[gmx-users] Limit on energygrp_table
Dear all, I am trying to use tabulated potentials in my simulation. However, there is a limit on energygrp_table and the grompp reports error. The interaction happens between any two of atoms, and their might be more than 3000 possible couples. What should I do to remove the limit? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Limit on energygrp_table
The error shows as "An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095." On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham wrote: > On 30/11/2011 5:09 PM, Liu, Liang wrote: > > Dear all, > > I am trying to use tabulated potentials in my simulation. However, there > is a limit on energygrp_table and the grompp reports error. > > > What error? > > > The interaction happens between any two of atoms, and their might be > more than 3000 possible couples. > What should I do to remove the limit? Thanks. > > > We don't know what limit you are observing. > > 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 > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Limit on energygrp_table
While, is it needed to list all the possible interacting (two) atoms in the energygrp_table option? I have more than 3000 possible two-atom pairs, corresponding to more than 3000 table_*.xvg files. On Wed, Nov 30, 2011 at 12:29 AM, Mark Abraham wrote: > On 30/11/2011 5:25 PM, Liu, Liang wrote: > > The error shows as "An input file contains a line longer than 4095 > characters, while the buffer passed to fgets2 has size 4095." > > > No text table file needs a line this long. We still don't have information > from you, but I expect you have a malformed file. > > Mark > > > > On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham > wrote: > >> On 30/11/2011 5:09 PM, Liu, Liang wrote: >> >> Dear all, >> >> I am trying to use tabulated potentials in my simulation. However, >> there is a limit on energygrp_table and the grompp reports error. >> >> >> What error? >> >> >> The interaction happens between any two of atoms, and their might be >> more than 3000 possible couples. >> What should I do to remove the limit? Thanks. >> >> >> We don't know what limit you are observing. >> >> 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 >> > > > > -- > Best, > Liang Liu > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] simulation with position constraint by a harmonic potential
I am running Gromacs for RNAs, and I got a problem during the simulation: How to perform the simulation with each heavy atom constrained to its initial position by a harmonic potential, E = k(r-r0)^2? -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] simulation with position constraint by a harmonic potential
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Re: [gmx-users] simulation with position constraint by a harmonic potential
Thanks. Is this position restraint same to the one "Position Restrained MD". I see some tutorial shows there are always three step to perform a simulation: Energy minimization, Position Restrained MD and MD Simulation. Is it possible to fulfill the position restraint during Position Restrained MD? Thanks. On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Firstly I want to thank for your reply, yes, it should be position >> restraint. >> >> I don't know how to reply in the thread, actually that was my first post. >> Therefore I have to ask you here, hope it also work to you. >> >> > Simply reply to the message. The discussion needs to stay on the list. > The members are not private tutors. > > My question is how to perform a position restraint simulation with the >> heavy atom constrained to its initial position by a harmonic potential >> E=k(r-r0)^2, >> which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? >> >> > You can adjust the force constant in the posre.itp file. There is no > automated way of decreasing or increasing a restraint; independent > simulations must be run on the different topologies. > > -Justin > > Thanks, and any helps will be highly appreciated. >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] simulation with position constraint by a harmonic potential
> > > Thanks. > > > > Is this position restraint same to the one "Position Restrained MD". I > > see some tutorial shows there are always three step to perform a > > simulation: Energy minimization, Position Restrained MD and MD > Simulation. > > "Always" is too strong, but this is common. > > > Is it possible to fulfill the position restraint during Position > > Restrained MD? Thanks. > > Yes, hence the name. How well they can be fulfilled depends on the > initial and simulation conditions. > Thanks for this information. But how to perform a harmonic potential to all the heavy atoms of RNA? Justin said this one should be adjusted in the posre.itp file, and what I see in the file is all 1000. Does this means k=1000 in the equation of E = k (r-r0)^2? Thanks. > > Mark > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] simulation with position constraint by a harmonic potential
It is weird why I always receive the digest of the mailing list but the specific topic? On Tue, Sep 27, 2011 at 9:14 AM, Liu, Liang wrote: > > Thanks. >> > >> > Is this position restraint same to the one "Position Restrained MD". I >> > see some tutorial shows there are always three step to perform a >> > simulation: Energy minimization, Position Restrained MD and MD >> Simulation. >> >> "Always" is too strong, but this is common. >> >> >> > Is it possible to fulfill the position restraint during Position >> > Restrained MD? Thanks. >> >> Yes, hence the name. How well they can be fulfilled depends on the >> initial and simulation conditions. >> > > Thanks for this information. > But how to perform a harmonic potential to all the heavy atoms of RNA? > Justin said this one should be adjusted in the posre.itp file, and what I > see in the file is all 1000. Does this means k=1000 in the equation of E = k > (r-r0)^2? > Thanks. > > >> >> Mark >> > > -- > Best, > Liang Liu > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] simulation with position constraint by a harmonic potential
Liu, Liang wrote: >* > Thanks.*>* >*>* > Is this position restraint same to the >one "Position Restrained*>* MD". I*>* > see some tutorial shows there >are always three step to perform a*>* > simulation: Energy minimization, >Position Restrained MD and MD*>* Simulation.*>* *>* "Always" is too >strong, but this is common.*>* *>* > Is it possible to fulfill the >position restraint during Position*>* > Restrained MD? Thanks.*>* *>* >Yes, hence the name. How well they can be fulfilled depends on the*>* >initial and simulation conditions.*>* *>* *>* Thanks for this information.*>* >But how to perform a harmonic potential to all the heavy atoms of RNA?*>* >Justin said this one should be adjusted in the posre.itp file, and what *>* I >see in the file is all 1000. Does this means k=1000 in the equation of *>* E = >k (r-r0)^2?* Yes. See my previous message. I explained the contents of the file, which are also discussed in the manual. -Justin --- perfect, thanks a lot. Does this conflict with the bond restraint, e.g. LINCS algorithm, during simulation? -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as "Need at least two replicas for replica exchange (option -multi)", what is this for? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
Does that mean I have to use MPI? I got an error "mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support" after run "mdrun -s md.tpr -multi 10 -replex 10" On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Hi everyone, >> I tried to use Gromacs to run REMD simulation. >> Firstly a set of (md#).mdp file are make and the grompp command can >> generate the same amount of (md#).tpr file. >> Assume # = 10, >> then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. >> >> However, a fetal error shows as "Need at least two replicas for replica >> exchange (option -multi)", what is this for? Thanks. >> >> >> > You have to use the -multi flag. Otherwise all mdrun does is run md.tpr > and try to do REMD with nothing. > > http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
Thanks for the information. I installed the mpi version with "sudo apt-get install gromacs-openmpi" under Ubuntu. Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another error appears, "The number of nodes (1) is not a multiple of the number of simulations (10)". What is this for? On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Does that mean I have to use MPI? I got an error "mdrun -multi is not >> supported with the thread library.Please compile GROMACS with MPI support" >> after run "mdrun -s md.tpr -multi 10 -replex 10" >> >> > Per the error message, yes. > > -Justin > > On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Hi everyone, >>I tried to use Gromacs to run REMD simulation. >>Firstly a set of (md#).mdp file are make and the grompp command >>can generate the same amount of (md#).tpr file. >>Assume # = 10, >>then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. >> >>However, a fetal error shows as "Need at least two replicas for >>replica exchange (option -multi)", what is this for? Thanks. >> >> >> >>You have to use the -multi flag. Otherwise all mdrun does is run >>md.tpr and try to do REMD with nothing. >> >>http://www.gromacs.org/__**Documentation/How-tos/REMD#__** >> Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >> >> <http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >> > >> >>-Justin >> >>-- ==**__== >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>> >> before posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-request@**gromacs.org >> >. >> >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command "mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50". Is this right? How to choose the numbers for np, multi or replex? Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Thanks for the information. I installed the mpi version with "sudo apt-get >> install gromacs-openmpi" under Ubuntu. >> >> Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another error >> appears, "The number of nodes (1) is not a multiple of the number of >> simulations (10)". What is this for? >> >> > You have to run mdrun_mpi as a process under mpirun, e.g.: > > mpirun -np 10 mdrun_mpi -s md.tpr (etc) > > -Justin > > On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Does that mean I have to use MPI? I got an error "mdrun -multi >>is not supported with the thread library.Please compile GROMACS >>with MPI support" after run "mdrun -s md.tpr -multi 10 -replex 10" >> >> >>Per the error message, yes. >> >>-Justin >> >>On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Liu, Liang wrote: >> >> Hi everyone, >> I tried to use Gromacs to run REMD simulation. >> Firstly a set of (md#).mdp file are make and the grompp >>command >> can generate the same amount of (md#).tpr file. >> Assume # = 10, >> then I tried to run REMD as mdrun -s md.tpr -np 10 >>-replex 10. >> >> However, a fetal error shows as "Need at least two >>replicas for >> replica exchange (option -multi)", what is this for? Thanks. >> >> >> >> You have to use the -multi flag. Otherwise all mdrun does is >> run >> md.tpr and try to do REMD with nothing. >> >> http://www.gromacs.org/** >> Documentation/How-tos/REMD#___**_Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >><http://www.gromacs.org/__**Documentation/How-tos/REMD#__** >> Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >> > >> <http://www.gromacs.org/__** >> Documentation/How-tos/REMD#__**Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >><http://www.gromacs.org/**Documentation/How-tos/REMD#** >> Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >> >> >> >> -Justin >> >> -- ==**== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >>231-9080 >> >> >> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin >> >> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >> > >> >> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> >> >> ==**== >> -- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>**> >> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> &
Re: [gmx-users] REMD problem
So if my personal computer have 2 cores, the np should be set to 2? Does it relate to -multi? How to choose a reasonable number for -replex? the smaller the better? Thanks again. On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> This works. Thanks a lot. >> >> Currently I am running on an RNA molecule and I want to a 1 ns REMD >> simulations with 50 temperatures, >> would you please have a look at the following command "mpirun -np 50 >> mdrun_mpi -s md.tpr -multi 50 -replex 50". Is this right? >> How to choose the numbers for np, multi or replex? >> >> > Current Gromacs versions allow more than one processor per REMD simulation. > Please refer to the link I provided before for specifics. You need all of > the replicas to run at roughly the same speed so the number of processors > per simulation should be the same. > > > Is the simulation time still set in the mdp file with nsteps and dt? e.g. >> nsteps = 50 and dt = 0.002 to run a 1ns simulation? >> >> > It's just like any other simulation in this regard. > > -Justin > > Any helps will be highly appreciated. >> >> On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Thanks for the information. I installed the mpi version with >>"sudo apt-get install gromacs-openmpi" under Ubuntu. >> >>Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another >>error appears, "The number of nodes (1) is not a multiple of the >>number of simulations (10)". What is this for? >> >> >>You have to run mdrun_mpi as a process under mpirun, e.g.: >> >>mpirun -np 10 mdrun_mpi -s md.tpr (etc) >> >>-Justin >> >>On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Liu, Liang wrote: >> >> Does that mean I have to use MPI? I got an error "mdrun >>-multi >> is not supported with the thread library.Please compile >>GROMACS >> with MPI support" after run "mdrun -s md.tpr -multi 10 >>-replex 10" >> >> >> Per the error message, yes. >> >> -Justin >> >> On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul >> mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Liu, Liang wrote: >> >> Hi everyone, >> I tried to use Gromacs to run REMD simulation. >> Firstly a set of (md#).mdp file are make and the >>grompp >> command >> can generate the same amount of (md#).tpr file. >> Assume # = 10, >> then I tried to run REMD as mdrun -s md.tpr -np 10 >> -replex 10. >> >> However, a fetal error shows as "Need at least two >> replicas for >> replica exchange (option -multi)", what is this >>for? Thanks. >> >> >> >> You have to use the -multi flag. Otherwise all mdrun >>does is run >> md.tpr and try to do REMD with nothing. >> >>http://www.gromacs.org/__** >> Documentation/How-tos/REMD#___**___Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >><http://www.gromacs.org/**Documentation/How-tos/REMD#___** >> _Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >> > >> <http://www.gromacs.org/** >> Documentation/How-tos/REMD#___**_Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >><http://www.gromacs.org/__**Documentation/How-tos/REMD#__** >> Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >> >> >>
Re: [gmx-users] REMD problem
Well, although this makes sense, why all the 50 replicas are running when I run "mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own computer with only 2 cores? By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Well, although this makes sense, why all the 50 replicas are running when >> I run "mpirun >> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own computer >> with only 2 cores? >> >> > I can offer no explanation for this behavior, but I expect that either not > all of them are actually running, or at the very least you will get horribly > slow performance. > > > By the way, would you please show me where I can find the reasonable >> replex number information in the literature? I did not find it in the link >> you posted and the manual either. >> >> > A few minutes of real literature searching will be far more valuable than > some random person on the Internet giving you a value that you blindly use > ;) > > -Justin > > Thanks. >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 <-> 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+040.0e+00 PotentialKinetic En. Total Energy Conserved En.Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+105.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Thanks. currently what I see is the program runs very slowly, but get .log >> file for all the 50 replicas, does this mean all of them are running? >> >> > Are the log files being updated, or do they all simply contain a fatal > error message that there are insufficient nodes? I cannot think of a reason > why 50 simulations could possibly run on 2 processors. > > -Justin > > On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Well, although this makes sense, why all the 50 replicas are >>running when I run "mpirun >> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own >>computer with only 2 cores? >> >> >>I can offer no explanation for this behavior, but I expect that >>either not all of them are actually running, or at the very least >>you will get horribly slow performance. >> >> >>By the way, would you please show me where I can find the >>reasonable replex number information in the literature? I did >>not find it in the link you posted and the manual either. >> >> >>A few minutes of real literature searching will be far more valuable >>than some random person on the Internet giving you a value that you >>blindly use ;) >> >>-Justin >> >>Thanks. >> >> >>-- Best, >>Liang Liu >> >> >>-- ==**__== >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Sear
Re: [gmx-users] REMD problem
Not know. I will update the result tomorrow, as the 5 steps take really long time :( On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham wrote: > On 29/09/2011 7:20 AM, Justin A. Lemkul wrote: > >> >> >> Liu, Liang wrote: >> >>> Yes, they are updated like: >>> ... >>> Replica exchange at step 5700 time 11.4 >>> Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 >>> 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 >>> 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 >>> 43 x 44 45 x 46 47 48 49 >>> Repl pr1.0 1.0 1.0 .00 1.0 1.0 >>> .00 1.0 1.0 1.0 1.0 .00 1.0 .00 >>> 1.0 .00 1.0 .00 .46 .00 1.0 >>> .78 1.0 .00 >>> >>> Replica exchange at step 5750 time 11.5 >>> Repl 0 <-> 1 dE = -7.583e+00 >>> Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x >>> 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 >>> 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x >>> 43 44 45 46 47 48 49 >>> Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 >>> 1.0 1.0 1.0 .48 .11 1.0 .00 >>> 1.0 .00 1.0 .00 .00 .01 1.0 1.0 >>> .00 .01 .01 >>> >>> Step Time Lambda >>> 5800 11.60.0 >>> >>> Energies (kJ/mol) >>> AngleProper Dih. Improper Dih. LJ-14 >>> Coulomb-14 >>>9.69806e+021.32207e+033.34938e+014.93171e+02 >>> -3.9e+03 >>>LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position >>> Rest. >>>3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 >>> 0.0e+00 >>> PotentialKinetic En. Total Energy Conserved En. >>> Temperature >>> -1.78987e+054.57462e+04 -1.33240e+051.23302e+10 >>> 5.62201e+02 >>> Pres. DC (bar) Pressure (bar) Constr. rmsd >>> -2.12803e+02 -5.47109e+022.21484e-05 >>> ... >>> >>> >> Perhaps someone else can offer an explanation. It should not be possible >> to run multiple replicas on a single processor. Also note that your >> exchange probability is extremely high; you're likely not obtaining >> meaningful sampling. >> > > If the MPI configuration allows physical processors to be over-allocated, > then GROMACS is none the wiser. > > Mark > > > >> -Justin >> >> On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote: >>> >>> >>> >>>Liu, Liang wrote: >>> >>>Thanks. currently what I see is the program runs very slowly, >>>but get .log file for all the 50 replicas, does this mean all of >>>them are running? >>> >>> >>>Are the log files being updated, or do they all simply contain a >>>fatal error message that there are insufficient nodes? I cannot >>>think of a reason why 50 simulations could possibly run on 2 >>> processors. >>> >>>-Justin >>> >>>On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul >>> mailto:jalem...@vt.edu> >>> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >>> >>> >>> >>> Liu, Liang wrote: >>> >>> Well, although this makes sense, why all the 50 replicas >>> are >>> running when I run "mpirun >>> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on >>>my own >>> computer with only 2 cores? >>> >>> >>> I can offer no explanation for this behavior, but I expect that >>> either not all of them are actually running, or at the very >>> least >>> you will get horribly slow performance. >>> >>> >>> By the way, would you please show me where I can find the >>> reasonable replex number information in the literature? >>> I did >>> not find it in the link you posted and th
Re: [gmx-users] REMD problem
After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My question is how to obtain the structure information? (I will need pdb file). On Thu, Sep 29, 2011 at 6:23 AM, Manuel Prinz wrote: > Am Do, 29.09.2011, 01:38 schrieb Mark Abraham: > > If the MPI configuration allows physical processors to be > > over-allocated, then GROMACS is none the wiser. > > Over-allocation is the default in Open MPI[1]. So it's technically > possible to run 50 MPI processes on 2 cores. Whether or not this is a good > idea is left on as an exercise to the reader. ;) > > Best regards, > Manuel > > [1] When not run from a resource manager that takes care of setting the > "right" configuration options. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My question is how to obtain the structure information? (I will need pdb file). -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] REMD problem
Thanks. Actually I applied just because the tutorial said so :( What I need is the structures only, I googled, but did not obtain useful information about Gromacs with REMD. Maybe I need to read the manual again :( I am totally fresh to MD simulation, just worked on this for 1 week ... On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham wrote: > On 30/09/2011 2:50 AM, Liu, Liang wrote: > > After running for more than 12 hours, the REMD simulation is completed and > what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. > > > Yep. One for each simulation. > > > Not sure if the result is reasonable. > > > Justin told you yesterday they would not be, because you have made a number > of totally arbitrary choices. > > > I tried to analyze the result, and after applying demux.pl, two > files replica_index.xvg replica_temp.xvg are obtained. > > > Why did you want to demux? > > > My question is how to obtain the structure information? (I will need pdb > file). > > > Do all the tutorial material you can find - even if not strictly relevant - > to get an idea about good workflows. Then try to replicate (part of) a > published REMD study to see how things work there. Search the web and check > out the GROMACS web page - there's lots of material out there. Stabbing in > the dark is a great way to waste your time, and people here don't have the > time to teach every person every thing. > > 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 > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 obtain structures with large RMSD?
Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very close to the initial one, with RMSD < 0.2. I am wondering how to obtain large-RMSD structures? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 obtain structures with large RMSD?
Thanks. Will the constrain help? On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Hi, all, >> >> I am trying to use Gromacs to obtain structural ensembles around native >> structures (PDB structures). >> However the simulated structures are always very close to the initial one, >> with RMSD < 0.2. >> I am wondering how to obtain large-RMSD structures? Thanks. >> >> > Large RMSD values would indicate non-native structures, which doesn't sound > like what you're looking for. If your goal is simply enhanced sampling, try > REMD. > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 obtain structures with large RMSD?
How's position restraint? If the force constant is reduced (reduce the number in posre.itp ?), the simulation will lead to more flexible structure? On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Thanks. >> >> Will the constrain help? >> >> > Bond constraints? Well, in general, they're useful, and likely necessary > at high temperature to keep your system stable. Please be more specific. > > -Justin > > On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Hi, all, >> >>I am trying to use Gromacs to obtain structural ensembles around >>native structures (PDB structures). >>However the simulated structures are always very close to the >>initial one, with RMSD < 0.2. >>I am wondering how to obtain large-RMSD structures? Thanks. >> >> >>Large RMSD values would indicate non-native structures, which >>doesn't sound like what you're looking for. If your goal is simply >>enhanced sampling, try REMD. >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>> >> before posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 obtain structures with large RMSD?
Well, I am only trying to get structures with some of them far from the initial structure (large RMSD) and some of them close to the initial one... On Mon, Oct 10, 2011 at 10:37 AM, Tsjerk Wassenaar wrote: > Hi Liang Liu, > > You will never get broader sampling by adding restraints. If you want > to have broader sampling, raise the temperature or add denaturants. > But also ask yourself the question if what you think you want is what > you should be wanting. What is the actual question you're trying to > solve? > > Cheers, > > Tsjerk > > On Mon, Oct 10, 2011 at 5:32 PM, Liu, Liang wrote: > > How's position restraint? If the force constant is reduced (reduce the > > number in posre.itp ?), the simulation will lead to more flexible > structure? > > > > On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul > wrote: > >> > >> > >> Liu, Liang wrote: > >>> > >>> Thanks. > >>> > >>> Will the constrain help? > >>> > >> > >> Bond constraints? Well, in general, they're useful, and likely > necessary > >> at high temperature to keep your system stable. Please be more > specific. > >> > >> -Justin > >> > >>> On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul >>> <mailto:jalem...@vt.edu>> wrote: > >>> > >>> > >>> > >>>Liu, Liang wrote: > >>> > >>>Hi, all, > >>> > >>>I am trying to use Gromacs to obtain structural ensembles around > >>>native structures (PDB structures). > >>>However the simulated structures are always very close to the > >>>initial one, with RMSD < 0.2. > >>>I am wondering how to obtain large-RMSD structures? Thanks. > >>> > >>> > >>>Large RMSD values would indicate non-native structures, which > >>>doesn't sound like what you're looking for. If your goal is simply > >>>enhanced sampling, try REMD. > >>> > >>>-Justin > >>> > >>>-- ==__== > >>> > >>>Justin A. Lemkul > >>>Ph.D. Candidate > >>>ICTAS Doctoral Scholar > >>>MILES-IGERT Trainee > >>>Department of Biochemistry > >>>Virginia Tech > >>>Blacksburg, VA > >>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > >>> > >>>http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin > >>><http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > >>> > >>>==__== > >>>-- gmx-users mailing listgmx-users@gromacs.org > >>><mailto:gmx-users@gromacs.org> > >>>http://lists.gromacs.org/__mailman/listinfo/gmx-users > >>><http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>>Please search the archive at > >>>http://www.gromacs.org/__Support/Mailing_Lists/Search > >>><http://www.gromacs.org/Support/Mailing_Lists/Search> before > posting! > >>>Please don't post (un)subscribe requests to the list. Use the www > >>>interface or send it to gmx-users-requ...@gromacs.org > >>><mailto:gmx-users-requ...@gromacs.org>. > >>>Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists > >>><http://www.gromacs.org/Support/Mailing_Lists> > >>> > >>> > >>> > >>> > >>> -- > >>> Best, > >>> Liang Liu > >> > >> -- > >> > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> MILES-IGERT Trainee > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> Please don't post (un)subscribe requests to the list. Use t
Re: [gmx-users] How to obtain structures with large RMSD?
Well, the thing is even I turn off the position restraint and raise the temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA hairpin. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 to remove clashes?
Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the "most" stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 to remove clashes?
This is a "reasonable" answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, meaning no need to check the "NOTE" of "System has non-zero total charge" in the output of grompp command? And also update the topology file automatically too? On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Hi, all, >> I am wondering if Gromacs can do the following work? >> >> Assuming I have a pdb file of an RNA molecule. Some atoms may be too >> close or even overlap, I am wondering if Gromacs can move the atoms to >> reasonable positions and remove the bad contacts? The final structure is >> supposed to be the "most" stable structure with minimal energy. I know >> AMBER minimization can do this work, and I am wondering if Gromacs can do >> the same? >> >> > Gromacs is perfectly capable of energy minimization. Whether or not > minimization succeeds and gives a reasonable output is mostly dependent > upon the feasibility of the starting structure. If the minimization > crashes, it's not Gromacs' fault ;) > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 to remove clashes?
Thanks. Do you know how to use a new force field, not amber or charm, but a force field built by someone else, and it's already in Gromacs format (tons of xvg file, right?) On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> This is a "reasonable" answer :) >> >> Thanks for that, and I just tried Gromacs for minimization, and looks the >> final structure does not have clashes anymore, and also are very close to >> the initial structure. >> >> Another question is if there is a way to add ions automatically, meaning >> no need to check the "NOTE" of "System has non-zero total charge" in the >> output of grompp command? And also update the topology file automatically >> too? >> >> > That depends on the system. For a simple solute in water, the running > total charge of the solute is recorded in the qtot column of the .top file. > If you have a complex system with lots of charged things, no, there is no > convenient way to get the charge aside from calculating it by hand or > reading the grompp output. > > The topology can be modified automatically by genion after ions are added > by using the -p flag. > > -Justin > > On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Hi, all, >>I am wondering if Gromacs can do the following work? >> >>Assuming I have a pdb file of an RNA molecule. Some atoms may be >>too close or even overlap, I am wondering if Gromacs can move >>the atoms to reasonable positions and remove the bad contacts? >>The final structure is supposed to be the "most" stable >>structure with minimal energy. I know AMBER minimization can do >>this work, and I am wondering if Gromacs can do the same? >> >> >>Gromacs is perfectly capable of energy minimization. Whether or not >>minimization succeeds and gives a reasonable output is mostly >>dependent upon the feasibility of the starting structure. If the >>minimization crashes, it's not Gromacs' fault ;) >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>> >> before posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**
[gmx-users] import force field
I have a serial of tabulated potentials with the name of *.xvg, which are the function of atom distance. I am wondering how to use them in gromacs simulation? Will that replace the force field, e.g. amber03? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 select option for genion command automatically?
I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 select option for genion command automatically?
Yes, I found it. THanks. On Mon, Nov 14, 2011 at 9:45 PM, Terry wrote: > > This is what you are looking for: > > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting > > Terry > > > On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang wrote: > >> I am wondering if there is a flag to make the command select SOL >> automatically instead of pressing some number each time? I have thousands >> of structures, it is really time-consuming to select one by one. >> >> -- >> Best, >> Liang Liu >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. 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 > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] import force field
The tabulated potentials I am using is non-bonded interactions. The question is the application of these potentials will only modify the force field, e.g. amber03, or will take place of the force field? On Mon, Nov 14, 2011 at 6:40 PM, Mark Abraham wrote: > On 15/11/2011 9:33 AM, Liu, Liang wrote: > > I have a serial of tabulated potentials with the name of *.xvg, which are > the function of atom distance. > I am wondering how to use them in gromacs simulation? Will that replace > the force field, e.g. amber03? Thanks. > > > There are sections in the manual that describe the use of tabulated > potentials for either bonded or non-bonded interactions. Such tables modify > the force field in the expected manner. > > 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 > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 tabulated potentials
I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 tabulated potentials
Thanks for help. If I have more atoms and they can interact each other or itself, like PP, PC, PN, CP, CN, CC How's the energygrp_table looking like? I know there should be a option in the grompp, but how to do that? And how to generate the index file? I am sorry for so many questions, I am really not familiar with it. On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak wrote: > >From your system information, I understand that you need to specify > tabulated potentials between atoms P and P, and between atoms C and P, and > so on. > > To achieve this, you need to create energy groups with atom types P and C, > and specify energygrp_table options in the grompp such as following > > > > energygrps = P C ; (and rest of the groups in your system, you will need > to specify index file containing energy groups ) > energygrp_table = P P P C > > > > so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run > directory, and uses it for P-P and P-C interactions, whereas for all other > interactions default table.xvg file is used. > > > I hope this helps. > > Regards > Sikandar > > > On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang wrote: > >> I am trying to use a serial of tabulated potentials, which are the >> functions of the distance between atoms and the names are table.xvg, >> table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some >> RNA structures. >> The procedure I apply is as following: >> >> pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce >> editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 >> genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top >> grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 >> mdrun -v -s em.tpr -c em.pdb -table table.xvg >> >> And the em.mdp file is: >> cpp = /usr/bin/cpp; Preprocessor >> include = -I../top; Directories to include >> in the topology format >> define = -DFLEX_SPC >> integrator = steep ; Algorithm options >> dt = 0.002; ps ! ; run control, the time >> step >> nsteps = 1000; run steps, simulation >> length = dt*nsteps >> nstenergy = 10 ; Write energies to disk >> every nstenergy steps >> nstxtcout = 10 ; Write coordinates to >> disk every nstxtcout steps >> xtc_grps= RNA ; Which coordinate >> group(s) to write to disk >> energygrps = RNA ; Whici energy group(s) to >> write to disk >> nstlist = 10 ; Frequency to update the >> neighbor list and long range forces >> ns_type = grid; Method to determine >> neighbor list and long range forces (simple, grid) >> rlist = 1.0 ; Cut-off for making >> neighbor list (short range forces) >> vdw-type= user >> coulombtype = user; Treatment of long range >> electrostatic interactions >> rcoulomb= 1.0 ; long range electrostatic >> cut-off >> rvdw= 1.0 ; long range Van der Walls >> cut-off >> constraints = none >> pbc = xyz >> emtol = 5000.0 >> emstep = 0.01 >> >> All the procedure and file are right? Thanks. >> >> -- >> Best, >> Liang Liu >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. 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 > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 tabulated potentials
Thanks, I will try to figure it out. On Tue, Nov 15, 2011 at 9:50 PM, Mark Abraham wrote: > On 16/11/2011 2:45 PM, Liu, Liang wrote: > > Thanks for help. > If I have more atoms and they can interact each other or itself, like PP, > PC, PN, CP, CN, CC How's the energygrp_table looking like? > I know there should be a option in the grompp, but how to do that? > > > See manual sections 7.3.12 and 6.7.2. > > > And how to generate the index file? I am sorry for so many questions, I > am really not familiar with it. > > > http://www.gromacs.org/Documentation/File_Formats/Index_File > > Mark > > > > On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak > wrote: > >> >From your system information, I understand that you need to specify >> tabulated potentials between atoms P and P, and between atoms C and P, and >> so on. >> >> To achieve this, you need to create energy groups with atom types P and >> C, and specify energygrp_table options in the grompp such as following >> >> >> >> energygrps = P C ; (and rest of the groups in your system, you will need >> to specify index file containing energy groups ) >> energygrp_table = P P P C >> >> >> >> so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run >> directory, and uses it for P-P and P-C interactions, whereas for all other >> interactions default table.xvg file is used. >> >> >> I hope this helps. >> >> Regards >> Sikandar >> >> >> On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang wrote: >> >>> I am trying to use a serial of tabulated potentials, which are the >>> functions of the distance between atoms and the names are table.xvg, >>> table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some >>> RNA structures. >>> The procedure I apply is as following: >>> >>> pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce >>> editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 >>> genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top >>> grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 >>> mdrun -v -s em.tpr -c em.pdb -table table.xvg >>> >>> And the em.mdp file is: >>> cpp = /usr/bin/cpp; Preprocessor >>> include = -I../top; Directories to include >>> in the topology format >>> define = -DFLEX_SPC >>> integrator = steep ; Algorithm options >>> dt = 0.002; ps ! ; run control, the time >>> step >>> nsteps = 1000; run steps, simulation >>> length = dt*nsteps >>> nstenergy = 10 ; Write energies to disk >>> every nstenergy steps >>> nstxtcout = 10 ; Write coordinates to >>> disk every nstxtcout steps >>> xtc_grps= RNA ; Which coordinate >>> group(s) to write to disk >>> energygrps = RNA ; Whici energy group(s) >>> to write to disk >>> nstlist = 10 ; Frequency to update the >>> neighbor list and long range forces >>> ns_type = grid; Method to determine >>> neighbor list and long range forces (simple, grid) >>> rlist = 1.0 ; Cut-off for making >>> neighbor list (short range forces) >>> vdw-type= user >>> coulombtype = user; Treatment of long range >>> electrostatic interactions >>> rcoulomb= 1.0 ; long range >>> electrostatic cut-off >>> rvdw= 1.0 ; long range Van der >>> Walls cut-off >>> constraints = none >>> pbc = xyz >>> emtol = 5000.0 >>> emstep = 0.01 >>> >>> All the procedure and file are right? Thanks. >>> >>> -- >>> Best, >>> Liang Liu >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-use
[gmx-users] calculate potentials of structure
Dear all, I am wondering if there is a way to calculate the potential of a given RNA structure? No minimization, no simulation, but calculate the potential. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] calculate potential with tabulated non-bonded interactions
Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build the topology file, I have to choose a force field. What should I do for that? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] calculate potential with tabulated non-bonded interactions
Well, I already have the xvg files from others. However I don't know how to use it. On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Dear all, >> >> I am trying to calculate potentials for RNA structures with a serial of >> tabulated potentials (non-bonded). >> And the only potential I am going to use is the tabulated potentials, and >> the effect from force field should be removed. >> However, when I use pdb2gmx to build the topology file, I have to choose >> a force field. What should I do for that? Thanks. >> >> > It sounds like you need to be constructing your own force field, > completely, from scratch. If you're not looking to use the existing force > fields, this sounds like the only real solution. You can take the time to > make .xvg files for bonded and nonbonded interactions (see the manual), but > that is probably just as much work and your simulations will be much slower. > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] calculate potential with tabulated non-bonded interactions
Well my first question is: if the pdb2gmx command must take a force file? I guess it should be necessary. Then the available list contains amber and others, but not user-specified potential. This will affect the future simulation or calculation? On Thu, Nov 17, 2011 at 10:06 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Well, I already have the xvg files from others. However I don't know how >> to use it. >> >> > Start with the manual, where modifications to the topology and relevant > commands and files are described. Then refer to the how-to online, which > has specific instructions. Then, ask specific questions of problems you > are having. I doubt anyone on this list will be able or willing to guess > where your problems are at this point. > > -Justin > > On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Dear all, >> >>I am trying to calculate potentials for RNA structures with a >>serial of tabulated potentials (non-bonded). >>And the only potential I am going to use is the tabulated >>potentials, and the effect from force field should be removed. >>However, when I use pdb2gmx to build the topology file, I have >>to choose a force field. What should I do for that? Thanks. >> >> >>It sounds like you need to be constructing your own force field, >>completely, from scratch. If you're not looking to use the existing >>force fields, this sounds like the only real solution. You can take >>the time to make .xvg files for bonded and nonbonded interactions >>(see the manual), but that is probably just as much work and your >>simulations will be much slower. >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>> >> before posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] what's the math algorithm?
Dear all, Assuming I have a some tabulated potentials, table.xvg, tablep.xvg, table_P_P.xvg, table_P_C.xvg and so on. Also there are non-zero values in the first column of both table.xvg and tablep.xvg; while the first column (x), the six column (h(x)) and the last column (h'(x)) have non-zero numbers. All other columns have only 0. So what's the math behind it? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
