5.0.35 and gcc 4.7.2 on fedora linux, but it only gives me a segementation fault (core dump) on mdrun startup. Same compiling options on gmx 4.6.1 gives me a running mdrun. Did anyone encounter the same problem? Thanks, Johannes -- 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] How to compile/run Gromacs on native Infiniband?
Dear all, My cluster has a FDR (56 Gb/s) Infiniband network. It is well known that there is a big difference between using IPoIB (IP over IB) with a normal sockets application and using native InfiniBand with an application that has been coded directly to the native IB verbs interface. The latter one gets much higher throughput and lower latency, while spending less CPU on networking. Therefore, I wonder if Gromacs has the native IB verbs interface. If so, how to compile and run Gromacs on native Infiniband? Any suggestions will be appreciated. Best Regards, Bert -- 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] CG angle distribution
Dear Gmx Users, I am building coarse-grained model for my protein. I group them int0 5-10 atoms. I wish to reproduce atomistic equilibrium angles as well as the spring constant. Shall I use g_angle -od option and calulate distributions? Then I will use equilibrium th0 as the centre of the gaussian distribution and adjust spring constant to match this curve? Please, advise. Steven -- 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] frame
Hi, if I run 20ns MD, and want to get the pdb at 19532ps trjconv -s md_0_1.tpr -f md_0_1.xtc -o bovin19532.gro -dt 1 -b 19532 -e 19532 editconf -f bovin19532.gro -o bovin19532.pdb If is it right? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-tp5008727.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] frame
better to convert ur frames in a time (ps) and use trjconv -dump to write out the frame. -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475 email: johan...@picb.ac.cn and Heidelberg Institut for Theoretical Studies HITS gGmbH Schloß-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone: +49-6221-533254 fax: +49 6221 533298 email: johannes.wag...@h-its.org http://www.h-its.org _ Amtsgericht Mannheim / HRB 337446 Managing Directors: Dr. h.c. Klaus Tschira Prof. Dr.-Ing. Andreas Reuter On 03.06.2013, at 15:33, maggin maggin.c...@gmail.com wrote: Hi, if I run 20ns MD, and want to get the pdb at 19532ps trjconv -s md_0_1.tpr -f md_0_1.xtc -o bovin19532.gro -dt 1 -b 19532 -e 19532 editconf -f bovin19532.gro -o bovin19532.pdb If is it right? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-tp5008727.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] using previous window restart file
Dear All, (Sorry for long mail!) (Thanks Thomas Schlesier for clarifying previous umbrella queries) I wish to run umbrella samplings using restart file of previous window. e.g. initial distance between A (reference) and B (pulled group) is 1 nm (10 Angs) then I intend to run 10 windows after each 1 Angstrom. Due to some reasons I want to use restart file of previous window, so if suppose 1st window (10 Angstrom window) is done then I will use last restart file of 1st window for 2nd window (9 Angstrom window) (This is different from Justin's tutorial in which initial configurations are generated in single pulling experiment). In such case as I said I want to use last restart of 1st Window for 2nd window so obviously the distance will not be exactly 9 Angstrom between A and B for 1st window restart file. What approach I should use for adjusting initial distance being 9 Angstrom to get initial configuration for 2nd window Knowing the distance between A and B in the restart file of 1st window (say 'x') then for second window y = 9 - x (where x can be or 9), First approach: pull_rate1 = (y/1000) or even slower Second approach: pull_init1 = y pull_rate1 = 0.0 Please Note for both the cases I can use pull_vec1 or pull rates (- or +) for positive or negative relative movement to get exact 9 Angstrom window distance regards, Jiomm -- 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: gmx 4.6 mpi installation through openmpi?
Hello all, I have a very similar problem, but compiling both Gromacs 4.6 and 4.6.1 with cmake and MPI support (no problems with non-MPI installation). I have cmake version 2.8.7, openmpi version 1.4.1, and I am using gcc version 4.6.3 in a linux Ubuntu 4.6.3. I use the cmake options: cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi A summary of the output given by this command is: CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version 3.2) -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 -- Configuring done -- Generating done -- Build files have been written to: /home/smith/gromacs-4.6 I believe that not having CUDA installed is not a problem, as I do not plan to run in GPU, and nowhere in the installation manual says that it is obligatory. After running make, the simulation stops with the following message: Linking C shared library libgmx_mpi.so [ 53%] Built target gmx Scanning dependencies of target gromacs_include_links [ 53%] Generating gromacs [ 53%] Built target gromacs_include_links Scanning dependencies of target template [ 53%] Building C object share/template/CMakeFiles/template.dir/template.c.o Linking C executable template ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__mth_i_dfloatuk' ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__builtin_va_gparg1' ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__pgdbg_stub' collect2: ld returned 1 exit status make[2]: *** [share/template/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 It looks like I lack one library somehow, but I do not know which one. I tried to install fftw before installing gromacs, and tried with both shared and dynamic libraries with the same result. Can anybody help? Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-mpi-installation-through-openmpi-tp5006975p5008730.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] gmx 4.6.2 segementation fault (core dump)
Thanks for reporting this. he best would be a redmine bug with a tpr, command line invocation for reproduction as well log output to see what software and hardware configuration are you using. Cheers, -- Szilárd On Mon, Jun 3, 2013 at 2:46 PM, Johannes Wagner johannes.wag...@h-its.org wrote: Hi there, trying to set up gmx-4.6.2, compiled with cuda 5.0.35 and gcc 4.7.2 on fedora linux, but it only gives me a segementation fault (core dump) on mdrun startup. Same compiling options on gmx 4.6.1 gives me a running mdrun. Did anyone encounter the same problem? Thanks, Johannes -- 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] gmx 4.6.2 segementation fault (core dump)
hi, thanks for the prompt replies ~/programs/gromacs-4.6.2/bin$ ./mdrun -version Program: ./mdrun Gromacs version:VERSION 4.6.2 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Fri May 31 18:44:32 CEST 2013 Built by: xx...@-its.org [CMAKE] Build OS/arch: Linux 3.8.8-100.fc17.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-3550 CPU @ 3.30GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/lib64/ccache/cc GNU cc (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2) C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -march=core-avx-i -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/lib64/ccache/c++ GNU c++ (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2) C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA driver:5.0 CUDA runtime: 5.0 ~/programs/gromacs-4.6.2/bin/mdrun -o gpu.log -s gpu.tpr -v Back Off! I just backed up md.log to ./#md.log.1# Reading file gpu.tpr, VERSION 4.6.2 (single precision) Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GT 640, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected for this run: #0 Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'triazole' 10 steps,100.0 ps. Segmentation fault (core dumped) .log file: 1,1Anfang Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1.004 Coulomb: 1 LJ: 1 System total charge: 0.000 Generated table with 1002 data points for Ewald. Tabscale = 500 points/nm Generated table with 1002 data points for LJ6. Tabscale = 500 points/nm Generated table with 1002 data points for LJ12. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 LJ12. Tabscale = 500 points/nm Using CUDA 8x8 non-bonded kernels Potential shift: LJ r^-12: 1.000 r^-6 1.000, Ewald 1.000e-05 Initialized non-bonded Ewald correction tables, spacing: 6.52e-04 size: 1536 Removing pbc first time Pinning threads with an auto-selected logical core stride of 1 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest PLEASE READ AND CITE THE FOLLOWING REFERENCE G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 --- Thank You --- There are: 18206 Atoms Initial temperature: 299.372 K Started mdrun on node 0 Mon Jun 3 16:09:59 2013 Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.04376e+042.58927e+049.76653e+001.50764e+02 -5.89359e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential -2.69867e+05 -3.86496e+04 -4.94959e+043.97160e+03 -3.08139e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 6.80836e+04 -2.40055e+052.99864e+02 -1.42021e+02 thats basically it. not much information, hence my email here in this list… cheers, Johannes -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475 email: johan...@picb.ac.cn and Heidelberg Institut for Theoretical Studies HITS gGmbH Schloß-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone: +49-6221-533254 fax: +49 6221 533298 email: johannes.wag...@h-its.org http://www.h-its.org _ Amtsgericht Mannheim / HRB 337446 Managing Directors: Dr. h.c. Klaus
Re: [gmx-users] gmx 4.6.2 segementation fault (core dump)
I can't reproduce it on a very similar hardware and software configuration. Can you provide a tpr? Is the segfault reproducible with multiple configurations? Does mdrun work without GPUs (-nb cpu or GMX_DISABLE_GPU_DETECTION=1 env. var)? -- Szilárd On Mon, Jun 3, 2013 at 4:12 PM, Johannes Wagner johannes.wag...@h-its.org wrote: hi, thanks for the prompt replies ~/programs/gromacs-4.6.2/bin$ ./mdrun -version Program: ./mdrun Gromacs version:VERSION 4.6.2 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Fri May 31 18:44:32 CEST 2013 Built by: xx...@-its.org [CMAKE] Build OS/arch: Linux 3.8.8-100.fc17.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-3550 CPU @ 3.30GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/lib64/ccache/cc GNU cc (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2) C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -march=core-avx-i -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/lib64/ccache/c++ GNU c++ (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2) C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA driver:5.0 CUDA runtime: 5.0 ~/programs/gromacs-4.6.2/bin/mdrun -o gpu.log -s gpu.tpr -v Back Off! I just backed up md.log to ./#md.log.1# Reading file gpu.tpr, VERSION 4.6.2 (single precision) Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GT 640, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected for this run: #0 Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'triazole' 10 steps,100.0 ps. Segmentation fault (core dumped) .log file: 1,1Anfang Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1.004 Coulomb: 1 LJ: 1 System total charge: 0.000 Generated table with 1002 data points for Ewald. Tabscale = 500 points/nm Generated table with 1002 data points for LJ6. Tabscale = 500 points/nm Generated table with 1002 data points for LJ12. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 LJ12. Tabscale = 500 points/nm Using CUDA 8x8 non-bonded kernels Potential shift: LJ r^-12: 1.000 r^-6 1.000, Ewald 1.000e-05 Initialized non-bonded Ewald correction tables, spacing: 6.52e-04 size: 1536 Removing pbc first time Pinning threads with an auto-selected logical core stride of 1 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest PLEASE READ AND CITE THE FOLLOWING REFERENCE G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 --- Thank You --- There are: 18206 Atoms Initial temperature: 299.372 K Started mdrun on node 0 Mon Jun 3 16:09:59 2013 Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.04376e+042.58927e+049.76653e+001.50764e+02 -5.89359e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential -2.69867e+05 -3.86496e+04 -4.94959e+043.97160e+03 -3.08139e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 6.80836e+04 -2.40055e+052.99864e+02 -1.42021e+02 thats basically it. not much information, hence my email here in this list… cheers, Johannes -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology
[gmx-users] Setting total simulation time
Hi GMX-users, If I wanted to run a 1 ns simulation take snapshots every 1 ps would these be the correct input parameters? Thanks! ; Run parameters integrator = md nsteps = 50 dt = 0.002 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 -- 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: frame
How to convert ur frames in a time (ps)? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: gmx 4.6 mpi installation through openmpi?
That looks like there's a PGI compiler getting used at some point (perhaps the internal FFTW build is picking up the CC environment var? I forget how that gets its compiler!). If you do find * -name config.log then perhaps you can see in that file what the FFTW build thinks about its compiler. Mark On Mon, Jun 3, 2013 at 4:00 PM, escajarro juan-manuel.casti...@mv.uni-kl.de wrote: Hello all, I have a very similar problem, but compiling both Gromacs 4.6 and 4.6.1 with cmake and MPI support (no problems with non-MPI installation). I have cmake version 2.8.7, openmpi version 1.4.1, and I am using gcc version 4.6.3 in a linux Ubuntu 4.6.3. I use the cmake options: cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi A summary of the output given by this command is: CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version 3.2) -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 -- Configuring done -- Generating done -- Build files have been written to: /home/smith/gromacs-4.6 I believe that not having CUDA installed is not a problem, as I do not plan to run in GPU, and nowhere in the installation manual says that it is obligatory. After running make, the simulation stops with the following message: Linking C shared library libgmx_mpi.so [ 53%] Built target gmx Scanning dependencies of target gromacs_include_links [ 53%] Generating gromacs [ 53%] Built target gromacs_include_links Scanning dependencies of target template [ 53%] Building C object share/template/CMakeFiles/template.dir/template.c.o Linking C executable template ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__mth_i_dfloatuk' ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__builtin_va_gparg1' ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__pgdbg_stub' collect2: ld returned 1 exit status make[2]: *** [share/template/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 It looks like I lack one library somehow, but I do not know which one. I tried to install fftw before installing gromacs, and tried with both shared and dynamic libraries with the same result. Can anybody help? Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-mpi-installation-through-openmpi-tp5006975p5008730.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Setting total simulation time
Try smaller numbers and periods for a test run, and see the machinery work. gmxcheck on the output files is your friend! Mark On Mon, Jun 3, 2013 at 4:40 PM, Parker de Waal parker.dewaa...@kzoo.eduwrote: Hi GMX-users, If I wanted to run a 1 ns simulation take snapshots every 1 ps would these be the correct input parameters? Thanks! ; Run parameters integrator = md nsteps = 50 dt = 0.002 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 -- 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] Re: frame
You chose your time step... ;-) Mark On Mon, Jun 3, 2013 at 4:50 PM, maggin maggin.c...@gmail.com wrote: How to convert ur frames in a time (ps)? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: frame
well, you basically just did it… 20ns is 20,000ps. so trjconv -dump 19532 -s xxx -f xxx -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475 email: johan...@picb.ac.cn and Heidelberg Institut for Theoretical Studies HITS gGmbH Schloß-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone: +49-6221-533254 fax: +49 6221 533298 email: johannes.wag...@h-its.org http://www.h-its.org _ Amtsgericht Mannheim / HRB 337446 Managing Directors: Dr. h.c. Klaus Tschira Prof. Dr.-Ing. Andreas Reuter On 03.06.2013, at 16:50, maggin maggin.c...@gmail.com wrote: How to convert ur frames in a time (ps)? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] frame in VMD
Hi, I use VMD to see GROMACS trajectory, I run 20ns md, there are 10,000,000 step, when load to VMD, it total 2777 frames. I don't known if there something wrong in it ? How to get the frame about 19532ps? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-in-VMD-tp5008737.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] frame in VMD
Probably, VMD tries to load the whole trajectory into memory, and that runs out. You should be using trjconv to get a particular frame. Also see http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume to avoid generating redundant information to throw away later. Mark On Mon, Jun 3, 2013 at 5:03 PM, maggin maggin.c...@gmail.com wrote: Hi, I use VMD to see GROMACS trajectory, I run 20ns md, there are 10,000,000 step, when load to VMD, it total 2777 frames. I don't known if there something wrong in it ? How to get the frame about 19532ps? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-in-VMD-tp5008737.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Vritual Sites and simulation time-step
Hi James, Not related to the integration stability as such, but since the vsites affect the hydrogens by definition perhaps g_hbond can reveal systematic differences between simulations with and without vsites. I believe Feenstra et al did this in the paper describing vsites in the first place. Erik On 3 Jun 2013, at 14:03, James Starlight jmsstarli...@gmail.com wrote: Mark, I've performed 50 ns simulation of water-soluble protein with and without VS. As the consequence I've observed similar behavior of both systems in case of secondfary structure conservation as well as overal degree of conformational dynamics. Also I didnt observed any fluctuation in energy and temperature (using SD as the thermostat and 2ps coupling). Is there any other Gromacs build-in tools on what I should paid more attention during investigation stability of the system with VS ? James 2013/6/2 Mark Abraham mark.j.abra...@gmail.com On Sun, Jun 2, 2013 at 4:56 PM, James Starlight jmsstarli...@gmail.com wrote: Mark, could you also provide me with some examples when usage of VS could give artifacts in simulations ? I don't know of any particular examples. This kind of thing tends to be tested ad hoc - how far can the time step be pushed and still reproduce some relevant observable? See GROMACS generalized Born paper. There is certainly some scope for people to investigate and publish such findings. See, for example, recent publications by Michael Shirts. In particular I'm interesting in usage of VS on hydrogens with membrane proteins. I really don't know anything there :-) I imagine people often use a united-atom lipid for a reason. 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 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] Creating a monolayer from Martini bilayer
Hello everybody, I am a new user to Gromacs and am working on lipid simulations with the Martini forcefield. The Martini website provides a pre-equilibrated DPPC bilayer, and I was wondering if there were any told that would allow me to convert this bilayer into a monolayer. For periodic boundary conditions to work, I was thinking of a stack that would go like Water Lipid Heads Tails Vacuum Tails Lipid Heads Water Is there any way to split apart the provided bilayer using some combination of Gromacs tools and introduce a space of at least 10 nm which is apparently the distance needed for the tails to not interact with each other? If there is no way of simply splitting the bilayer, what would you recommend for creating a simulation of lipid monolayers from a single DPPC molecule? I feel like I could use genconf but it might require too much equilibration. I am hopeful that there is some way of simply working with the provided bilayer. Any help would be appreciated! -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Setting total simulation time
Thanks Mark, Using the above I ran gmxcheck -f nvt.trr Here is the resulting out put Last frame500 time 1000.000 Item#frames Timestep (ps) Step 5012 Time 5012 Lambda 5012 Coords 5012 Velocities 5012 Forces 0 Box5012 Does this mean I can interpret this as 1 ns of simulation with output every 2 ps? Also I thought when I assigned values for output at 1000, such as nstxout = 1000, that I would get an write of data every 1 ps? I'm moderately confused! Parker On Mon, Jun 3, 2013 at 11:02 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Try smaller numbers and periods for a test run, and see the machinery work. gmxcheck on the output files is your friend! Mark On Mon, Jun 3, 2013 at 4:40 PM, Parker de Waal parker.dewaa...@kzoo.edu wrote: Hi GMX-users, If I wanted to run a 1 ns simulation take snapshots every 1 ps would these be the correct input parameters? Thanks! ; Run parameters integrator = md nsteps = 50 dt = 0.002 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 -- 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] Creating a monolayer from Martini bilayer
You could try packmol or the MembraneEditor. http://www.cellmicrocosmos.org/index_cm2.php Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 03.06.2013 um 18:43 schrieb Neha nshafi...@wesleyan.edu: Hello everybody, I am a new user to Gromacs and am working on lipid simulations with the Martini forcefield. The Martini website provides a pre-equilibrated DPPC bilayer, and I was wondering if there were any told that would allow me to convert this bilayer into a monolayer. For periodic boundary conditions to work, I was thinking of a stack that would go like Water Lipid Heads Tails Vacuum Tails Lipid Heads Water Is there any way to split apart the provided bilayer using some combination of Gromacs tools and introduce a space of at least 10 nm which is apparently the distance needed for the tails to not interact with each other? If there is no way of simply splitting the bilayer, what would you recommend for creating a simulation of lipid monolayers from a single DPPC molecule? I feel like I could use genconf but it might require too much equilibration. I am hopeful that there is some way of simply working with the provided bilayer. Any help would be appreciated! -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Creating a monolayer from Martini bilayer
Hey :) Just center the bilayer around z=0, solvate and put all molecules in the box with trjconv. Then add 10 to the PBC Z-component (third number from the last line in the .gro file). Cheers, Tsjerk On Mon, Jun 3, 2013 at 6:55 PM, Gunther Lukat g.lu...@gmx.net wrote: You could try packmol or the MembraneEditor. http://www.cellmicrocosmos.org/index_cm2.php Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 03.06.2013 um 18:43 schrieb Neha nshafi...@wesleyan.edu: Hello everybody, I am a new user to Gromacs and am working on lipid simulations with the Martini forcefield. The Martini website provides a pre-equilibrated DPPC bilayer, and I was wondering if there were any told that would allow me to convert this bilayer into a monolayer. For periodic boundary conditions to work, I was thinking of a stack that would go like Water Lipid Heads Tails Vacuum Tails Lipid Heads Water Is there any way to split apart the provided bilayer using some combination of Gromacs tools and introduce a space of at least 10 nm which is apparently the distance needed for the tails to not interact with each other? If there is no way of simply splitting the bilayer, what would you recommend for creating a simulation of lipid monolayers from a single DPPC molecule? I feel like I could use genconf but it might require too much equilibration. I am hopeful that there is some way of simply working with the provided bilayer. Any help would be appreciated! -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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: About the binary identical results by restarting from the checkpoint file
Hi Mark, Thanks for your reply. I tested restarting simulations with .cpt files by GROMACS 4.6.1. and the problems are still there, i.e. I cannot get binary identical results from restarted simulations with those from continuous simulations. The command I used for restarting is as the following (Only one processor is used during the simulations.): mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod For further information, I attach my original .mdp file below: constraints = all-bonds ; convert all bonds to constraints. integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 2 ns. nstcomm = 10; frequency for center of mass motion removal. nstxout= 5 ; collect data every 10.0 ps. nstxtcout = 5 ; frequency to write coordinate to xtc trajectory. nstvout= 5 ; frequency to write velocities to output trajectory. nstfout = 5 ; frequency to write forces to output trajectory. nstlog = 5 ; frequency to write energies to log file. nstenergy= 5 ; frequency to write energies to energy file. nstlist = 1 ; frequency to update the neighbor list. ns_type = grid rlist = 1.4 coulombtype = PME rcoulomb= 1.4 vdwtype = cut-off rvdw = 1.4 pme_order = 8 ; use 6,8 or 10 when running in parallel ewald_rtol = 1e-5 optimize_fft= yes DispCorr = no ; don't apply any correction ;open LINCS constraint_algorithm = LINCS lincs_order = 4 ;highest order in the expansion of the constraint coupling matrix lincs_warnangle = 30 ;maximum angle that a bond can rotate before LINCS will complain lincs_iter = 1;number of iterations to correct for a rotational lengthening in LINCS ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps = HEP ref_t = 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; generate velocity is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 Is there something wrong with my .mdp file or my command? Thanks a lot. Cheers, Cuiying On Sun, Jun 2, 2013 at 10:37 PM, Cuiying Jian cuiying_j...@hotmail.comwrote: Hi GROMACS Users, These days, I am testing restarting simulaitions with .cpt files. I already set nlist=1 in the .mdp file. I can restart my simulations (which are stopped manually) with the following commands (version 4.0.7): mpiexec mdrun_s_mpi -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod -reprod is used to force binary identical simulaitons. During the restarted simulations, same number of processors are used as that in the simulation interrupted. The only case, in which I can get binary identical results with those from the continuous simulations (which are not stopped manually), is for SPC water molecules. Any other molecules (like -heptane), I can never get binary identical results with those from the continuous simulations. I also try to get new .tpr files by: tpbconv_s -s md.tpr -f md.trr -e md.edr -c md_c.tpr -cont and then: mpiexec mdrun_s_mpi -v -s md_c.tpr -cpt 0 -cpi md.cpt -deffnm md_c -reprod But I still cannot get binary identical results. I also test the simulations with only one processor and binary identical results are still not obtained. Using double precision does not solve the problems. I think that the above problems are caused by some information may not be stored during the running of the simulations. That seems likely. The leading candidate would be a random number generator you're using for a stochastic integrator. Your .mdp file would have been useful. On the other hand, if I run two independent simulations using the exactly same number of processors, the same commands and the same input files, i.e. mpiexec mdrun_s_mpi -v -s md.tpr -deffnm md -reprod I can always get binary identical results from these two independent simulations. I understand that MD is chaotic and if we run simulation for enough long time, simulation results should converge. Also, there are factors which may affect the reproducibility as described in the GROMACS website. But for my
Re: [gmx-users] Creating a monolayer from Martini bilayer
On 03.06.2013 18:43, Neha wrote: I am a new user to Gromacs and am working on lipid simulations with the Martini forcefield. The Martini website provides a pre-equilibrated DPPC bilayer, and I was wondering if there were any told that would allow me to convert this bilayer into a monolayer. For periodic boundary conditions to work, I was thinking of a stack that would go like Water Lipid Heads Tails Vacuum Tails Lipid Heads Water Is this the 128 DPPC system from http://md.chem.rug.nl/cgmartini/index.php/downloads/example-applications/66-dppc-membrane (2x 64 DPPC + 2000 W)? Is there any way to split apart the provided bilayer using some combination of Gromacs tools and introduce a space of at least 10 nm which is apparently the distance needed for the tails to not interact with each other? The layers are, 'afaics', somehow interdigitated and placed in a box normal to z with a z height of 10nm and centered at about 5nm. They are not sorted (first 64 lower, secod 64 upper layer). If there is no way of simply splitting the bilayer, what would you recommend for creating a simulation of lipid monolayers from a single DPPC molecule? I feel like I could use genconf but it might require too much equilibration. I am hopeful that there is some way of simply working with the provided bilayer. What I would do: write a simple script, read 12 lines (one molecule) and check for the z coordinate of the NC3 type (first entry of each 12 line record). Then, decide: - if NC3[z] 6 then add 1.0 to all 12 z coordinates (nm) - if NC3[z] 4 then keep it write the 12 lines back to another file, either modified or unmodified. next 12 lines/molecule (128 times total) Then, the waters. This is somehow arbitrary. Maybe you could check if each water's (W) z coordinate is below 5, so keep it - or above 5, so move it up. This will, of course, require some steepest descent minimization afterwards. -- 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: About the binary identical results by restarting from the checkpoint file
On Mon, Jun 3, 2013 at 6:59 PM, Cuiying Jian cuiying_j...@hotmail.comwrote: Hi Mark, Thanks for your reply. I tested restarting simulations with .cpt files by GROMACS 4.6.1. and the problems are still there, i.e. I cannot get binary identical results from restarted simulations with those from continuous simulations. The command I used for restarting is as the following (Only one processor is used during the simulations.): mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod This is not generally enough to generate a serial run in 4.6, by the way. GROMACS tries very hard to automatically use all the resources available in the best way. See mdrun -h for various -nt* options, and consult the pre-step-0 part of the .log file for feedback. For further information, I attach my original .mdp file below: constraints = all-bonds ; convert all bonds to constraints. integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 2 ns. nstcomm = 10; frequency for center of mass motion removal. nstxout= 5 ; collect data every 10.0 ps. nstxtcout = 5 ; frequency to write coordinate to xtc trajectory. nstvout= 5 ; frequency to write velocities to output trajectory. nstfout = 5 ; frequency to write forces to output trajectory. nstlog = 5 ; frequency to write energies to log file. nstenergy= 5 ; frequency to write energies to energy file. nstlist = 1 ; frequency to update the neighbor list. ns_type = grid rlist = 1.4 coulombtype = PME rcoulomb= 1.4 vdwtype = cut-off rvdw = 1.4 pme_order = 8 ; use 6,8 or 10 when running in parallel ewald_rtol = 1e-5 optimize_fft= yes DispCorr = no ; don't apply any correction ;open LINCS constraint_algorithm = LINCS lincs_order = 4 ;highest order in the expansion of the constraint coupling matrix lincs_warnangle = 30 ;maximum angle that a bond can rotate before LINCS will complain lincs_iter = 1;number of iterations to correct for a rotational lengthening in LINCS ; Temperature coupling is on Tcoupl = v-rescale This coupling algorithm has a stochastic component, and at least at some points in history the random number generator was either not checkpointed properly, or not propagated in parallel properly. I'm not sure offhand if any of that has been fixed yet (I doubt it), but you can test (parts of) this hypothesis by using Berendsen (in any GROMACS 4.x), or really being sure you've run a single thread. If Berendsen is fully reproducible, then the RNG is the issue. While that's irritating, it probably won't get fixed before GROMACS 5 (as a side effect of other stuff going on). Mark tau_t = 0.1 tc-grps = HEP ref_t = 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; generate velocity is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 Is there something wrong with my .mdp file or my command? Thanks a lot. Cheers, Cuiying On Sun, Jun 2, 2013 at 10:37 PM, Cuiying Jian cuiying_j...@hotmail.com wrote: Hi GROMACS Users, These days, I am testing restarting simulaitions with .cpt files. I already set nlist=1 in the .mdp file. I can restart my simulations (which are stopped manually) with the following commands (version 4.0.7): mpiexec mdrun_s_mpi -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod -reprod is used to force binary identical simulaitons. During the restarted simulations, same number of processors are used as that in the simulation interrupted. The only case, in which I can get binary identical results with those from the continuous simulations (which are not stopped manually), is for SPC water molecules. Any other molecules (like -heptane), I can never get binary identical results with those from the continuous simulations. I also try to get new .tpr files by: tpbconv_s -s md.tpr -f md.trr -e md.edr -c md_c.tpr -cont and then: mpiexec mdrun_s_mpi -v -s md_c.tpr -cpt 0 -cpi md.cpt -deffnm md_c -reprod But I still cannot get binary identical
[gmx-users] Re: Creating a monolayer from Martini bilayer
Hi, thank you so much! This way seems promising, however I am not sure how to center the bilayer around z=0. I thought I could use editconf but I might be confused as to how Gromacs centers its objects. If I put -center 0 0 0 does that mean the bilayer is centered around z = 0? Also I thought that trjconv only dealt with trajectory files. What I have right now is a structure file, a topology file and an map file. After I have solvated, I will still only have a new structure file, so what would the trjconv be acting on? Thank you so much for helping out a newbie! Hey :) Just center the bilayer around z=0, solvate and put all molecules in the box with trjconv. Then add 10 to the PBC Z-component (third number from the last line in the .gro file). Cheers, Tsjerk -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008747.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Creating a monolayer from Martini bilayer
Hi Neha, A single structure is like a trajectory with only one frame :p trjconv works on those as well. Right, set the center at 0,0,0 and choose the lipids as group for centering. Cheers, Tsjerk On Mon, Jun 3, 2013 at 7:31 PM, Neha nshafi...@wesleyan.edu wrote: Hi, thank you so much! This way seems promising, however I am not sure how to center the bilayer around z=0. I thought I could use editconf but I might be confused as to how Gromacs centers its objects. If I put -center 0 0 0 does that mean the bilayer is centered around z = 0? Also I thought that trjconv only dealt with trajectory files. What I have right now is a structure file, a topology file and an map file. After I have solvated, I will still only have a new structure file, so what would the trjconv be acting on? Thank you so much for helping out a newbie! Hey :) Just center the bilayer around z=0, solvate and put all molecules in the box with trjconv. Then add 10 to the PBC Z-component (third number from the last line in the .gro file). Cheers, Tsjerk -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008747.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. -- 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] How to compile/run Gromacs on native Infiniband?
There's no ibverbs support, s o pick your favorite/best MPI implementation, more than that you can't do. -- Szilárd On Mon, Jun 3, 2013 at 2:54 PM, Bert bert.u...@gmail.com wrote: Dear all, My cluster has a FDR (56 Gb/s) Infiniband network. It is well known that there is a big difference between using IPoIB (IP over IB) with a normal sockets application and using native InfiniBand with an application that has been coded directly to the native IB verbs interface. The latter one gets much higher throughput and lower latency, while spending less CPU on networking. Therefore, I wonder if Gromacs has the native IB verbs interface. If so, how to compile and run Gromacs on native Infiniband? Any suggestions will be appreciated. Best Regards, Bert -- 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: Creating a monolayer from Martini bilayer
Hi Tsjerk, Thank you so much for being so patient! I have yet another question. The membrane I got from the Martini website already has water in it. Do I need to add more water and if so why? Also how exactly do I use trjconv to put all molecules in the box? Sorry for being so annoying need a lot of elaboration! Tsjerk Wassenaar wrote Hi Neha, A single structure is like a trajectory with only one frame :p trjconv works on those as well. Right, set the center at 0,0,0 and choose the lipids as group for centering. Cheers, Tsjerk On Mon, Jun 3, 2013 at 7:31 PM, Neha lt; nshafique@ gt; wrote: Hi, thank you so much! This way seems promising, however I am not sure how to center the bilayer around z=0. I thought I could use editconf but I might be confused as to how Gromacs centers its objects. If I put -center 0 0 0 does that mean the bilayer is centered around z = 0? Also I thought that trjconv only dealt with trajectory files. What I have right now is a structure file, a topology file and an map file. After I have solvated, I will still only have a new structure file, so what would the trjconv be acting on? Thank you so much for helping out a newbie! Hey :) Just center the bilayer around z=0, solvate and put all molecules in the box with trjconv. Then add 10 to the PBC Z-component (third number from the last line in the .gro file). Cheers, Tsjerk -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008747.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008751.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] CG angle distribution
In my experience parametrizing with the Martini forcefield that works fine. You might have to do it in a iterative manner though, since non-bonded (VDW) iteractions might shift the equilibrium with respect to the value you set (unless you exclude all the problematic non-bonded interactions, of course.) Djurre From: Steven Neumann s.neuman...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 3 June 2013, 15:11 Subject: [gmx-users] CG angle distribution Dear Gmx Users, I am building coarse-grained model for my protein. I group them int0 5-10 atoms. I wish to reproduce atomistic equilibrium angles as well as the spring constant. Shall I use g_angle -od option and calulate distributions? Then I will use equilibrium th0 as the centre of the gaussian distribution and adjust spring constant to match this curve? Please, advise. Steven -- 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] Re: Creating a monolayer from Martini bilayer
Hi Neha, You can use trjconv with option -pbc mol to put all molecules in the box. If you want a vacuum, you probably don't want to add more water. But just play with it and see what comes out. CG simulations are fast enough for that kind of trial-and-error. Cheers, Tsjerk On Mon, Jun 3, 2013 at 8:26 PM, Neha nshafi...@wesleyan.edu wrote: Hi Tsjerk, Thank you so much for being so patient! I have yet another question. The membrane I got from the Martini website already has water in it. Do I need to add more water and if so why? Also how exactly do I use trjconv to put all molecules in the box? Sorry for being so annoying need a lot of elaboration! Tsjerk Wassenaar wrote Hi Neha, A single structure is like a trajectory with only one frame :p trjconv works on those as well. Right, set the center at 0,0,0 and choose the lipids as group for centering. Cheers, Tsjerk On Mon, Jun 3, 2013 at 7:31 PM, Neha lt; nshafique@ gt; wrote: Hi, thank you so much! This way seems promising, however I am not sure how to center the bilayer around z=0. I thought I could use editconf but I might be confused as to how Gromacs centers its objects. If I put -center 0 0 0 does that mean the bilayer is centered around z = 0? Also I thought that trjconv only dealt with trajectory files. What I have right now is a structure file, a topology file and an map file. After I have solvated, I will still only have a new structure file, so what would the trjconv be acting on? Thank you so much for helping out a newbie! Hey :) Just center the bilayer around z=0, solvate and put all molecules in the box with trjconv. Then add 10 to the PBC Z-component (third number from the last line in the .gro file). Cheers, Tsjerk -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008747.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008751.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. -- 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: Have your ever got a real NVE simulation (good energy conservation) in gromacs?
Hi guys I am using the set of parameters that I added before and I am getting energy Conservation THANKS John -- View this message in context: http://gromacs.5086.x6.nabble.com/Have-your-ever-got-a-real-NVE-simulation-good-energy-conservation-in-gromacs-tp5008501p5008756.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Specific question regarding SPC water model
Dear group, I am not sure how SPC energy actually works - is there really just one VdW interaction - just between two oxygen atoms? If so, when I place a hydrogen atom of one water molecule at the location of the oxygen from another water, the two oxygens are separated by the distance of H-O bond length i.e. 1.0A. The only VdW interaction is repulsive but finite (and equal ~4E6) but the electrostatic between H and O is -Inf = 1/0.0 What's wrong? Tim -- View this message in context: http://gromacs.5086.x6.nabble.com/Specific-question-regarding-SPC-water-model-tp5008757.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] eletrical filed issue
Dear Gromacs Developers or Users I am trying to apply a constant electrical field in Gromacs. I have made a charged fullerene in vacuum for testing. A electrical field in x direction is applied as: ; Electric field E-x = 1 2 1 However, the C60 moves only around 0.1 nm in 10 ps and then stops. My whole simulation period is 50 ps, in the following 40 ps, the C60 is just donging relaxation (likely). The first thing I have done is change the simulation step size from 1 fs to 0.5 fs, the simulation result is the same. Then, I have used the output conformation for another sequential simulation, then this happens again (another 0.1 nm in 10 ps). I also changed the box size to understand the surface effect of PBC, the difference is pretty small. The I removed the PBC, it didn't change, either. I have read the manual, it says: the first number: the number of cosines, only 1 is implemented (with frequency 0). However, I didn't quite get this 'frequency 0'. Does this mean there is one cosine in one second? Or one cosine in the whole simulation period? Or in one simulation time step? Another thing is I have checked the field output, it is as below. I guess this means constant force field, but not quite sure. Thanks a lot for your help! 0 2 0 0 #FIELD 0.0005 2 0 0 #FIELD 0.001 2 0 0 #FIELD 0.0015 2 0 0 #FIELD 0.002 2 0 0 #FIELD 0.0025 2 0 0 #FIELD 0.003 2 0 0 #FIELD 0.0035 2 0 0 #FIELD 0.004 2 0 0 #FIELD 0.0045 2 0 0 #FIELD 0.005 2 0 0 #FIELD 0.0055 2 0 0 #FIELD 0.006 2 0 0 #FIELD 0.0065 2 0 0 #FIELD 0.007 2 0 0 #FIELD 0.0075 2 0 0 #FIELD 0.008 2 0 0 #FIELD 0.0085 2 0 0 #FIELD 0.009 2 0 0 #FIELD 0.0095 2 0 0 #FIELD 0.01 2 0 0 #FIELD 0.0105 2 0 0 #FIELD 0.011 2 0 0 #FIELD 0.0115 2 0 0 #FIELD 0.012 2 0 0 #FIELD 0.0125 2 0 0 #FIELD 0.013 2 0 0 #FIELD 0.0135 2 0 0 #FIELD 0.014 2 0 0 #FIELD 0.0145 2 0 0 #FIELD 0.015 2 0 0 #FIELD 0.0155 2 0 0 #FIELD 0.016 2 0 0 #FIELD Tong Li email t14...@qut.edu.au -- 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] About low PH simulation of DPPC liposomes
Hi guys I need to simulate DPPC liposomes in low PH environment I have been looking for literature but I have not found a good option. Any suggestion?? Thanks John Michael -- View this message in context: http://gromacs.5086.x6.nabble.com/About-low-PH-simulation-of-DPPC-liposomes-tp5008759.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Specific question regarding SPC water model
Thanks for the answer. You're introducing atomic overlap and thus an energetic singularity from the infinite Coulombic attraction. Is there anything I can do with this? I posted this question because I'm trying to run a Monte Carlo simulation of a water box but eventually it finds the global energy minimum (-Inf) and can't escape from it. 2013/6/4 Justin Lemkul [via GROMACS] ml-node+s5086n5008760...@n6.nabble.com On 6/3/13 7:49 PM, tnorgd wrote: Dear group, I am not sure how SPC energy actually works - is there really just one VdW interaction - just between two oxygen atoms? Yep. A lot of force fields work like that. Given the size of H atoms relative to their heavy atom counterparts, the heavy atom to which they are connected generally governs the vdW interactions. If so, when I place a hydrogen atom of one water molecule at the location of the oxygen from another water, the two oxygens are separated by the distance of H-O bond length i.e. 1.0A. The only VdW interaction is repulsive but finite (and equal ~4E6) but the electrostatic between H and O is -Inf = 1/0.0 What's wrong? Nothing. That makes perfect sense. You're introducing atomic overlap and thus an energetic singularity from the infinite Coulombic attraction. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 list[hidden email]http://user/SendEmail.jtp?type=nodenode=5008760i=0 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5008760i=1. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Specific-question-regarding-SPC-water-model-tp5008757p5008760.html To unsubscribe from Specific question regarding SPC water model, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5008757code=dG5vcmdkQGdtYWlsLmNvbXw1MDA4NzU3fC0xODM5OTYzNjc= . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- 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] assembling trajectory files
Dear Gromacs users, I have simulated my system for two separately 10 ns with continuation option in order to continue the first 10 ns simulation. In order to do some analysis , I'm aiming to assemble both trajectory and tpr files. I would be very grateful if someone could help me in this issue. -- 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] assembling trajectory files
On 6/3/13 8:54 PM, Souilem Safa wrote: Dear Gromacs users, I have simulated my system for two separately 10 ns with continuation option in order to continue the first 10 ns simulation. In order to do some analysis , I'm aiming to assemble both trajectory and tpr files. I would be very grateful if someone could help me in this issue. trjcat concatenates trajectories. There is no need to concatenate .tpr files; there are no time-dependent quantities in them so it doesn't make sense to do so. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Specific question regarding SPC water model
On 6/3/13 8:12 PM, Someone Else wrote: Thanks for the answer. You're introducing atomic overlap and thus an energetic singularity from the infinite Coulombic attraction. Is there anything I can do with this? I posted this question because I'm trying to run a Monte Carlo simulation of a water box but eventually it finds the global energy minimum (-Inf) and can't escape from it. That sounds like something done outside of Gromacs, is it not? I would think that properly accounting for Coulombic interactions would have prevented this from occurring, but I don't do MC so I can't go beyond speculation. -Justin 2013/6/4 Justin Lemkul [via GROMACS] ml-node+s5086n5008760...@n6.nabble.com On 6/3/13 7:49 PM, tnorgd wrote: Dear group, I am not sure how SPC energy actually works - is there really just one VdW interaction - just between two oxygen atoms? Yep. A lot of force fields work like that. Given the size of H atoms relative to their heavy atom counterparts, the heavy atom to which they are connected generally governs the vdW interactions. If so, when I place a hydrogen atom of one water molecule at the location of the oxygen from another water, the two oxygens are separated by the distance of H-O bond length i.e. 1.0A. The only VdW interaction is repulsive but finite (and equal ~4E6) but the electrostatic between H and O is -Inf = 1/0.0 What's wrong? Nothing. That makes perfect sense. You're introducing atomic overlap and thus an energetic singularity from the infinite Coulombic attraction. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 list[hidden email]http://user/SendEmail.jtp?type=nodenode=5008760i=0 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5008760i=1. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Specific-question-regarding-SPC-water-model-tp5008757p5008760.html To unsubscribe from Specific question regarding SPC water model, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5008757code=dG5vcmdkQGdtYWlsLmNvbXw1MDA4NzU3fC0xODM5OTYzNjc= . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- Justin A. Lemkul, Ph.D. Research Scientist 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] assembling trajectory files
Dear Justin, Thank you very much for your quick reply, that is helpful to me On 4 June 2013 10:05, Justin Lemkul jalem...@vt.edu wrote: On 6/3/13 8:54 PM, Souilem Safa wrote: Dear Gromacs users, I have simulated my system for two separately 10 ns with continuation option in order to continue the first 10 ns simulation. In order to do some analysis , I'm aiming to assemble both trajectory and tpr files. I would be very grateful if someone could help me in this issue. trjcat concatenates trajectories. There is no need to concatenate .tpr files; there are no time-dependent quantities in them so it doesn't make sense to do so. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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] About Concatenation of several trajectory files
Dear Justin, Mark other gromacs users Thank you fro your previuos replies I need to concatenate several .trr , .xtc and .edr files . Is there is any gromacs tools availble ? or Is it enough to use cat command in Linux Thanks In ADVANCE -- 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] About Concatenation of several trajectory files
On 6/3/13 10:15 PM, vidhya sankar wrote: Dear Justin, Mark other gromacs users Thank you fro your previuos replies I need to concatenate several .trr , .xtc and .edr files . Is there is any gromacs tools availble ? or Is it enough to use cat command in Linux trjcat for .xtc and .trr and eneconv for .edr - the manual describes all of this. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: frame
hi, Wagner It works! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008768.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
