[gmx-users] remd
sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 vs MD
Hi, well I guess it depends on what models you mean... REMD is a technique to enhance the conformational sampling. So if you have a e.g. a protein that is disordered or has large disordered parts. Using REMD several copies of the same system are simulated, each replica at a different temperature. Then, each replica can explore a different portion of the conformational space: the higher temperature replicas are able to move between different regions of the potential energy surface without staying in any of them, while the lowest temperature replicas can get trapped in local minima and are able to accurately explore the regions of the potential energy surface. This way you can obtain more information about conformational space then by simple MD. This paper might help: Y. Sugita, Y. Okamoto, Chem. Phys. Let., 314, 261 (1999) best Date: Thu, 5 Sep 2013 11:34:47 +0800 From: pqah...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] REMD vs MD Hi all, I just want to ask you which is about REMD..I just understanding about the MD simulation which is the basic one..If i have a several models that i need to see the interaction between them is it okay to use MD?Or i need to use REMD instead? Thanks in advance, -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD vs MD
Hi all, I just want to ask you which is about REMD..I just understanding about the MD simulation which is the basic one..If i have a several models that i need to see the interaction between them is it okay to use MD?Or i need to use REMD instead? Thanks in advance, -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 run on higher nodes.
Not sure what you're asking, but if you're providing twice as much hardware, then invoke mpiexec_mpt suitably to tell it to use all of that. Then, if you invoke mdrun_mpi the same way as you do now, it will work out it can use twice as much hardware per replica. Mark On Mon, Aug 5, 2013 at 7:55 AM, suhani nagpal suhani.nag...@gmail.com wrote: Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR setenv MPI_GROUP_MAX 1024 setenv MPI_UNBUFFERED_STDIO 1 #mpiexec_mpt -np 24 ./exefile mpiexec_mpt -np 96 /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend So each replica runs at one processor. Now, I want to run the remd at 16 nodes ( double ) so that each replica is subjected to 2 processors. Kindly assist ! Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 run on higher nodes.
Sir Yeah, I meant to use twice the hardware and i have already invoked mpiexec_mpt. the pbs script works fine if i start afresh mdrun of the tprs but if i extend the simulation run by -cpi filename -noappend the run doesnt take place. On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Not sure what you're asking, but if you're providing twice as much hardware, then invoke mpiexec_mpt suitably to tell it to use all of that. Then, if you invoke mdrun_mpi the same way as you do now, it will work out it can use twice as much hardware per replica. Mark On Mon, Aug 5, 2013 at 7:55 AM, suhani nagpal suhani.nag...@gmail.com wrote: Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR setenv MPI_GROUP_MAX 1024 setenv MPI_UNBUFFERED_STDIO 1 #mpiexec_mpt -np 24 ./exefile mpiexec_mpt -np 96 /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend So each replica runs at one processor. Now, I want to run the remd at 16 nodes ( double ) so that each replica is subjected to 2 processors. Kindly assist ! Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD run on higher nodes.
On 8/5/13 6:36 AM, suhani nagpal wrote: Sir Yeah, I meant to use twice the hardware and i have already invoked mpiexec_mpt. the pbs script works fine if i start afresh mdrun of the tprs but if i extend the simulation run by -cpi filename -noappend the run doesnt take place. AFAIK, you can't change the number of processors mid-job and then try to use mdrun -cpi since information related to DD, etc is stored in the checkpoint files, which now do not match the previous run. -Justin On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Not sure what you're asking, but if you're providing twice as much hardware, then invoke mpiexec_mpt suitably to tell it to use all of that. Then, if you invoke mdrun_mpi the same way as you do now, it will work out it can use twice as much hardware per replica. Mark On Mon, Aug 5, 2013 at 7:55 AM, suhani nagpal suhani.nag...@gmail.com wrote: Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR setenv MPI_GROUP_MAX 1024 setenv MPI_UNBUFFERED_STDIO 1 #mpiexec_mpt -np 24 ./exefile mpiexec_mpt -np 96 /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend So each replica runs at one processor. Now, I want to run the remd at 16 nodes ( double ) so that each replica is subjected to 2 processors. Kindly assist ! Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 run on higher nodes.
Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR setenv MPI_GROUP_MAX 1024 setenv MPI_UNBUFFERED_STDIO 1 #mpiexec_mpt -np 24 ./exefile mpiexec_mpt -np 96 /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend So each replica runs at one processor. Now, I want to run the remd at 16 nodes ( double ) so that each replica is subjected to 2 processors. Kindly assist ! Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] remd
Sir, I did an 80 ns Remd simulation, after completion of the simulation extended it up to 480 ns using tpbconv. Now the extended trajectories also write on old trajectory files(traj.trr)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
What does gmxcheck say about them? On Aug 2, 2013 8:08 AM, Shine A shin...@iisertvm.ac.in wrote: Sir, I did an 80 ns Remd simulation, after completion of the simulation extended it up to 480 ns using tpbconv. Now the extended trajectories also write on old trajectory files(traj.trr)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] remd
Hi! On 2013-07-12 07:58, Shine A wrote: Hi Sir, Is it possible to run an REMD simulation having 16 replicas in a cluster(group of cpu) having 8 nodes. Here each node have 8 processors. It is possible. If you have Gromacs (version = 4.6) compiled with MPI and you specify the number of replicas (-multi 16) in the mdrun command and 64 processors are allocated by mpirun, mdrun should start 4 MPI processes per each replica. It worked for me, at least. With OpenMP parallelization it would run faster, I have some problems with it though. Read the latest posts Problems with REMD in Gromacs 4.6.3. Best, G -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
Hi Sir, Is it possible to run an REMD simulation having 16 replicas in a cluster(group of cpu) having 8 nodes. Here each node have 8 processors. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
Sir, I did an REMD for a peptide using implicit solvent model(8 replica 10 ns each).The experimental structure of peptide in water look like betasheet(from circular dichroism). But almost all conformations from trajectory look like alpha-helices.Then how I can correlate experimental and theoretical results. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
On 7/8/13 11:13 AM, Shine A wrote: Sir, I did an REMD for a peptide using implicit solvent model(8 replica 10 ns each).The experimental structure of peptide in water look like betasheet(from circular dichroism). But almost all conformations from trajectory look like alpha-helices.Then how I can correlate experimental and theoretical results. Structural features are largely determined by the force field you've chosen to use. Some have intrinsic biases that are usually well described in the literature. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
Sir, I did a 10 ns REMD simulation for a peptide, 8 replicas using amber force field.Then extracted pdb file from the trajectory and clustered using g_cluster. The I viewed the average structure of the cluster in pymol .But here the atoms are merged togather.why it happends?Is there any problem with my force field? My md.mdp file as follows. RESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 1000 ; 1 ps = 10 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 500 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 376.32 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 270 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
Not sure exactly what merging together means, for visualisation I generally use vmd as this supports gromacs files directly. Your problem might be to do with, using rlist, rcoulomb, and rvdw set to 0 is not the standard way to do an infinite cut-off normally you set them to -1 as in the manual. Also the AMBER force field was parametrised with a cut-off it might, depending on what you are trying to do, be advisable to use the cut-off specified in the original papers and the wider literature for the AMBER force field. Richard On 02/07/13 10:07, Shine A wrote: Sir, I did a 10 ns REMD simulation for a peptide, 8 replicas using amber force field.Then extracted pdb file from the trajectory and clustered using g_cluster. The I viewed the average structure of the cluster in pymol .But here the atoms are merged togather.why it happends?Is there any problem with my force field? My md.mdp file as follows. RESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 1000 ; 1 ps = 10 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 500 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 376.32 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 270 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Not sure exactly what merging together means, for visualisation I generally use vmd as this supports gromacs files directly. If I understand correctly (and the OP can clarify if I haven't), it sounds like visualization of the average structure shows atoms overlapping one another. One should not necessarily expect anything reasonable from an average structure. http://www.gromacs.org/Documentation/Terminology/Average_Structure Your problem might be to do with, using rlist, rcoulomb, and rvdw set to 0 is not the standard way to do an infinite cut-off normally you set them to -1 as in the manual. I have never seen cutoffs set to -1. Is this a special trick in the code? The OP's settings are correct for infinite cutoffs and use of all-vs-all kernels. Also the AMBER force field was parametrised with a cut-off it might, depending on what you are trying to do, be advisable to use the cut-off specified in the original papers and the wider literature for the AMBER force field. This is an important point, but finite cutoffs like those used in explicit-solvent simulations (on the order of 1.0 nm) have, in my hands, produced terrible results in an implicit environment (poor energy conservation, loss of structure, etc). Longer cutoffs are generally recommended, and I only ever use infinite cutoffs in implicit systems. It is definitely worth some time doing validation of one's settings. Richard On 02/07/13 10:07, Shine A wrote: Sir, I did a 10 ns REMD simulation for a peptide, 8 replicas using amber force field.Then extracted pdb file from the trajectory and clustered using g_cluster. The I viewed the average structure of the cluster in pymol .But here the atoms are merged togather.why it happends?Is there any problem with my force field? My md.mdp file as follows. RESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 1000 ; 1 ps = 10 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 500 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 376.32 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 270 This doesn't make much sense to me. If you're generating velocities, you should be generating them for the target temperature. If not, your thermostat has to do some funny things to get it back on track. With V-rescale (or Berendsen, for that matter), you may not have an issue since it relaxes quickly. Other thermostats will cause you grief. -Justin gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of
Re: [gmx-users] remd
On 02/07/13 12:10, Justin Lemkul wrote: On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Not sure exactly what merging together means, for visualisation I generally use vmd as this supports gromacs files directly. If I understand correctly (and the OP can clarify if I haven't), it sounds like visualization of the average structure shows atoms overlapping one another. One should not necessarily expect anything reasonable from an average structure. http://www.gromacs.org/Documentation/Terminology/Average_Structure Your problem might be to do with, using rlist, rcoulomb, and rvdw set to 0 is not the standard way to do an infinite cut-off normally you set them to -1 as in the manual. I have never seen cutoffs set to -1. Is this a special trick in the code? The OP's settings are correct for infinite cutoffs and use of all-vs-all kernels. Yes sorry that's my mistake I should never respond to the mailing list before having my morning coffee. Infinite cutoffs are specified with rlist=0 etc. Sorry for the confusion. Richard Also the AMBER force field was parametrised with a cut-off it might, depending on what you are trying to do, be advisable to use the cut-off specified in the original papers and the wider literature for the AMBER force field. This is an important point, but finite cutoffs like those used in explicit-solvent simulations (on the order of 1.0 nm) have, in my hands, produced terrible results in an implicit environment (poor energy conservation, loss of structure, etc). Longer cutoffs are generally recommended, and I only ever use infinite cutoffs in implicit systems. It is definitely worth some time doing validation of one's settings. Richard On 02/07/13 10:07, Shine A wrote: Sir, I did a 10 ns REMD simulation for a peptide, 8 replicas using amber force field.Then extracted pdb file from the trajectory and clustered using g_cluster. The I viewed the average structure of the cluster in pymol .But here the atoms are merged togather.why it happends?Is there any problem with my force field? My md.mdp file as follows. RESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 1000 ; 1 ps = 10 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 500 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 376.32 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 270 This doesn't make much sense to me. If you're generating velocities, you should be generating them for the target temperature. If not, your thermostat has to do some funny things to get it back on track. With V-rescale (or Berendsen, for that matter), you may not have an issue since it relaxes quickly. Other thermostats will cause you grief. -Justin gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
[gmx-users] remd
Sir, I trying to calculate ground state conformational ensemble of a peptide by comparing experimental chemical shift and predicted chemical shifts.For that I did REMD simulation at 8 temperatures.Then using g_cluster clustered.Here is it reasonable to compare the chemical shift of average structure from a cluster to experimental chemical shift? But here the problem is atoms in the average structure look like overlapped to neighbor.why this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
Justin answered this question about average structures earlier today. Please read his answer. Mark On Tue, Jul 2, 2013 at 8:37 PM, Shine A shin...@iisertvm.ac.in wrote: Sir, I trying to calculate ground state conformational ensemble of a peptide by comparing experimental chemical shift and predicted chemical shifts.For that I did REMD simulation at 8 temperatures.Then using g_cluster clustered.Here is it reasonable to compare the chemical shift of average structure from a cluster to experimental chemical shift? But here the problem is atoms in the average structure look like overlapped to neighbor.why this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD
Wrong way around. Decide what you want to observe and how you will measure it *before* you do a simulation. Now you have a chance of doing the right simulation. On point, check out out chapter 8 of the manual. Mark On Thu, Jun 27, 2013 at 7:17 AM, Shine A shin...@iisertvm.ac.in wrote: Hai Sir, I did an REMD simulation for an intrinsically disordered peptide.Then I extracted thousands of conformations(pdb) from trajectory. Now I want to compare experimental Chemical Shifts and NOE distance for the peptide with all these conformations.How can I do this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD
Hai Sir, I did an REMD simulation for an intrinsically disordered peptide.Then I extracted thousands of conformations(pdb) from trajectory. Now I want to compare experimental Chemical Shifts and NOE distance for the peptide with all these conformations.How can I do this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 analysis
Sir, I did an remd simulation in implicit solvent for a peptide.I want to compare the NOE distances from NMR and various conformations from REMD output. Here how I get various conformations from remd trajectory? .Is any script is available to find distance between two particular atoms?.How I get kinetics of folding from g_kinetics? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 analysis
There's number of analysis tools briefly described in chapter 8 of the manual, and lots more detail in Appendix D. Have a look at what is there, and do your background reading of the literature to see the kinds of things people have done before you. Mark On Tue, Jun 25, 2013 at 1:18 PM, Shine A shin...@iisertvm.ac.in wrote: Sir, I did an remd simulation in implicit solvent for a peptide.I want to compare the NOE distances from NMR and various conformations from REMD output. Here how I get various conformations from remd trajectory? .Is any script is available to find distance between two particular atoms?.How I get kinetics of folding from g_kinetics? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD run showing temperature range more than the equilibrated.
On Tue, Jun 4, 2013 at 12:51 PM, suhani nagpal suhani.nag...@gmail.comwrote: Hi all ! well, I'm working on REMD with 96 replicas, with temperature range 280K to 425.04K. The NVT equilibration works well and graphs plotted show almost the required temperature after equilibration. Then, after 3 ns of remd run , the edr - xvg files show initial temperature atleast 40 -50 units up , and then gradually reduces to it's temperature. for example replica 0 has 280 temperature , for initial 40 ps, it shows temperature up till 335K an then, decline. Sounds like you're re-generating velocities, or mismatching input files. and around 21st to 22nd replica, the exchange probability is varying a lot from 20% to 60%. so, my queries are how to resolve this temperature issue and why is the exchange probability so abrupt at 21-22 replica ? Can't say. Might even be real! 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] REMD run showing temperature range more than the equilibrated.
Hi all ! well, I'm working on REMD with 96 replicas, with temperature range 280K to 425.04K. The NVT equilibration works well and graphs plotted show almost the required temperature after equilibration. Then, after 3 ns of remd run , the edr - xvg files show initial temperature atleast 40 -50 units up , and then gradually reduces to it's temperature. for example replica 0 has 280 temperature , for initial 40 ps, it shows temperature up till 335K an then, decline. and around 21st to 22nd replica, the exchange probability is varying a lot from 20% to 60%. so, my queries are how to resolve this temperature issue and why is the exchange probability so abrupt at 21-22 replica ? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [Spam:*****] [gmx-users] REMD analysis
An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266
Re: [Spam:*****] [gmx-users] REMD analysis
Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of
Re: [Spam:*****] [gmx-users] REMD analysis
You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63
Re: [Spam:*****] [gmx-users] REMD analysis
Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want
Re: [gmx-users] REMD analysis
Indeed the Repeat-3 seems good. But I would guess you did not run too long, right! That would explain the distribution of values! On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ??
Re: [gmx-users] REMD analysis
Okay, now I can start with large production runs . On Thu, May 16, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Indeed the Repeat-3 seems good. But I would guess you did not run too long, right! That would explain the distribution of values! On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well .
Re: [Spam:*****] [gmx-users] REMD analysis
On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? Probably. But exchange acceptance is a poor proxy for sampling efficiency - see recent discussions of REMD on this list. Mark So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png
Re: [Spam:*****] [gmx-users] REMD analysis
Sorry to ask this simple question but how to read the replica_index and replica_temp files. I tried to search a lot but didn't find any information. As I have concatenated all log files and demuxed them. Here's first 10 lines from both files:- replica_index: 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456978 10 11 12 6 1023459678 10 11 12 8 1203495768 10 11 12 10 1230947568 11 10 12 replica_temp 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456897 10 11 12 6 1023457896 10 11 12 8 2013468795 10 11 12 10 3012578694 11 10 12 On Thu, May 16, 2013 at 11:24 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? Probably. But exchange acceptance is a poor proxy for sampling efficiency - see recent discussions of REMD on this list. Mark So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are
Re: [Spam:*****] [gmx-users] REMD analysis
They show which structure is in which ensemble, and the inverse. Look at the exchange events reported in the .log files and work out which is which. Mark On Thu, May 16, 2013 at 5:25 PM, bharat gupta bharat.85.m...@gmail.comwrote: Sorry to ask this simple question but how to read the replica_index and replica_temp files. I tried to search a lot but didn't find any information. As I have concatenated all log files and demuxed them. Here's first 10 lines from both files:- replica_index: 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456978 10 11 12 6 1023459678 10 11 12 8 1203495768 10 11 12 10 1230947568 11 10 12 replica_temp 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456897 10 11 12 6 1023457896 10 11 12 8 2013468795 10 11 12 10 3012578694 11 10 12 On Thu, May 16, 2013 at 11:24 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? Probably. But exchange acceptance is a poor proxy for sampling efficiency - see recent discussions of REMD on this list. Mark So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I
Re: [Spam:*****] [gmx-users] REMD analysis
The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks
Re: [Spam:*****] [gmx-users] REMD analysis
The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
[gmx-users] REMD analysis
Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: [Spam:*****] [gmx-users] REMD analysis
You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: [Spam:*****] [gmx-users] REMD analysis
Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD average acceptance ratio
Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810 ) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD average acceptance ratio
Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810 ) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list
Re: [gmx-users] REMD average acceptance ratio
You are simulating in vacuo! Otherwise the temperature gaps are way too large … If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not importance … the temperature distribution has … make some test to see how the acceptance ratio evolves … On May 11, 2013, at 5:05 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810 ) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 --
Re: [gmx-users] REMD average acceptance ratio
Dear Sir, I tried again with the following temp. ditribution, this time with 30 replicas (280 K -624K) and 500 ps simulation time for each one. 0 280 1 287.8 2 295.9 3 304.2 4 312.7 5 321.5 6 330.5 7 339.8 8 349.3 9 359.1 10 369.1 11 379.5 12 390.1 13 401.0 14 412.3 15 423.8 16 435.7 17 447.9 18 460.4 19 473.3 20 486.6 21 500.2 22 514.3 23 528.7 24 543.5 25 558.7 26 574.4 27 590.4 28 607.0 29 624.0 The output of md29.log file is :- Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .68 .63 .62 .68 .71 .66 .69 .68 .71 .67 .64 .71 .69 .71 .66 .69 .73 .73 .72 .73 .69 .71 .71 .74 .73 .70 .72 .74 .71 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl 81 77 79 90 93 78 91 80 88 78 81 92 96 94 81 83 90 92 83 97 89 87 91 94 88 84 85 89 86 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .65 .62 .63 .73 .74 .63 .73 .65 .70 .63 .65 .74 .77 .76 .65 .67 .72 .74 .66 .78 .71 .70 .73 .76 .70 .68 .68 .72 .69 The average acceptance ration comes around 0.69 , which is very high. Now, in order to get the avg. acceptance ration between 0.2 to 0.3 and also all the replicas should exchange , what has to be done. Here's the link for remd_index and remd_temp files https://www.dropbox.com/s/sgpblcdg9zh7f52/remd_temp.png https://www.dropbox.com/s/6hvqlqmu64mb2jy/remd_index.png I want to that if I include water for the simulation, the same temp. distribution would work or not ?? On Sun, May 12, 2013 at 12:10 AM, XAvier Periole x.peri...@rug.nl wrote: You are simulating in vacuo! Otherwise the temperature gaps are way too large … If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not importance … the temperature distribution has … make some test to see how the acceptance ratio evolves … On May 11, 2013, at 5:05 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789
Re: [gmx-users] REMD average acceptance ratio
The values of exchange ratio look much better: they are similar over the range of temperatures. To reduce the ratio you have to increase the spacing between temperatures, which means increase the value of c in the formula I gave earlier. When you but the water in, the degrees of freedom (and thus the potential energy) will increase and the temperature distribution won't work at all! To cover the same temperature range you'll need much more temperatures. On May 11, 2013, at 19:59, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried again with the following temp. ditribution, this time with 30 replicas (280 K -624K) and 500 ps simulation time for each one. 0 280 1 287.8 2 295.9 3 304.2 4 312.7 5 321.5 6 330.5 7 339.8 8 349.3 9 359.1 10 369.1 11 379.5 12 390.1 13 401.0 14 412.3 15 423.8 16 435.7 17 447.9 18 460.4 19 473.3 20 486.6 21 500.2 22 514.3 23 528.7 24 543.5 25 558.7 26 574.4 27 590.4 28 607.0 29 624.0 The output of md29.log file is :- Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .68 .63 .62 .68 .71 .66 .69 .68 .71 .67 .64 .71 .69 .71 .66 .69 .73 .73 .72 .73 .69 .71 .71 .74 .73 .70 .72 .74 .71 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl 81 77 79 90 93 78 91 80 88 78 81 92 96 94 81 83 90 92 83 97 89 87 91 94 88 84 85 89 86 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .65 .62 .63 .73 .74 .63 .73 .65 .70 .63 .65 .74 .77 .76 .65 .67 .72 .74 .66 .78 .71 .70 .73 .76 .70 .68 .68 .72 .69 The average acceptance ration comes around 0.69 , which is very high. Now, in order to get the avg. acceptance ration between 0.2 to 0.3 and also all the replicas should exchange , what has to be done. Here's the link for remd_index and remd_temp files https://www.dropbox.com/s/sgpblcdg9zh7f52/remd_temp.png https://www.dropbox.com/s/6hvqlqmu64mb2jy/remd_index.png I want to that if I include water for the simulation, the same temp. distribution would work or not ?? On Sun, May 12, 2013 at 12:10 AM, XAvier Periole x.peri...@rug.nl wrote: You are simulating in vacuo! Otherwise the temperature gaps are way too large … If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not importance … the temperature distribution has … make some test to see how the acceptance ratio evolves … On May 11, 2013, at 5:05 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53
Re: [gmx-users] REMD Statistics
On Mon, May 6, 2013 at 3:48 AM, Kong xq xqkong...@gmail.com wrote: Hi Mark, Thanks for your great help. I am sorry for the negligence to state the variation value correctly( it should be 0.011 rather than 0.11). Does this somewhat small value indicate the generalized equilibrium achieved? It might be consistent with it, but it is never diagnostic of it. FWIW, I have never seen an REMD study that attempted to address whether generalized equilibrium was achieved. I will search the papers you suggested. I am wondering whether the histogram is the gold standard for effectively constructing REMD flow. Moreover, how to do the potential energy overlap analysis in Gromacs, from the edr file for each replica ？Does any tool avalible in Gromacs to do this job ? g_energy to get the data for each replica, then your favorite analysis package to form histograms, and graphing program to overlay the plots. The histograms can be done with g_analyze. 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] REMD Statistics
Dear GMX users, I have some concerns about the statistics analysis of REMD which do need your generous help. I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas spaning from 300K to 390K. Then I want to do some statistics analysis for the results. First, I calculated the acceptance ratio for the adjacent pairs of temperatures (showing below). It seems that most of the values are uniform ( 0.25 +/- 0.11) . Second, I followed the track of replica 1 in the temperature space with the information from replica_temp.xvg generated by demux.pl(demux.pl md0.log) scipt. However, the histogram（table below) indicated that the distribution of replica 1 in temperature space is not very uniform. So my question is why did the nonuniform temperature distribution of replica 1 occur given the fact that the acceptance ratio indicated a free random walk in temperature space ? What's more, whether a longer simulation was needed to make a more flatter temperature distribution for each replica? By the way, I want to double check that each column except the first in replica_temp.xvg represents a constant temperature corresponding to that specified in tpr file, we may need to follow the replica index (such as 0 for the first replica) among different coloumns (or temperatures). Does this make sense? Best regards! Xiangqian Kong *The frequency of replica 1 in temperature space * TemperatureFrequency31016.91%32011.58%33013.68%34013.79%35012.64%36011.60% 3704.38%3805.26%39010.16% -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 Statistics
On Sun, May 5, 2013 at 5:14 PM, Kong xq xqkong...@gmail.com wrote: Dear GMX users, I have some concerns about the statistics analysis of REMD which do need your generous help. I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas spaning from 300K to 390K. Then I want to do some statistics analysis for the results. First, I calculated the acceptance ratio for the adjacent pairs of temperatures (showing below). It seems that most of the values are uniform ( 0.25 +/- 0.11) . That is an abnormally high variation in my experience. That could suggest lack of generalized equilibrium on this time scale. Second, I followed the track of replica 1 in the temperature space with the information from replica_temp.xvg generated by demux.pl(demux.pl md0.log) scipt. However, the histogram（table below) indicated that the distribution of replica 1 in temperature space is not very uniform. So my question is why did the nonuniform temperature distribution of replica 1 occur given the fact that the acceptance ratio indicated a free random walk in temperature space ? The acceptance ratio is only a proxy for the existence of a random walk. It would be an amusing exercise to construct a toy system with replicas that would only exchange over a few adjacent temperatures. With suitable overlap of replicas constrained-temperature subranges, you could synthesise uniform exchange rates with no interesting replica flow. For example, if * state A is possible in the lower two-thirds of your temperature range, and * state B is possible in the upper two-thirds of your temperature range, and * no other states are possible, and * your initial configurations include examples of both A and B, and * A and B have no available interconversion pathways, then you can see apparently uniform neighbour exchange rates, and the REMD simulation is probably not being very useful in the normal case of trying to enhance statistics at the lowest temperature. The possibility of this kind of kinetic trapping is discussed in the REMD literature (including some rather old mentions). The extreme challenge of actually achieving replica flow efficiently is discussed in a series of papers from Nadler and Hansmann. Even spacing the temperatures for even replica flow for met-enkephalin is not trivial. What's more, whether a longer simulation was needed to make a more flatter temperature distribution for each replica? Probably, but as above, not necessarily meaningful. It might be instructive to construct some random walks following the GROMACS REMD protocal with acceptance rate 0.25 and see whether your intuition is valid :-) By the way, I want to double check that each column except the first in replica_temp.xvg represents a constant temperature corresponding to that specified in tpr file, we may need to follow the replica index (such as 0 for the first replica) among different coloumns (or temperatures). Does this make sense? Look at the first row and column, and back at the .log files to see what exchanges take place. That's much better than trying a written description! Mark Best regards! Xiangqian Kong *The frequency of replica 1 in temperature space * TemperatureFrequency31016.91%32011.58%33013.68%34013.79%35012.64%36011.60% 3704.38%3805.26%39010.16% -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD Statistics
Hi Mark, Thanks for your great help. I am sorry for the negligence to state the variation value correctly( it should be 0.011 rather than 0.11). Does this somewhat small value indicate the generalized equilibrium achieved? I will search the papers you suggested. I am wondering whether the histogram is the gold standard for effectively constructing REMD flow. Moreover, how to do the potential energy overlap analysis in Gromacs, from the edr file for each replica ？Does any tool avalible in Gromacs to do this job ? Xiangqian Kong 2013/5/6 Mark Abraham mark.j.abra...@gmail.com On Sun, May 5, 2013 at 5:14 PM, Kong xq xqkong...@gmail.com wrote: Dear GMX users, I have some concerns about the statistics analysis of REMD which do need your generous help. I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas spaning from 300K to 390K. Then I want to do some statistics analysis for the results. First, I calculated the acceptance ratio for the adjacent pairs of temperatures (showing below). It seems that most of the values are uniform ( 0.25 +/- 0.11) . That is an abnormally high variation in my experience. That could suggest lack of generalized equilibrium on this time scale. Second, I followed the track of replica 1 in the temperature space with the information from replica_temp.xvg generated by demux.pl(demux.pl md0.log) scipt. However, the histogram（table below) indicated that the distribution of replica 1 in temperature space is not very uniform. So my question is why did the nonuniform temperature distribution of replica 1 occur given the fact that the acceptance ratio indicated a free random walk in temperature space ? The acceptance ratio is only a proxy for the existence of a random walk. It would be an amusing exercise to construct a toy system with replicas that would only exchange over a few adjacent temperatures. With suitable overlap of replicas constrained-temperature subranges, you could synthesise uniform exchange rates with no interesting replica flow. For example, if * state A is possible in the lower two-thirds of your temperature range, and * state B is possible in the upper two-thirds of your temperature range, and * no other states are possible, and * your initial configurations include examples of both A and B, and * A and B have no available interconversion pathways, then you can see apparently uniform neighbour exchange rates, and the REMD simulation is probably not being very useful in the normal case of trying to enhance statistics at the lowest temperature. The possibility of this kind of kinetic trapping is discussed in the REMD literature (including some rather old mentions). The extreme challenge of actually achieving replica flow efficiently is discussed in a series of papers from Nadler and Hansmann. Even spacing the temperatures for even replica flow for met-enkephalin is not trivial. What's more, whether a longer simulation was needed to make a more flatter temperature distribution for each replica? Probably, but as above, not necessarily meaningful. It might be instructive to construct some random walks following the GROMACS REMD protocal with acceptance rate 0.25 and see whether your intuition is valid :-) By the way, I want to double check that each column except the first in replica_temp.xvg represents a constant temperature corresponding to that specified in tpr file, we may need to follow the replica index (such as 0 for the first replica) among different coloumns (or temperatures). Does this make sense? Look at the first row and column, and back at the .log files to see what exchanges take place. That's much better than trying a written description! Mark Best regards! Xiangqian Kong *The frequency of replica 1 in temperature space * TemperatureFrequency31016.91%32011.58%33013.68%34013.79%35012.64%36011.60% 3704.38%3805.26%39010.16% -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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! *
[gmx-users] REMD temperature spacing formula
Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 temperature spacing formula
Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD temperature spacing formula
Thanks for that link. I have used it, but it only takes system size properties. It doesn't take the potential energy values at all. I am looking if someone has used any alternate for temperature spacing generation? On Thu, Apr 4, 2013 at 1:16 PM, rama david ramadavidgr...@gmail.com wrote: Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD temperature spacing formula
On Thu, Apr 4, 2013 at 10:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Thanks for that link. I have used it, but it only takes system size properties. It doesn't take the potential energy values at all. Actually it does, inasmuch as it uses parameters fitted to observed energy values, which you'd know from reading the abstract of the cited paper ;-). I am looking if someone has used any alternate for temperature spacing generation? Not sure what you're asking for. But you could try the REMD how-to guide in shameless plughttp://pubs.acs.org/doi/abs/10.1021/ct800016r/shameless plug, or the works of DA Kofke or UHE Hansmann will likely be instructive. Mark On Thu, Apr 4, 2013 at 1:16 PM, rama david ramadavidgr...@gmail.com wrote: Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD general protocol ...
Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. I will be very grateful to you for your help and suggestion. With Best Regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 general protocol ...
On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -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] REMD general protocol ...
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? Erik -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 general protocol ...
I would look on some paper which temperature ranges and conditions (NPT/NVT) were used for systems of a similar size and with a similar aim. 2013/4/2 rama david ramadavidgr...@gmail.com Dear friends , Thank you justin and Mark for your suggestion I increases my temp range from 310-360 K Now I get 20 replicas . Is in such large temp range wlll it be good to use NPT. Would you tell me the temp differences in which box instability generally arises .. Is my working-flow right or need to change much Thank you With Best Regards.. On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? Erik -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD general protocol ...
Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your suggestion. On Tue, Apr 2, 2013 at 6:45 PM, massimo sandal deviceran...@gmail.comwrote: I would look on some paper which temperature ranges and conditions (NPT/NVT) were used for systems of a similar size and with a similar aim. 2013/4/2 rama david ramadavidgr...@gmail.com Dear friends , Thank you justin and Mark for your suggestion I increases my temp range from 310-360 K Now I get 20 replicas . Is in such large temp range wlll it be good to use NPT. Would you tell me the temp differences in which box instability generally arises .. Is my working-flow right or need to change much Thank you With Best Regards.. On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? Erik -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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
Re: [gmx-users] REMD general protocol ...
On 4/2/13 7:38 AM, Erik Marklund wrote: On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? I suppose, but then why bother with the exchange overhead? Seems to me that if you're only interested in temperature-dependent quantities, you can do that with independent simulations at different temperatures. -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] REMD general protocol ...
On 4/2/13 9:24 AM, rama david wrote: Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your suggestion. The best training experience would be to take a simple example from the literature and reproduce it. It is very hard to try to teach someone completely via email, especially since we do not know the scope and goals of what you are doing. With respect to the question about pressure coupling stability over 310 - 360 K, I don't know offhand what to expect, but in general, I think this is a standard limitation within REMD and you'll probably encounter it. Again, find a protocol for a similar system and try to get things working. It will be easier to help you if you have a known objective that has been demonstrated to work. -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] REMD general protocol ...
Thank you justin. I will do the same. On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 9:24 AM, rama david wrote: Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your suggestion. The best training experience would be to take a simple example from the literature and reproduce it. It is very hard to try to teach someone completely via email, especially since we do not know the scope and goals of what you are doing. With respect to the question about pressure coupling stability over 310 - 360 K, I don't know offhand what to expect, but in general, I think this is a standard limitation within REMD and you'll probably encounter it. Again, find a protocol for a similar system and try to get things working. It will be easier to help you if you have a known objective that has been demonstrated to work. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD temperature spacing error
On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all. We are trying to run REMD on two proteins : 292 and 44 aa residues using GROMACS 4.6. We are unable to obtain the temperature spacing using REMD temperature generator (http://folding.bmc.uu.se/remd/) as it is giving myriad temperature ranges (in the order of 150 for 250-550K range) Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD temperature spacing error
I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all. We are trying to run REMD on two proteins : 292 and 44 aa residues using GROMACS 4.6. We are unable to obtain the temperature spacing using REMD temperature generator (http://folding.bmc.uu.se/remd/) as it is giving myriad temperature ranges (in the order of 150 for 250-550K range) Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? 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] REMD temperature spacing error
k is dimensionless. It does not relate to Boltzmann's constant. The exponential spacing it produces would lead to replica exchange rates that are constant over the T range, under certain assumptions (e.g. papers by David A Kofke). In practice, it normally would not lead to such rates. Whether constant exchange rate is even useful/meaningful is another matter (e.g. papers by Walter Nadler Ulrich Hansmann). Mark On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all. We are trying to run REMD on two proteins : 292 and 44 aa residues using GROMACS 4.6. We are unable to obtain the temperature spacing using REMD temperature generator (http://folding.bmc.uu.se/remd/) as it is giving myriad temperature ranges (in the order of 150 for 250-550K range) Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD temperature spacing error
Sorry. I thought it was related to Boltzmann constt. Then how is 'k' calculated ? On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote: k is dimensionless. It does not relate to Boltzmann's constant. The exponential spacing it produces would lead to replica exchange rates that are constant over the T range, under certain assumptions (e.g. papers by David A Kofke). In practice, it normally would not lead to such rates. Whether constant exchange rate is even useful/meaningful is another matter (e.g. papers by Walter Nadler Ulrich Hansmann). Mark On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all. We are trying to run REMD on two proteins : 292 and 44 aa residues using GROMACS 4.6. We are unable to obtain the temperature spacing using REMD temperature generator (http://folding.bmc.uu.se/remd/) as it is giving myriad temperature ranges (in the order of 150 for 250-550K range) Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 temperature spacing error
People often vary it to try to have an average exchange acceptance rate of a level they think is useful. But that is only a proxy for what they really want to achieve, which is replica flow, and it turns out that is a complex thing and often requires a irregular spacing anyway. Mark On Wed, Mar 13, 2013 at 6:02 PM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Sorry. I thought it was related to Boltzmann constt. Then how is 'k' calculated ? On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham mark.j.abra...@gmail.com wrote: k is dimensionless. It does not relate to Boltzmann's constant. The exponential spacing it produces would lead to replica exchange rates that are constant over the T range, under certain assumptions (e.g. papers by David A Kofke). In practice, it normally would not lead to such rates. Whether constant exchange rate is even useful/meaningful is another matter (e.g. papers by Walter Nadler Ulrich Hansmann). Mark On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all. We are trying to run REMD on two proteins : 292 and 44 aa residues using GROMACS 4.6. We are unable to obtain the temperature spacing using REMD temperature generator (http://folding.bmc.uu.se/remd/) as it is giving myriad temperature ranges (in the order of 150 for 250-550K range) Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD simulation
Hi all, and thanks Mark, Chris and Xavier for your comments. I finally managed to run the REMD simulation but i can not restart the simulation or continue the simulation after it finished. I tried with a test system and run two replicas for just 20 ps. After it finished correctly i extended the time in each .tpr file and tried to continue the REMD simulation using the checkpoint files but i always get the same error message Multi-checking simulation part ... OK Multi-checking simulation part ... OK Reading file test0.tpr, VERSION 4.5.5 (single precision) Reading file test1.tpr, VERSION 4.5.5 (single precision) Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... ERROR: 0031-250 task 6: Segmentation fault ERROR: 0031-250 task 7: Segmentation fault ERROR: 0031-250 task 2: Segmentation fault ERROR: 0031-250 task 1: Segmentation fault ERROR: 0031-250 task 5: Segmentation fault ERROR: 0031-250 task 3: Segmentation fault ERROR: 0031-250 task 0: Terminated ERROR: 0031-250 task 4: Terminated I used Gromacs 4.5.5 and the following commands: to start the REMD simulation: mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500 to extend the time of the simulation in the .tpr files: tpbconv_d -s test_#.tpr -extend 20 -o test_#.tpr to continue the REMD simualtion: mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500 Do i need to use any specific option to be able to continue the REMD simulation? Thanks in advanced Kenny Virtual sites also have a hidden benefit - not only can you take a longer time step, but the width of the distribution of PE is relatively wider, so you can have higher exchange probability for the same temperatures. Mark On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Xavier is right, except that you can also reduce the size of your system. You can take larger steps in temperature if you have fewer atoms. If you are using a cubic system, you can move to a rhombic dodecahedron. Even constraining all bonds will help a bit here (vs. harmonic bonds). There are lots of papers on this topic. To see why you don't get any exchanges, construct histograms of your potential energies and you will see that they don't overlap. Also, it is inefficient to take evenly spaced temperatures. This is not your major problem, but read a bit on exponentially spaced temperatures for REMD. Chris. -- original message -- Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried the serverhttp://folding.bmc.uu.se/remd/index.php but for my system it gives 50 replicas. If i try to take 24 evenly spaced values from the obtained list of temperature then the replicas do not exchange at all. I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 atoms for the solute. Thanks in advanced Kenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Readhttp://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? Readhttp://www.gromacs.org/Support/Mailing_Lists -- Kenny Bravo Rodriguez Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany Phone: +49 (0)208 306 2160 Email:ke...@mpi-muelheim.mpg.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 simulation
That looks very strange. Please file an issue at redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to me. Mark On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez ke...@mpi-muelheim.mpg.de wrote: Hi all, and thanks Mark, Chris and Xavier for your comments. I finally managed to run the REMD simulation but i can not restart the simulation or continue the simulation after it finished. I tried with a test system and run two replicas for just 20 ps. After it finished correctly i extended the time in each .tpr file and tried to continue the REMD simulation using the checkpoint files but i always get the same error message Multi-checking simulation part ... OK Multi-checking simulation part ... OK Reading file test0.tpr, VERSION 4.5.5 (single precision) Reading file test1.tpr, VERSION 4.5.5 (single precision) Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... ERROR: 0031-250 task 6: Segmentation fault ERROR: 0031-250 task 7: Segmentation fault ERROR: 0031-250 task 2: Segmentation fault ERROR: 0031-250 task 1: Segmentation fault ERROR: 0031-250 task 5: Segmentation fault ERROR: 0031-250 task 3: Segmentation fault ERROR: 0031-250 task 0: Terminated ERROR: 0031-250 task 4: Terminated I used Gromacs 4.5.5 and the following commands: to start the REMD simulation: mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500 to extend the time of the simulation in the .tpr files: tpbconv_d -s test_#.tpr -extend 20 -o test_#.tpr to continue the REMD simualtion: mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500 Do i need to use any specific option to be able to continue the REMD simulation? Thanks in advanced Kenny Virtual sites also have a hidden benefit - not only can you take a longer time step, but the width of the distribution of PE is relatively wider, so you can have higher exchange probability for the same temperatures. Mark On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Xavier is right, except that you can also reduce the size of your system. You can take larger steps in temperature if you have fewer atoms. If you are using a cubic system, you can move to a rhombic dodecahedron. Even constraining all bonds will help a bit here (vs. harmonic bonds). There are lots of papers on this topic. To see why you don't get any exchanges, construct histograms of your potential energies and you will see that they don't overlap. Also, it is inefficient to take evenly spaced temperatures. This is not your major problem, but read a bit on exponentially spaced temperatures for REMD. Chris. -- original message -- Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried the serverhttp://folding.bmc.uu.**se/remd/index.phphttp://folding.bmc.uu.se/remd/index.php but for my system it gives 50 replicas. If i try to take 24 evenly spaced values from the obtained list of temperature then the replicas do not exchange at all. I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 atoms for the solute. Thanks in advanced Kenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Readhttp://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Readhttp://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists --
[gmx-users] REMD with umbrella sampling in Gromacs 4.5.5
Hi all, I've read some earlier posts in the forum about replica exchange combined with umbrella sampling but still not sure if the restrain potential defined in the pull code will be included in the exchange criterion: P(i-j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) - U(Rj,Dj)) ] where i, j are 2 replica and beta, R, D are the respective inverse temperature, Cartesian coordinates and parameters in the pull code (force constant, equilibrium position etc.). Can anyone clarify that? Thanks, Dejun-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 with umbrella sampling in Gromacs 4.5.5
Hi all, I've read some earlier posts in the forum about replica exchange combined with umbrella sampling but still not sure if the restrain potential defined in the pull code will be included in the exchange criterion: P(i-j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) - U(Rj,Dj)) ] where i, j are 2 replica and beta, R, D are the respective inverse temperature, Cartesian coordinates and parameters in the pull code (force constant, equilibrium position etc.). Can anyone clarify that? Thanks, Dejun -- View this message in context: http://gromacs.5086.n6.nabble.com/REMD-with-umbrella-sampling-in-Gromacs-4-5-5-tp5003172.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD simulation
Virtual sites also have a hidden benefit - not only can you take a longer time step, but the width of the distribution of PE is relatively wider, so you can have higher exchange probability for the same temperatures. Mark On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Xavier is right, except that you can also reduce the size of your system. You can take larger steps in temperature if you have fewer atoms. If you are using a cubic system, you can move to a rhombic dodecahedron. Even constraining all bonds will help a bit here (vs. harmonic bonds). There are lots of papers on this topic. To see why you don't get any exchanges, construct histograms of your potential energies and you will see that they don't overlap. Also, it is inefficient to take evenly spaced temperatures. This is not your major problem, but read a bit on exponentially spaced temperatures for REMD. Chris. -- original message -- Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried the server http://folding.bmc.uu.se/remd/index.php but for my system it gives 50 replicas. If i try to take 24 evenly spaced values from the obtained list of temperature then the replicas do not exchange at all. I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 atoms for the solute. Thanks in advanced Kenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD simulation
Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried the server http://folding.bmc.uu.se/remd/index.php but for my system it gives 50 replicas. If i try to take 24 evenly spaced values from the obtained list of temperature then the replicas do not exchange at all. I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 atoms for the solute. Thanks in advanced Kenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 simulation
Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried the server http://folding.bmc.uu.se/remd/index.php but for my system it gives 50 replicas. If i try to take 24 evenly spaced values from the obtained list of temperature then the replicas do not exchange at all. I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 atoms for the solute. Thanks in advanced Kenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] REMD simulation
Xavier is right, except that you can also reduce the size of your system. You can take larger steps in temperature if you have fewer atoms. If you are using a cubic system, you can move to a rhombic dodecahedron. Even constraining all bonds will help a bit here (vs. harmonic bonds). There are lots of papers on this topic. To see why you don't get any exchanges, construct histograms of your potential energies and you will see that they don't overlap. Also, it is inefficient to take evenly spaced temperatures. This is not your major problem, but read a bit on exponentially spaced temperatures for REMD. Chris. -- original message -- Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried the server http://folding.bmc.uu.se/remd/index.php but for my system it gives 50 replicas. If i try to take 24 evenly spaced values from the obtained list of temperature then the replicas do not exchange at all. I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 atoms for the solute. Thanks in advanced Kenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 with Frozen DNA and Moving Protein
Dear Gromacs Users, I would like to study structure of a positively charged protein in the vicinity of DNA. To do this, I want to perform replica exchange molecular dynamics simulations in which DNA is frozen and only the protein moves. This way I can efficiently obtain the free energy landscape of the protein close to [frozen] DNA. The reason why I keep the DNA frozen is that this may reduce the computational cost in two ways: 1. DNA atom coordinates are not updated. 2. Maybe I can have a smaller simulation box (and less number of water molecules), because in principle I can exclude DNA-DNA interactions via energygrp_excl. so, I would like to ask you if you think this is a reasonable approach? What could go wrong in such simulations? Any input would be appreciated. Thanks in advance, Saber -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 with Frozen DNA and Moving Protein
On 11/9/12 9:02 AM, saber naderi wrote: Dear Gromacs Users, I would like to study structure of a positively charged protein in the vicinity of DNA. To do this, I want to perform replica exchange molecular dynamics simulations in which DNA is frozen and only the protein moves. This way I can efficiently obtain the free energy landscape of the protein close to [frozen] DNA. The reason why I keep the DNA frozen is that this may reduce the computational cost in two ways: 1. DNA atom coordinates are not updated. Frozen groups do not improve performance. 2. Maybe I can have a smaller simulation box (and less number of water molecules), because in principle I can exclude DNA-DNA interactions via energygrp_excl. This is also not true, as there are protein-DNA and protein-water interactions that cannot be ignored. so, I would like to ask you if you think this is a reasonable approach? What could go wrong in such simulations? Any input would be appreciated. Are you sure that there is no potential for the protein to induce any structural change in the DNA? If you freeze the DNA, you assume that no remodeling occurs. This assumption could impact the calculated free energy of binding. -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] REMD with Frozen DNA and Moving Protein
I second everything that Justin Lemkul wrote. This recent paper (C. A. Brackley, M. E. Cates, and D. Marenduzzo, Phys. Rev. Lett. 109:168103 (2012)) have a few weak points in my opinion, but demonstrate the artifacts that arise from freezing the DNA. Best, Erik 9 nov 2012 kl. 20.42 skrev Justin Lemkul: On 11/9/12 9:02 AM, saber naderi wrote: Dear Gromacs Users, I would like to study structure of a positively charged protein in the vicinity of DNA. To do this, I want to perform replica exchange molecular dynamics simulations in which DNA is frozen and only the protein moves. This way I can efficiently obtain the free energy landscape of the protein close to [frozen] DNA. The reason why I keep the DNA frozen is that this may reduce the computational cost in two ways: 1. DNA atom coordinates are not updated. Frozen groups do not improve performance. 2. Maybe I can have a smaller simulation box (and less number of water molecules), because in principle I can exclude DNA-DNA interactions via energygrp_excl. This is also not true, as there are protein-DNA and protein-water interactions that cannot be ignored. so, I would like to ask you if you think this is a reasonable approach? What could go wrong in such simulations? Any input would be appreciated. Are you sure that there is no potential for the protein to induce any structural change in the DNA? If you freeze the DNA, you assume that no remodeling occurs. This assumption could impact the calculated free energy of binding. -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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] remd jobs failed
hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 jobs failed
Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, Albert mailmd2...@gmail.com wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] remd jobs failed
hello David: thanks for kind reply. The .tpr file was created by grompp in cluster and there is no problem for that. thank you very much Albert On 10/19/2012 08:52 AM, Davide Mercadante wrote: Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, Albert mailmd2...@gmail.com wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] remd jobs failed
Hi Albert, Please accept my apologies, I must have misread your e-mail. Effectively everything seems to be right in the command line and I am not able to understand either why you get the error. Good luck. Cheers, Davide On 19/10/12 7:54 PM, Albert mailmd2...@gmail.com wrote: hello David: thanks for kind reply. The .tpr file was created by grompp in cluster and there is no problem for that. thank you very much Albert On 10/19/2012 08:52 AM, Davide Mercadante wrote: Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, Albert mailmd2...@gmail.com wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] remd jobs failed
On 10/19/12 2:37 AM, Albert wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 1579 Fatal error: File remd_.tpr not found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr ..) You should be executing mdrun instead of g_tune_pme. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD queries
Hi friends , I am new to the REMD simulation. I read some thread from archive but they not clarify by queries that why I am asking you on forum I have following Queries: 1. I want to simulate protein by remd at physiological temp ( 310). So my initial temp of replica should be 310 or less than that??? 2. I read some thread for archive but not get the exact protocol : As per the http://www.gromacs.org/Documentation/How-tos/REMD link I have to do the seperate NVT for each replica... But Should for NPT and Production run I have to do the same thing ??? Or please help me to set the proper protocol.. When I used the T-remd http://folding.bmc.uu.se/remd/ for NVT *ERROR*: Can not do constant volume yet! So how to determine temp for the nvt ??? Is it possible to run replica directly in the production run ??? These may be simple question but as new to REMD these question putting me in a great trouble For NPT with constrained I got following result Summary of input and derived variables. VariableValue Pdes0.1 Temperature range310 - 350 Number of water molecules3000 Number of protein atoms284 Including all H~ 431 Number of hydrogens in protein~ 62 Number of constraints~ 284 Number of vsites~ 0 Number of degrees of freedom~ 27568Energy loss due to constraints1.18 (kJ/mol K) Should I have to use these same value for NVT and production MD ??? or for production MD I have to use NPT Constraints in the protein: fully flexible I just confused with these options. So please give me proper protocol. Thank you in advance. With best wishes and regards Rama david, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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 in explicit solvent
Hi Gromacs Users I'm new to list, but hope to get a little help from someone experienced with setting up some replica exhange simulations in explicit solvent. It keeps exploding after app. 50 to 200 ps simulation time. It runs fine up to there, and then suddently one or a couple of atoms get unstable and move to much between timesteps. Heres what I have done. Build the peptide in extended configuration in pymol. Ran a 200 ps simulation with implicit solvent model to compact the structure. Generated a solvent box. Equilibrated the system for 200 ps. Generated a range of MDP file with varying temperatures and made individual .tpr files Ran the simulation with the switches -multi 16 -replex 1000 I tried to troubleshoot a little with lowering the dt and equilibrating and minimizing more. Also tried different temperature coupling, as I'm not sure what is the most appropriate for REMD simulations. Is there something wrong with the parameters of the mdp file? title= Yo cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 1000 nstxout = 1 nstvout = 1 nstlog = 1 nstenergy= 1000 nstxtcout= 1000 xtc_grps = Protein energygrps = Protein SOL nstlist = 10 ns_type = grid rlist= 0.8 coulombtype = PME rcoulomb = 0.8 rvdw = 0.8 tcoupl = Berendsen tc-grps = Protein SOL tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Berendsen tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds Best Regards Esben -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 in explicit solvent
On 19/06/2012 5:55 PM, Esben Jannik Bjerrum wrote: Hi Gromacs Users I'm new to list, but hope to get a little help from someone experienced with setting up some replica exhange simulations in explicit solvent. It keeps exploding after app. 50 to 200 ps simulation time. It runs fine up to there, and then suddently one or a couple of atoms get unstable and move to much between timesteps. All the advice of http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation and http://www.gromacs.org/Documentation/Terminology/Blowing_Up pertains to each individual system for REMD. In particular, you need to equilibrate each replica under its conditions and not expect them to tolerate a sharp jump in T and to pressure-coupling at the start. The fact that you are using gen-vel = yes is proof that you have not equilibrated yet :-) Heres what I have done. Build the peptide in extended configuration in pymol. Ran a 200 ps simulation with implicit solvent model to compact the structure. Generated a solvent box. Equilibrated the system for 200 ps. Generated a range of MDP file with varying temperatures and made individual .tpr files Ran the simulation with the switches -multi 16 -replex 1000 I tried to troubleshoot a little with lowering the dt and equilibrating and minimizing more. Also tried different temperature coupling, as I'm not sure what is the most appropriate for REMD simulations. Here's where your background reading comes in ;-) What's good for normal simulations is generally good for REMD. There is a school of thought that NVT REMD is not good because the pressure is artificially high (but I haven't seen anyone demonstrate artefacts from that), but NPT costs extra because the volume change affects your PME load balance and accuracy. Is there something wrong with the parameters of the mdp file? title= Yo cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 1000 nstxout = 1 nstvout = 1 nstlog = 1 nstenergy= 1000 nstxtcout= 1000 xtc_grps = Protein energygrps = Protein SOL nstlist = 10 ns_type = grid rlist= 0.8 coulombtype = PME rcoulomb = 0.8 Most would regard this set of PME parameters (most of which are coming from defaults) as too cheap to be effective. Mark rvdw = 0.8 tcoupl = Berendsen tc-grps = Protein SOL tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Berendsen tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds Best Regards Esben -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 question
Michael, Thank you for your answer. On the other hand, I´m not implementing, I´m using REMD.. I miss wrote it. Nathalia -Mensaje original- De: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] En nombre de Michael Shirts Enviado el: lunes, 28 de mayo de 2012 08:09 p.m. Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] REMD question Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibration at constant pressure. On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces natsgar...@gmail.com wrote: Dear Gromacs Users, We are implementing REMD method in Gromacs in protein folding, in your web page you give some steps that don´t mention any step about NPT stabilization. This step is necessary to run REMD simulations? Thank you in advance, Nathalia -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD question
Dear Gromacs Users, We are implementing REMD method in Gromacs in protein folding, in your web page you give some steps that don´t mention any step about NPT stabilization. This step is necessary to run REMD simulations? Thank you in advance, Nathalia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 question
Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibration at constant pressure. On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces natsgar...@gmail.com wrote: Dear Gromacs Users, We are implementing REMD method in Gromacs in protein folding, in your web page you give some steps that don´t mention any step about NPT stabilization. This step is necessary to run REMD simulations? Thank you in advance, Nathalia -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD - low temperature ranges
Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources and I am wondering if for studing 175 aa protein is better to start from 250K and up to 350 K or choose from 300-400K (just an example) Thanks! Best! tomek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 - low temperature ranges
On 27/04/2012 10:59 PM, Tomek Wlodarski wrote: Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources and I am wondering if for studing 175 aa protein is better to start from 250K and up to 350 K or choose from 300-400K (just an example) Depends on the temperature(s) at which you wish to make observations. Sampling is normally enhanced at higher temperatures, so unless you want the ensemble at some low temperatures, it is normal to start at your lowest observation temperature. Of course, you could always read the reasoning provided by the authors in their paper, or email them for clarification... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD - low temperature ranges
Hi Mark, Thanks for reply. The problem is that I have never found in the papers reasoning behind the the lower than 300K temperatures. Moreover, authors were interested in properties in 300K or above. I was wondering if this is not based on experience that REMD implemented in gromacs works better when you also include lower temperature.? best! tomek On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 27/04/2012 10:59 PM, Tomek Wlodarski wrote: Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources and I am wondering if for studing 175 aa protein is better to start from 250K and up to 350 K or choose from 300-400K (just an example) Depends on the temperature(s) at which you wish to make observations. Sampling is normally enhanced at higher temperatures, so unless you want the ensemble at some low temperatures, it is normal to start at your lowest observation temperature. Of course, you could always read the reasoning provided by the authors in their paper, or email them for clarification... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD - low temperature ranges
If you are only interested in conformational sampling, then it makes sense to start at 300 K or even higher - maybe 320 K. The main reason for working at lower temperatures is if your system is unstable - eg. if you expect that the molecule will be mostly unfolded at 300 K and you want to sample the folded state. Another reason might be having experimental data at lower T, but this is problematic, as it is hard to model temperature-dependent properties with simple force fields. Krzysztof Kuczera On 4/27/12 10:06 AM, Tomek Wlodarski wrote: Hi Mark, Thanks for reply. The problem is that I have never found in the papers reasoning behind the the lower than 300K temperatures. Moreover, authors were interested in properties in 300K or above. I was wondering if this is not based on experience that REMD implemented in gromacs works better when you also include lower temperature.? best! tomek On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 27/04/2012 10:59 PM, Tomek Wlodarski wrote: Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources and I am wondering if for studing 175 aa protein is better to start from 250K and up to 350 K or choose from 300-400K (just an example) Depends on the temperature(s) at which you wish to make observations. Sampling is normally enhanced at higher temperatures, so unless you want the ensemble at some low temperatures, it is normal to start at your lowest observation temperature. Of course, you could always read the reasoning provided by the authors in their paper, or email them for clarification... Mark -- gmx-users mailing list 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 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 -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD equilibration
Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
On 03/23/2012 10:41 AM, francesco oteri wrote: Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Depends on the ensemble you want to simulate. If the replica you are interested in should be simulated in NVT you should equilibrate this replica well and take care that all replicas have the same volume (meaning that the replicas with higher T have very high pressures). You also can simulate each replica in an NPT ensemble (and also equilibrate the replicas with NPT). When the pressure is included in the Metropolis criteria for the exchange of the trajectories. Thanks in advance, Francesco all the best Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] REMD equilibration
Hi Francesco, It should be the same ensemble, in which you want to carry out the production REMD. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of francesco oteri Sent: 23 March 2012 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Francesco Il giorno 23 marzo 2012 10:53, Kukol, Andreas a.ku...@herts.ac.uk ha scritto: Hi Francesco, It should be the same ensemble, in which you want to carry out the production REMD. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of francesco oteri Sent: 23 March 2012 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
francesco oteri wrote: I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Another very real concern is the stability of the simulations under NPT. At higher temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail. This phenomenon has been reported by a number of other users. With NVT, this does not happen. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
23 mar 2012 kl. 11.37 skrev Justin A. Lemkul: francesco oteri wrote: I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Another very real concern is the stability of the simulations under NPT. At higher temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail. This phenomenon has been reported by a number of other users. With NVT, this does not happen. -Justin Very true. The benefit from NPT is on the other hand that the replicas can be more distant in temperature space, so if it works then NPT is more efficient. Erik -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD error
Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied Can anybody suggest me how could I rectify this error. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 error
On 12/01/2012 11:54 AM, bharat gupta wrote: Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied You configured GROMACS to use shared libraries, but something about them or your current environment doesn't work. Try rebuilding GROMACS, building with static libraries, or discussing with your system admins. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD error
On Thursday 12,January,2012 08:54 AM, bharat gupta wrote: Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied Can you run a normal md smoothly? try: mdrun_mpi mdrun -deffnm prefix_0 if it works, then some of your trajectories not sound. means system does not equilibrium well. Can anybody suggest me how could I rectify this error. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
