Re: [gmx-users] replica exchange data in cpt file
This is, unfortunately, normal. The REMD implementation was never updated when the checkpointing mechanism was introduced, so this data is not checkpointed. Mark On Sat, Mar 16, 2013 at 12:07 PM, francesco oteri wrote: > Dear gromacs users, > I ran a REMD on a HPC cluster equipped with a queue system. > For this reason I carried out the simulation dividing it in chuncks. > Because of this, each run started using the .cpt file from the previous > one. > > The simulation ran fine, but I noticed that the informations regarding > attempts > and probabilities are not stored so in each .log the data restart from 0 > like > a new simulation. > > Have I done something wrong or is it a known (except to me) issue? > > 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 > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Problem building Gromacs-4.5.5 on BlueGene/Q
Blue Gene/Q does not support the flags "-qarch=450d -qtune=450" nor does it have the same FPU intrinsics as BGP. See https://wiki.alcf.anl.gov/parts/index.php/Blue_Gene/Q#Compiling for information about compiler flags and https://wiki.alcf.anl.gov/parts/index.php/Blue_Gene/Q#Intrinsics for links to information about the QPX vector intrinsics. Jeff -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhamm...@alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 8:34 AM, Shima Arasteh wrote: Thanks. As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file? Do you mean this? Am I right? Yes. Try it. One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command? Type 'help' at the prompt or otherwise search gromacs.org and Google for example usage. It is very easy to create index groups specifying subsets of residues or just their backbone atoms, etc. -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: Fwd: Fw: Fwd: [gmx-users] position restraints
Thanks. As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file? Do you mean this? Am I right? One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Saturday, March 16, 2013 3:39 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/16/13 7:09 AM, Shima Arasteh wrote: > Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? > It would not be possible because I don't see any option for seperate chains > when running genrestr command. > You need to provide a sensible index group to genrestr to create such groups. -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] Could anyone send me some *.tpr input files ( for testing) ?
Hi, everyone ~ I'm going to test performance of Gromacs4.6 on my cluster. However, I have no enough tpr files at hand. Could someone send me several tpr files for testing ? Thanks a lot! With Regards -- Daniel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Check point for restart
On 3/16/13 7:15 AM, vidhya sankar wrote: Dear Justin Thank you for previous reply, There is power cut when i run My simulation So My System Gets Automatically restarted (Due to Low ups Power Packing) Then I want To restart My simulation using the obtained Checkpoint so i am using the following Command to restart ./mdrun_d -s emdppccycN31_solionsfull.tpr -cpi emdppccycN31_solionsfull_prev.cpt -v -nt 4 -deffnm emdppccycN31_solionsfull -cpt 2 -append But I have Got the following Error Checksum wrong for 'emdppccycN31_solionsfull.log'. The file has been replaced or its contents has been modified. Could you please suggest me a solution ? Don't use -append. Concatenate the relevant output files later yourself. -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: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 7:09 AM, Shima Arasteh wrote: Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command. You need to provide a sensible index group to genrestr to create such groups. -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] About Check point for restart
Dear Justin Thank you for previous reply, There is power cut when i run My simulation So My System Gets Automatically restarted (Due to Low ups Power Packing) Then I want To restart My simulation using the obtained Checkpoint so i am using the following Command to restart ./mdrun_d -s emdppccycN31_solionsfull.tpr -cpi emdppccycN31_solionsfull_prev.cpt -v -nt 4 -deffnm emdppccycN31_solionsfull -cpt 2 -append But I have Got the following Error Checksum wrong for 'emdppccycN31_solionsfull.log'. The file has been replaced or its contents has been modified. Could you please suggest me a solution ? Thanks in Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command. Thanks in advance. Sincerely, Shima From: Mark Abraham To: Shima Arasteh ; Discussion list for GROMACS users Sent: Saturday, March 16, 2013 2:21 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh wrote: As you said I changed define in mdp file to define=-DPOSRE . > >I also included backbone.itp file as this: > > >; Include chain topologies >#include "topol_Protein_chain_A.itp" >#ifdef POSRE >#include "backbone_posre.itp" > >#endif >#include "topol_Protein_chain_B.itp" >#ifdef POSRE >#include "backbone_posre.itp" >#endif > > > ; Include POPC chain topology >#include "popc.itp" > >; Include water topology >#include "./charmm36-modified.ff/tip3p.itp" > >#ifdef POSRES_WATER >; Position restraint for each water oxygen >[ position_restraints ] >; i funct fcx fcy fcz > 1 1 1000 1000 1000 >#endif > > > >; Include topology for ions >#include "./charmm36-modified.ff/ions.itp" > >[ system ] >; Name >Protein > >[ molecules ] >; Compound #mols >Protein_chain_A 1 >Protein_chain_B 1 >POPC 238 >SOL 19936 >CL 2 > >But I get this fatal error that my include part for position restraints is not >correct: >Fatal error: >[ file backbone_posre.itp, line 79 ]: >Atom index (364) in position_restraints out of bounds (1-360). >This probably means that you have inserted topology section >"position_restraints" >in a part belonging to a different molecule than you intended to. >In that case move the "position_restraints" section to the right molecule. >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors > >Would you please give me suggestions? > The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean. Mark >Thanks in advance. > >Sincerely, >Shima > > >- Original Message - >From: Justin Lemkul >To: Shima Arasteh ; Discussion list for GROMACS >users >Cc: >Sent: Saturday, March 16, 2013 12:25 AM >Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints > > > >On 3/15/13 9:43 AM, Shima Arasteh wrote: >> I also included the position restraints as follows in my top file: >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #ifdef POSRE >> #include "backbone_posre.itp" >> #include "strong_posre.itp" >> #endif >> #include "topol_Protein_chain_B.itp" >> #ifdef POSRE >> #include "strong_posre.itp" >> #include "backbone_posre.itp" >> #endif >> >> As I described earlier, I included position restraints of backbone in top >> file and also added define = -DPOSRES to minim.mdp file. But it seems that >> the position restrains have not been included. Would you please suggest me >> how I can apply position restraints effectively? >> > >It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your >topology, what you need is -DPOSRE. It is very easy to tell when position >restraints are being applied. A position restraint energy term is written to >the .log and .edr files. If it's not there, you're not applying restraints. > >-Justin > >> Thanks in advance. >> Your suggestions would be appreciated. >> Shima >> >> >> -- Forwarded message -- >> From: Shima Arasteh >> Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) >> Subject: Fw: Fwd: [gmx-users] position restraints >> To: Discussion list for GROMACS users >> >> Dear users, >> >> >> Although I put the position restraints on backbone, I get RMSD around >> 0.2 nm. Is it usual? >> This deviation is just for a minimization step only. I' m on doubt >> about keeping the backbone in a fix secondary structure. >> I' d prefer to restraint the backbone completely. Is it possible? >> >> Thanks in advance. >> >> >> >> Restraints allow, by definition, for slight deviations. >> >> Erik >> * Please don't post (un)subscribe requests to the list. Use thewww >> interface or send it to gmx-users-requ...@gromacs.org. >> >> >> >> >> Dear gmx users, >> >> I want to use restraints on backbone of my protein to keep its secondary >> structure during minimization and equilibration steps. To do so, I >> generated backbone-restrain.itp and then included it to top file. Next, >> added define = -DPOSRES to minim.mdp file. >> After minimization, when I check the minimization output file, I saw >> that the backbone of input and output files are not exactly the same. >> Is there any step which I have not done to set the restraints correctly? >> >> >> Thanks in advance. >> >> Sincerely, >> Shima >> > >-- > > >Justin A. Lemkul, Ph.D. >Research Scientist >Department of Biochemistry >Virginia
Re: [gmx-users] Parallelization performance
On Sat, Mar 16, 2013 at 1:50 AM, Sonia Aguilera < sm.aguiler...@uniandes.edu.co> wrote: > Hi! > > I have been running MD simulations on a 6 processors machine. I just got an > account on a cluster. A nvt stabilization takes about 8 hours on my 6 > processors machine, but it takes about 12 hours on the cluster using 16 > processors. It is my understanding that the idea of running in parallel is > to be more efficient, wrigth? > Yes, but your performance depends on the hardware and the setup. 16 abacuses are not faster than 6 computers :-) Secondly, even if the hardware is comparable, if your 6-processor machine has 4 cores per processor, then OpenMP might be delivering more performance. Or your MPI environment might be configured wrongly and you're running 16 copies of the same simulation on superior hardware. You should inspect the top of the log files to see what GROMACS thinks your hardware is providing, and the bottom of the log file to see in which aspects of the simulation the two systems are delivering difference performance. > This is the command for the run on the 6 processors machine: > mdrun -v -s nvtOmpA.tpr -deffnm nvtOmpA > > This is the command for the run on 16 processor on the cluster: > mpirun -np 16 mdrun_mpi -v -s nvtOmpA.tpr -deffnm nvtOmpA > > With the last command I am imaging that my process is divided in 16 > processors that perform in parallel so that the wall time should be less > than in the 6 processor machine. My system is a protein in oil and water, > and the simulations are for FE calculations. I think it is spected that the > run on the 16 processor of the cluster should be faster, but I'm getting > the > opposite. Am I doing something wrong? > Not as far as we know. But you need to inspect your .log files for all the clues GROMACS provides. This is my mdp. I have used the same mdp for simulations in 4, 6 and 8 > processor machines and everytime is faster and runs quite well. Any help > will be grateful!! > > title= NVT equilibration > ; Run control > integrator = sd ; Langevin dynamics > There have been fixes for correctness and performance of the SD integrator - you should certainly not be using GROMACS 4.6. Mark > tinit= 0 > dt = 0.002 > nsteps = 15; 300 ps > nstcomm = 100 > ; Output control > nstxout = 500 > nstvout = 500 > nstfout = 0 > nstlog = 500 > nstenergy= 500 > nstxtcout= 0 > xtc-precision= 1000 > ; Neighborsearching and short-range nonbonded interactions > nstlist = 10 > ns_type = grid > pbc = xyz > rlist= 1.5 > ; Electrostatics > coulombtype = PME > rcoulomb = 1.5 > ; van der Waals > vdw-type = switch > rvdw-switch = 0.8 > rvdw = 0.9 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = EnerPres > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; EWALD/PME/PPPM parameters > pme_order= 6 > ewald_rtol = 1e-06 > epsilon_surface = 0 > optimize_fft = no > ; Temperature coupling > ; tcoupl is implicitly handled by the sd integrator > tc_grps = system > tau_t= 1.0 > ref_t= 300 > ; Pressure coupling is off for NVT > Pcoupl = No > tau_p= 0.5 > compressibility = 4.5e-05 > ref_p= 1.0 > ; Free energy control stuff > free_energy = yes > init_lambda = 0.1 > delta_lambda = 0 > foreign_lambda = 0.05 0.2 > sc-alpha = 0 > sc-power = 0 > sc-sigma = 0 > couple-moltype = Protein_chain_A ; name of moleculetype to > decouple > couple-lambda0 = vdw ; > couple-lambda1 = vdw-q ; > couple-intramol = yes > nstdhdl = 10 > ; Generate velocities to start > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > ; options for bonds > constraints = h-bonds ; we only have C-H bonds here > ; Type of constraint algorithm > constraint-algorithm = lincs > ; Do not constrain the starting configuration > continuation = no > ; Highest order in the expansion of the constraint coupling matrix > lincs-order = 12 > > > > Thanks in advance! > > Sonia Aguilera > Graduate assistant > > > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Parallelization-performance-tp5006357.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > h
[gmx-users] replica exchange data in cpt file
Dear gromacs users, I ran a REMD on a HPC cluster equipped with a queue system. For this reason I carried out the simulation dividing it in chuncks. Because of this, each run started using the .cpt file from the previous one. The simulation ran fine, but I noticed that the informations regarding attempts and probabilities are not stored so in each .log the data restart from 0 like a new simulation. Have I done something wrong or is it a known (except to me) issue? 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] Timesteps don't match
On Fri, Mar 15, 2013 at 7:10 PM, Alexander Peyser wrote: > Dear all, > > I'm receiving a "timesteps don't match" error, due to a wobble in the time > between steps for my xtc trajectory file. The source of the wobble is > mysterious. > > I'm running gromacs-4.5.5 with plumed patches for a very long trajectory > using double precision code with a time step of 2fs and xtc frames every > 200fs. The trajectory was run in 24 hour chunks, with a continuation with > -append over all the chunks. The timing fit precisely the values set over > many, many chunks. > > Unfortunately, I was trying to consolidate some disk space and lost my log > file, which kept me from simply running mdrun_d with -append to continue > the trajectory as I had been doing. I started a new trajectory with the > checkpoint file by extending the tpr with tpbconv, and then continued > appending to the output from that. The beginning time is correct, beginning > right after the end of the first trajectory. However, every frame is > separated from the next by 187.5 fs or 218.75 fs, repeatedly. I've checked > my input files, my cpt checkpoint and my tpr run file --- there are no step > values like that at all, and the xtc output time continues to be set as > every 100 steps, with a step time of 2fs. > > Where should I look to identify the source of this wobble? Has anyone seen > anything similar? > Sounds pretty weird. I haven't got any theories on how that could happen. If you've got input files that can reproduce the issue, please file it on redmine.gromacs.org. 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: Fwd: Fw: Fwd: [gmx-users] position restraints
On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh wrote: > As you said I changed define in mdp file to define=-DPOSRE . > > I also included backbone.itp file as this: > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #endif > #include "topol_Protein_chain_B.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #endif > > > ; Include POPC chain topology > #include "popc.itp" > > ; Include water topology > #include "./charmm36-modified.ff/tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > > > ; Include topology for ions > #include "./charmm36-modified.ff/ions.itp" > > [ system ] > ; Name > Protein > > [ molecules ] > ; Compound#mols > Protein_chain_A 1 > Protein_chain_B 1 > POPC238 > SOL19936 > CL2 > > But I get this fatal error that my include part for position restraints is > not correct: > Fatal error: > [ file backbone_posre.itp, line 79 ]: > Atom index (364) in position_restraints out of bounds (1-360). > This probably means that you have inserted topology section > "position_restraints" > in a part belonging to a different molecule than you intended to. > In that case move the "position_restraints" section to the right molecule. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Would you please give me suggestions? > The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean. Mark > > Thanks in advance. > > Sincerely, > Shima > > - Original Message - > From: Justin Lemkul > To: Shima Arasteh ; Discussion list for > GROMACS users > Cc: > Sent: Saturday, March 16, 2013 12:25 AM > Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints > > > > On 3/15/13 9:43 AM, Shima Arasteh wrote: > > I also included the position restraints as follows in my top file: > > > > ; Include chain topologies > > #include "topol_Protein_chain_A.itp" > > #ifdef POSRE > > #include "backbone_posre.itp" > > #include "strong_posre.itp" > > #endif > > #include "topol_Protein_chain_B.itp" > > #ifdef POSRE > > #include "strong_posre.itp" > > #include "backbone_posre.itp" > > #endif > > > > As I described earlier, I included position restraints of backbone in > top file and also added define = -DPOSRES to minim.mdp file. But it seems > that the position restrains have not been included. Would you please > suggest me how I can apply position restraints effectively? > > > > It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your > topology, what you need is -DPOSRE. It is very easy to tell when position > restraints are being applied. A position restraint energy term is written > to > the .log and .edr files. If it's not there, you're not applying > restraints. > > -Justin > > > Thanks in advance. > > Your suggestions would be appreciated. > > Shima > > > > > > -- Forwarded message -- > > From: Shima Arasteh > > Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) > > Subject: Fw: Fwd: [gmx-users] position restraints > > To: Discussion list for GROMACS users > > > > Dear users, > > > > > > Although I put the position restraints on backbone, I get RMSD around > > 0.2 nm. Is it usual? > > This deviation is just for a minimization step only. I' m on doubt > > about keeping the backbone in a fix secondary structure. > > I' d prefer to restraint the backbone completely. Is it possible? > > > > Thanks in advance. > > > > > > > > Restraints allow, by definition, for slight deviations. > > > > Erik > > * Please don't post (un)subscribe requests to the list. Use thewww > > interface or send it to gmx-users-requ...@gromacs.org. > > > > > > > > > > Dear gmx users, > > > > I want to use restraints on backbone of my protein to keep its secondary > > structure during minimization and equilibration steps. To do so, I > > generated backbone-restrain.itp and then included it to top file. Next, > > added define = -DPOSRES to minim.mdp file. > > After minimization, when I check the minimization output file, I saw > > that the backbone of input and output files are not exactly the same. > > Is there any step which I have not done to set the restraints correctly? > > > > > > Thanks in advance. > > > > Sincerely, > > Shima > > > > -- > > > 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:
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include "topol_Protein_chain_A.itp" #ifdef POSRE #include "backbone_posre.itp" #endif #include "topol_Protein_chain_B.itp" #ifdef POSRE #include "backbone_posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "./charmm36-modified.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-modified.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 19936 CL 2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: > I also included the position restraints as follows in my top file: > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #include "strong_posre.itp" > #endif > #include "topol_Protein_chain_B.itp" > #ifdef POSRE > #include "strong_posre.itp" > #include "backbone_posre.itp" > #endif > > As I described earlier, I included position restraints of backbone in top > file and also added define = -DPOSRES to minim.mdp file. But it seems that > the position restrains have not been included. Would you please suggest me > how I can apply position restraints effectively? > It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin > Thanks in advance. > Your suggestions would be appreciated. > Shima > > > -- Forwarded message -- > From: Shima Arasteh > Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) > Subject: Fw: Fwd: [gmx-users] position restraints > To: Discussion list for GROMACS users > > Dear users, > > > Although I put the position restraints on backbone, I get RMSD around > 0.2 nm. Is it usual? > This deviation is just for a minimization step only. I' m on doubt > about keeping the backbone in a fix secondary structure. > I' d prefer to restraint the backbone completely. Is it possible? > > Thanks in advance. > > > > Restraints allow, by definition, for slight deviations. > > Erik > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > > > > > Dear gmx users, > > I want to use restraints on backbone of my protein to keep its secondary > structure during minimization and equilibration steps. To do so, I > generated backbone-restrain.itp and then included it to top file. Next, > added define = -DPOSRES to minim.mdp file. > After minimization, when I check the minimization output file, I saw > that the backbone of input and output files are not exactly the same. > Is there any step which I have not done to set the restraints correctly? > > > Thanks in advance. > > Sincerely, > Shima > -- 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: Fwd: Fw: Fwd: [gmx-users] position restraints
As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include "topol_Protein_chain_A.itp" #ifdef POSRE #include "backbone_posre.itp" #endif #include "topol_Protein_chain_B.itp" #ifdef POSRE #include "backbone_posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "./charmm36-modified.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-modified.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 19936 CL 2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: > I also included the position restraints as follows in my top file: > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #include "strong_posre.itp" > #endif > #include "topol_Protein_chain_B.itp" > #ifdef POSRE > #include "strong_posre.itp" > #include "backbone_posre.itp" > #endif > > As I described earlier, I included position restraints of backbone in top > file and also added define = -DPOSRES to minim.mdp file. But it seems that > the position restrains have not been included. Would you please suggest me > how I can apply position restraints effectively? > It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin > Thanks in advance. > Your suggestions would be appreciated. > Shima > > > -- Forwarded message -- > From: Shima Arasteh > Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) > Subject: Fw: Fwd: [gmx-users] position restraints > To: Discussion list for GROMACS users > > Dear users, > > > Although I put the position restraints on backbone, I get RMSD around > 0.2 nm. Is it usual? > This deviation is just for a minimization step only. I' m on doubt > about keeping the backbone in a fix secondary structure. > I' d prefer to restraint the backbone completely. Is it possible? > > Thanks in advance. > > > > Restraints allow, by definition, for slight deviations. > > Erik > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > > > > > Dear gmx users, > > I want to use restraints on backbone of my protein to keep its secondary > structure during minimization and equilibration steps. To do so, I > generated backbone-restrain.itp and then included it to top file. Next, > added define = -DPOSRES to minim.mdp file. > After minimization, when I check the minimization output file, I saw > that the backbone of input and output files are not exactly the same. > Is there any step which I have not done to set the restraints correctly? > > > Thanks in advance. > > Sincerely, > Shima > -- 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
