Re: [gmx-users] Removing Water from Final Simulation
FYI you can also take the complement of an existing group with make_ndx using the ! symbol. e.g. if water is group 0, you could make a group of everything but water using: !0 This might be easier/more foolproof than concatenating all other groups when generating the appropriate index file as suggested in the previous email. Best, - Reid On Sun, Jun 2, 2013 at 10:40 PM, Dallas Warren wrote: > What group did you select from the list offered when you ran the script? > Did it include all of your molecules, minus water? Or did you just select > something like "Protein"? > > You need to run make_ndx and general a group that contains all of the > molecules you want. So you will want to do something like "1 | 2 | 3" when > running make_ndx What those numbers are depends on what is contained > within the gro file you feed it. > > 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 11:53 AM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Removing Water from Final Simulation > > > > Thanks Warren for your help, those were exactly the functions I was > > looking > > for! > > > > However I'm still experiencing a bit of trouble because my simulated > > protein contained a heme cofactor and it seems to only let me extract > > one > > object. > > > > Have you had any experience with this? > > > > Parker > > On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren > > wrote: > > > > > 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 > -- > 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 > -- Reid Van Lehn NSF/MIT Presidential Fellow Alfredo Alexander-Katz Research Group Ph.D Candidate - Materials Science -- gmx-users mailing listgmx-users@gromacs.
RE: [gmx-users] Removing Water from Final Simulation
What group did you select from the list offered when you ran the script? Did it include all of your molecules, minus water? Or did you just select something like "Protein"? You need to run make_ndx and general a group that contains all of the molecules you want. So you will want to do something like "1 | 2 | 3" when running make_ndx What those numbers are depends on what is contained within the gro file you feed it. 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 11:53 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Removing Water from Final Simulation > > Thanks Warren for your help, those were exactly the functions I was > looking > for! > > However I'm still experiencing a bit of trouble because my simulated > protein contained a heme cofactor and it seems to only let me extract > one > object. > > Have you had any experience with this? > > Parker > On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren > wrote: > > > 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 -- 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] Removing Water from Final Simulation
Thanks Warren for your help, those were exactly the functions I was looking for! However I'm still experiencing a bit of trouble because my simulated protein contained a heme cofactor and it seems to only let me extract one object. Have you had any experience with this? Parker On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren wrote: > 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] Removing Water from Final Simulation
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] 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] About the binary identical results by restarting from the checkpoint file
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. 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. Cheers, Cuiying -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Aw: [gmx-users] Nose-Hover chains for membrane protein simulation
Off subject, I thought a good pop up for the end of file processing etc...would be ___ "Government spies are everywhere, they're in your home, they're in your hair they're down the street and hiding in walls They're waiting to take you away" Fabulous flying freak brothers. ___ from the 60's 70's commic... Stephan Watkins -- 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] fattyn acid parameter in OPLSAA forcefield
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? Anyone has better suggestion? Fatemeh Ramezani -- 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] Pressure coupling
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
Re: [gmx-users] cation-pi interaction
Chapter 8 of the manual names a tool that sounds like what the OP wants ;-) Mark On Sat, Jun 1, 2013 at 10:25 AM, Dr. Vitaly Chaban wrote: > Can g_angle not handle this? > > > Dr. Vitaly Chaban > > > > > > On Sat, Jun 1, 2013 at 10:15 AM, larif sofiene >wrote: > > > Greeting > > I'm trying to find the angle between a cation and a benzene cycle from a > MD > > trajectory. I'm really confused is there a tool for such calculations ? > > because i must find angle using a plan passing by the center of the cycle > > and vector (from cation to the mass center of the benzene cycle). > > How can i do it please ?. > > 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 > > > -- > 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
On Sun, Jun 2, 2013 at 4:56 PM, James Starlight 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] cation-pi interaction
I've always wondered why people do this. There are no pi electrons in your force field so it seems to me that if you find a stable "cation-pi" interaction in your simulations then that just implies that a real cation-pi interaction is not necessary to stabilize this particular conformation. That is, unless one is just after pretty pictures. Am I missing something? Chris. -- original message -- I'm trying to find the angle between a cation and a benzene cycle from a MD trajectory. I'm really confused is there a tool for such calculations ? because i must find angle using a plan passing by the center of the cycle and vector (from cation to the mass center of the benzene cycle). How can i do it please ?. 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] structure alignement :g_rmsdist
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 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 > > > See g_rmsdist -h > > > > Mark > > > > > > On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele > 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
[gmx-users] double sum over neighbor list
Hi I am tyring to compute total virial, i.e. sum_i sum_j (rij*Fij). To achieve this, I am making modifications in the gmx_nb_generic_kernel() function in nb_generic.c. In it, I see that atoms I and j are accessed from neighbor lists to determine forces on atom I . My question is that in this loop do I have to take care of double counting pair forces, i.e. will the pair of atom I and j be accessed twice or just once? Thanks Sikandar -- 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
Mark, could you also provide me with some examples when usage of VS could give artifacts in simulations ? In particular I'm interesting in usage of VS on hydrogens with membrane proteins. James 2013/6/1 James Starlight > Thanks for so detailed explanation! > > I've also forced with the problem of barostat during simulation of my > membrane protein with N-H chains ( see adjacent topic). I'll be also very > thankful for you suggestion in that case too. > > James > > > 2013/6/1 Mark Abraham > >> On Fri, May 31, 2013 at 5:19 PM, James Starlight > >wrote: >> >> > 3) Also I've already performed small simulation with the time step 5 fs >> > (defining virtual sites by means of pdb2gmx -vsites and introducing >> heavy >> > hydrogens. I've not observed any errors during my simulation. When I've >> > tried to increase dt up to 7 fs I've obtained warnings according to >> that I >> > should increase tau_p (from 2 ps with Parinello coupling). How tau_p is >> > relevant to the timestep and when I could obtain more information about >> > such constants ? E.g if i increase tau_p doest it means that I provide >> > weaker coupling to the system with pressure bath ? (higher constant- >> higher >> > relaxation times ) >> > >> >> You're integrating forces calculated at one instant and assuming they are >> applicable over a finite time period. Obviously this is an approximation, >> and it gets worse with longer time step. The worse approximation means the >> sampling is from a shadow Hamiltonian that is even further from the real >> one. P-R is not very stable if the sampling is not from equilibrium, so >> probably the change suggested in the warning helps keep P-R working. >> >> The absence of the simulation crashing is not a suitable proxy for >> assuming >> there are no problems. You should compare observables with those from >> conservative parameter sets and see whether differences exist. >> >> Mark >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] water position restraints
On 6/2/13 7:57 AM, Shima Arasteh wrote: I just applied genrestr command: #genrestr -f minim.gro -o water_posre.itp -fc 10 10 10 And then I just chose the water to create the water_posre.itp. Would not that work? No, it won't. You can't run genrestr on a configuration with multiple molecules. Position restraints are applied based on moleculetype-specific numbering, not atom numbering in a coordinate file; thus genrestr only works if using a single molecule in the input (note that the help text tells you this). The approach outlined before is redundant and will cause a fatal error due to atom numbering. If you want to restrain water molecules, the default #ifdef that is already built into the topology does all the work for you. You don't need to do anything. If, for some reason, you feel a stronger force constant is required, just change it using a text editor. -Justin Sincerely, Shima From: Mark Abraham To: Shima Arasteh ; Discussion list for GROMACS users Sent: Sunday, June 2, 2013 3:35 PM Subject: Re: [gmx-users] water position restraints What's in that .itp? You can only restrain all the waters that have that moleculetype. See http://www.gromacs.org/Documentation/How-tos/Position_Restraints On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh wrote: Dear GMX users, I' d like to put the position restraints on water oxygen atoms. To do so, I made a water_posre.itp file. Then I modified the top file, as this, but didn't work: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #include "water_posre.itp" #endif Would you please help me here? I don't know how I change the fcx, fcy, and fcz. Is it possible to change the fc values 1000 to 10 in top file by just text editing as below: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 10 10 10 #include "water_posre.itp" #endif Sincerely, Shima -- 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 -- 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] Compilation error
On 6/2/13 9:03 AM, vidhya sankar wrote: Dear Gromacs user Thank you for your previous reply When i Compile gromacs 4.5.6 I have Gor following error collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.6/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.6/src' make: *** [all-recursive] Error 1 I configure with Following Command ./configure --enable-double --with-fft=fftpack --program-suffix=_d I Have fftw3.3.2 but i have Not used that I am using the deh=fault fftpack Using fftpack will be much slower than FFTW. How to Solve this error What went wrong? No idea. The real error message precedes the output you posted. -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: Nose-Hover chains for membrane protein simulation
And I my point was I didn't think that there was going to be a measurable ergodicity difference between NH chains and NH. Given the size of the system, the chaoticness of atomic motions will likely give you configurational sampling indistinguishable from full ergodicity. Most of the errors that are solved by NH chains are for small toy systems. On Sun, Jun 2, 2013 at 2:17 AM, James Starlight wrote: > Michael, > > > thanks for suggestions. > > the main reason of ussage N-H with chains is the assumption that simple N-H > does not provide ergodicity of the system assuming that I'd like to sample > all temperature acceptable conformations on the 100 ns trajectory. > > But as I understood the chain regime does not compatible with the membrane > protein simulation due to the artifacts arising with MTTK batostat. > > James > > 2013/6/1 Michael Shirts > >> I can't think of any instance where nose-hoover chains provides an >> advantage over nose-hoover in a large system -- all the demonstrations >> of superiority are in model systems that are not particularly chaotic. >> As the system gets more chaotic, it matters less. >> >> I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman >> with semiisotropic scaling. >> >> On Sat, Jun 1, 2013 at 1:07 AM, James Starlight >> wrote: >> > Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK >> > barostat 5ps coupling ) I've observed non-physical behaviour of my system >> > with the constant drift of the protein molecule as the rigid body in the >> > y-z plane >> > >> > Energy Average Err.Est. RMSD Tot-Drift >> > >> --- >> > Pressure -760.137 --193.776218.059 >> (bar) >> > >> > >> > >From manual I've noticed that MMTK doest not support *semiisotropic >> > scalling. *Doest it means that with the Nose-hover chains and md-vv I >> > should use only weaker coupling during productions runs (I cant use >> > Parinello;s barostat with such options too) >> > >> > Thanks for help >> > >> > James >> > >> > >> > >> > 2013/5/31 James Starlight >> > >> >> Dear Gromacs users! >> >> >> >> I'd like to perform simulation of the membrane protein in lipid-water >> >> system using Nose-Hover with chains. >> >> >> >> From manual I've found that with such thermostat I should use (1) md-vv >> >> integrator (2) MTTK instead of Parinello's batostat and (3) shake >> instead >> >> of LINCS. >> >> >> >> >> >> How doest such options compatible with the simulation of membrane >> proteins >> >> in general ? On what other options should I pay attention during >> simulation >> >> of membrane protein with NH chains ? >> >> >> >> >> >> >> >> Thanks for help, >> >> James >> >> >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > * Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > 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] Compilation error
Dear Gromacs user Thank you for your previous reply When i Compile gromacs 4.5.6 I have Gor following error collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.6/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.6/src' make: *** [all-recursive] Error 1 I configure with Following Command ./configure --enable-double --with-fft=fftpack --program-suffix=_d I Have fftw3.3.2 but i have Not used that I am using the deh=fault fftpack How to Solve this error What went wrong? I am using gcc 4.6.3 in Ubunt12.04 OS already I have Successfully installed gromacs 4.6 it run well 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] water position restraints
I just applied genrestr command: #genrestr -f minim.gro -o water_posre.itp -fc 10 10 10 And then I just chose the water to create the water_posre.itp. Would not that work? Sincerely, Shima From: Mark Abraham To: Shima Arasteh ; Discussion list for GROMACS users Sent: Sunday, June 2, 2013 3:35 PM Subject: Re: [gmx-users] water position restraints What's in that .itp? You can only restrain all the waters that have that moleculetype. See http://www.gromacs.org/Documentation/How-tos/Position_Restraints On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh wrote: Dear GMX users, > >I' d like to put the position restraints on water oxygen atoms. >To do so, I made a water_posre.itp file. Then I modified the top file, as >this, but didn't work: > > >#ifdef POSRES_WATER >; Position restraint for each water oxygen >[ position_restraints ] >; i funct fcx fcy fcz > 1 1 1000 1000 1000 >#include "water_posre.itp" >#endif > > >Would you please help me here? I don't know how I change the fcx, fcy, and >fcz. Is it possible to change the fc values 1000 to 10 in top file by just >text editing as below: > >#ifdef POSRES_WATER >; Position restraint for each water oxygen >[ position_restraints ] >; i funct fcx fcy fcz > 1 1 10 10 10 >#include "water_posre.itp" >#endif > > > > > > >Sincerely, >Shima >-- >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] structure alignement :g_rmsdist
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 > See g_rmsdist -h > > Mark > > > On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele 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
Re: [gmx-users] structure alignement :g_rmsdist
See g_rmsdist -h Mark On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele 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
Re: [gmx-users] About Checkpoint error in gromacs 4.6
-append is the default behaviour. You can turn it off. But you can't turn it off and have behaviour like it is on. You will need to deal with your file size problem yourself by concatenating files later on, if you need to. Mark On Sun, Jun 2, 2013 at 6:14 AM, vidhya sankar wrote: > > > Deat Justin Thank you for your Previuos Reply, > > But When I Run tne the following command with Append Option > > mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 > -deffnm CNTPEPRSOLNPT -append > > > > I Have got the following error > The original run wrote a file called 'CNTPEPRSOLNPT.trr' which is larger > than 2 GB, but mdrun did not support large file offsets. Can not append. > Run mdrun with -noappend > > How to Solve this ? > But When i Run With -noappend option It run Well But it Produce different > File Name files Are not merged (are not Continues) > > 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 > -- 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] water position restraints
What's in that .itp? You can only restrain all the waters that have that moleculetype. See http://www.gromacs.org/Documentation/How-tos/Position_Restraints On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh wrote: > Dear GMX users, > > I' d like to put the position restraints on water oxygen atoms. > To do so, I made a water_posre.itp file. Then I modified the top file, as > this, but didn't work: > > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #include "water_posre.itp" > #endif > > > Would you please help me here? I don't know how I change the fcx, fcy, and > fcz. Is it possible to change the fc values 1000 to 10 in top file by > just text editing as below: > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 10 10 10 > #include "water_posre.itp" > #endif > > > > > > > Sincerely, > Shima > -- > 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] structure alignement :g_rmsdist
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
Re: [gmx-users] viscosity
On 2013-06-02 06:40, Marcelo Vanean wrote: *On 2013-06-01 17:11, Marcelo Vanean wrote: * *On 2013-06-01 02:24, Marcelo Vanean wrote: * *Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. * *I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. * *Maybe you can post the energy file on that site as well. Have you tried to compute the pressure autocorrelation (using g_energy)?* I didn't the pressure autocorrelation. A question: what does this analysis tell me? Check the equations in the manual and relevant literature. The viscosity is computed from the pressure ACF. I posted the energy file here: http://www.4shared.com/file/SSAU1reN/ener.html. That website does not work. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water position restraints
Dear GMX users, I' d like to put the position restraints on water oxygen atoms. To do so, I made a water_posre.itp file. Then I modified the top file, as this, but didn't work: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #include "water_posre.itp" #endif Would you please help me here? I don't know how I change the fcx, fcy, and fcz. Is it possible to change the fc values 1000 to 10 in top file by just text editing as below: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 #include "water_posre.itp" #endif Sincerely, Shima -- 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
