[gmx-users] How do I monitor dynamics of helices and domain rotation?
Hi all, 1) I am looking at see if two adjacent helices are changing their conformation in space. I would like to monitor whether they are orthogonal to each other or have become parallel to each other during simulations. Is it possible in Gromacs to follow such changes, and if so, what command would I use to track such changes? 2a) Also how would I track domain rotations? To check if a domain A is rotating with respect to domain B. I am thinking of picking 2 amino acids on domains A and B and monitor the dihederal angle to see if there is rotation between domains A and B. Is it possible to do such an analysis using Gromacs and if so how and what command should I be using? or if there is a different way please do share. 2b) Also I am looking to monitor whether domain A is in the same plane as domain B or if it has gone up or down in space with respect to domain B? How can I monitor this feature? I appreciate your help. Thank you James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] analysing helix dynamics
Hi all, During MD simulations of a protein,I find that there are two helices switch periodically from being parallel and perpendicular to each other. I'd like to plot out the orientation of these two helices with respect to each other, is there a command to extract this information? JJ http://www.chick.com/reading/tracts/1071/1071_01.asp -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Turning OFF/ON distance restraints during a simulation
Hi all, Is it possible to turn OFF/ON distance restraints after simulating a system for a certain period of time? If yes, how do I command GMX to do such a job? Thank you James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] distance restrained D simulations
Yes you are right particle decomposition does not work too! On Thu, Sep 30, 2010 at 12:19 AM, XAvier Periole wrote: > > What is happening is that you've got bonds too long and the > dd can not manage to cut things in 4 subsystems ... > > try particle decomposition but you might end up with the same > problem :(( > > On Sep 29, 2010, at 5:35 PM, jayant james wrote: > > > Hi! > I am trying to perform distance restrained MD simulations of a protein with > Gromacs4.0.5. > I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am > incorporating simular to NOE distance restraints in NMR. > When I use one processor for the simulations its all fine, but, when I use > multiple processors I get a bunch of errors > lets me start with the "NOTE" found below. Well do not want to increase the > cut-off distance but want the program to use multiple processors. How can I > overcome this problem? > I would appreciate your input > Thanks > JJ > > NOTE: atoms involved in distance restraints should be within the longest > cut-off distance, if this is not the case mdrun generates a fatal error, in > that case use particle decomposition (mdrun option -pd) > > > WARNING: Can not write distance restraint data to energy file with domain > decomposition > Loaded with Money > > > --- > Program mdrun_mpi, VERSION 4.0.5 > Source code file: ../../../src/mdlib/domdec.c, line: 5873 > > Fatal error: > There is no domain decomposition for 4 nodes that is compatible with the > given box and a minimum cell size of 8.89355 nm > Change the number of nodes or mdrun option -rdd or -dds > Look in the log file for details on the domain decomposition > --- > > "What Kind Of Guru are You, Anyway ?" (F. Zappa) > > Error on node 0, will try to stop all the nodes > Halting parallel program mdrun_mpi on CPU 0 out of 4 > > gcq#21: "What Kind Of Guru are You, Anyway ?" (F. Zappa) > > -- > mpirun has exited due to process rank 2 with PID 28700 on > node compute-3-73.local exiting without calling "finalize". This may > have caused other processes in the application to be > terminated by signals sent by mpirun (as reported here). > - > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode -1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -- > > > > > > > > > -- > Jayasundar Jayant James > > www.chick.com/reading/tracts/0096/0096_01.asp) > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. 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 > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] distance restrained D simulations
Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR. When I use one processor for the simulations its all fine, but, when I use multiple processors I get a bunch of errors lets me start with the "NOTE" found below. Well do not want to increase the cut-off distance but want the program to use multiple processors. How can I overcome this problem? I would appreciate your input Thanks JJ NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) WARNING: Can not write distance restraint data to energy file with domain decomposition Loaded with Money --- Program mdrun_mpi, VERSION 4.0.5 Source code file: ../../../src/mdlib/domdec.c, line: 5873 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 8.89355 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- "What Kind Of Guru are You, Anyway ?" (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 4 gcq#21: "What Kind Of Guru are You, Anyway ?" (F. Zappa) -- mpirun has exited due to process rank 2 with PID 28700 on node compute-3-73.local exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). - MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. ------ -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] CL atom not being recognised
Hi! I am using the gromos9643a1 forcefield and the chloride is described as given below in the rtp file. I have described the CL as CL- in my pdb input file and still it is not accepting! I am using V 4.0.5 [ CL- ] [ atoms ] CL CL--1.0 0 [ bonds ] [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type On Mon, Jun 28, 2010 at 4:15 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi! >> The protein I am attempting to simulate has a CL atom. When I run pdb2gmx >> I get the following error message. Any help in overcoming this problem would >> be appreciated. >> Thanks >> James -- >> Program pdb2gmx, VERSION 4.0 >> Source code file: pdb2gmx.c, line: 429 >> >> Fatal error: >> Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms >> while sorting atoms >> --- >> > > You haven't told us which force field you're trying to use, but I'm > guessing that the chloride .rtp entry is probably named "CL" instead of > "CL-" (which is used by the ffG* force fields). You can check the .rtp file > to be sure. > > Also, I would strongly suggest upgrading to version 4.0.7 - there have been > numerous bug fixes and performance upgrades since version 4.0. > > -Justin > > >> >> -- >> Jayasundar Jayant James >> >> www.chick.com/reading/tracts/0096/0096_01.asp < >> http://www.chick.com/reading/tracts/0096/0096_01.asp>) >> >> > -- > > > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CL atom not being recognised
Hi! The protein I am attempting to simulate has a CL atom. When I run pdb2gmx I get the following error message. Any help in overcoming this problem would be appreciated. Thanks James -- Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms while sorting atoms --- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] load imbalance
Hi All! i have been getting this messsage in my log file. Started mdrun on node 0 Tue Apr 13 14:28:28 2010 Step Time Lambda 00.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Improper Dih. LJ-14 3.63316e+042.60311e+032.05878e+038.63051e+02 -4.53144e+01 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coul. recip. 5.46208e+042.42763e+05 -4.16328e+03 -1.65989e+06 -2.39317e+05 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.56418e+062.63757e+05 -1.30042e+063.00341e+02 -4.19843e+03 Cons. rmsd () 9.18296e-06 DD step 9 load imb.: force 1.3% DD step 9 load imb.: force 2.1% Step Time Lambda 10 200.20.0 IT IS SOME THING TO DO WITH IMBALANCE. and the force increases with time! I have a few questions based on this above report in my log file 1. Is this some serious problem? 2. Can I ignore this and proceed or do some thing to rectify the problem, if so please tell me what? I am using gromacs 4.0.5 and using 4 nodes, Any help would be appreciated. Thank you Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parts of protein unfolds during MD simulations
Hi! I have an issue with my protein modelling. I find that some of the helices (not all) have greatly unfolded during a 8ns distance restrained MD run. I am using the parameters below for the MD run. Is there any thing that can treat the system better than PME? thanks Jayant James title = Yo cpp = /usr/bin/cpp define = -DDISRES constraints = none ;constraint_algorithm = lincs ;lincs_order = 4 integrator = md dt = 0.001; ps ! nsteps = 100 ; total 1.0ns. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes disre = simple disre_weighting = equal ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = tnc Non-Protein tnt NMR tni tau_t = 0.1 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 300 ; Energy monitoring energygrps = Protein Non-Protein ;tnc Non-Protein tnt NMR tni ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] stopping and restarting a simulations after adding more constraints
Hi! I have been performing a distance restrained simulation for 7ns and now I feel that its time to throw in a few more distance restraints. So this is what I am planning to to 1. Stop the simulation .The command would be, killall mdrun 2. Add the two constraints into the disres.itp 3. use grompp and later the mdrun command. The question is, Since I am restarting the simulation from 7ns I shoudn't give gen_vel=Yes. Am I right? Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] handling particle decomposition with distance restraints
The energy minimization went on without any problem on 4 processors but the problem occurs when I perform the MD run. Also, I did not get any error message with relevance to LINCS etc... JJ On Wed, Jun 24, 2009 at 6:53 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Yes my distance restraints are long because I am using FRET distances as >> distance restraints while performing MD simulations. Upon usage of this >> command >> >> mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro -pd >> & >> >> I get the following error!! I did try giving yes after -pd but even then >> the same error message is repeated. >> >> > Anything else printed to the screen or log file? LINCS warnings or > anything else? Did energy minimization complete successfully? > > -Justin > > Back Off! I just backed up md.log to ./#md.log.9# >> Reading file pr.tpr, VERSION 4.0 (single precision) >> NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain >> NODEID=1 argc=13 >> NODEID=3 argc=13 >> [localhost:17514] *** Process received signal *** >> [localhost:17514] Signal: Segmentation fault (11) >> [localhost:17514] Signal code: Address not mapped (1) >> [localhost:17514] Failing at address: 0x134 >> [localhost:17514] [ 0] /lib64/libpthread.so.0 [0x38dec0f0f0] >> [localhost:17514] [ 1] /lib64/libc.so.6(memcpy+0x15b) [0x38de08432b] >> [localhost:17514] [ 2] >> /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(ompi_convertor_pack+0x152) >> [0x3886e45392] >> [localhost:17514] [ 3] >> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0x13d) >> [0x7f39dd118a4d] >> [localhost:17514] [ 4] >> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_rndv+0x140) >> [0x7f39dd735230] >> [localhost:17514] [ 5] >> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x748) >> [0x7f39dd72e508] >> [localhost:17514] [ 6] >> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_split_bintree+0x91c) >> [0x7f39dc6f735c] >> [localhost:17514] [ 7] >> /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(MPI_Bcast+0x15c) [0x3886e4c40c] >> [localhost:17514] [ 8] mdrun_mpi(bcast_state+0x26c) [0x56d59c] >> [localhost:17514] [ 9] mdrun_mpi(mdrunner+0x1067) [0x42b807] >> [localhost:17514] [10] mdrun_mpi(main+0x3b4) [0x431c34] >> [localhost:17514] [11] /lib64/libc.so.6(__libc_start_main+0xe6) >> [0x38de01e576] >> [localhost:17514] [12] mdrun_mpi [0x413339] >> [localhost:17514] *** End of error message *** >> mpirun noticed that job rank 0 with PID 17514 on node >> localhost.localdomain exited on signal 11 (Segmentation fault). >> 3 additional processes aborted (not shown) >> >> >> >> On Wed, Jun 24, 2009 at 6:04 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>jayant james wrote: >> >> >>I just replaced the old gmx 4.0 version with the 4.0.5 version >>and still the same problem >> >>NOTE: atoms involved in distance restraints should be within the >>longest cut-off distance, if this is not the case mdrun >>generates a fatal error, in that case use particle decomposition >>(mdrun option -pd) >> >>Well, does it work with -pd? It looks like your distance restraints >>are indeed quite long, so this looks like it is your only option. >> >>-Justin >> >> >> >>WARNING: Can not write distance restraint data to energy file >>with domain decomposition >> >> >> >>On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> jayant james wrote: >> >> Hi! >> I am performing an mpi MD (on a quad core system) run with >> distance restraints. When I execute this command below >> without >> position restraints the MD run is distributed over 4 nodes >> perfectly well. But when I incorporate the distance >>restraints I >> hit a road block >>mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr >>-c pr.gro & >>I get this error message (below). My pr.mdp and dist
Re: [gmx-users] handling particle decomposition with distance restraints
Yes my distance restraints are long because I am using FRET distances as distance restraints while performing MD simulations. Upon usage of this command mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro -pd & I get the following error!! I did try giving yes after -pd but even then the same error message is repeated. Back Off! I just backed up md.log to ./#md.log.9# Reading file pr.tpr, VERSION 4.0 (single precision) NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain NODEID=1 argc=13 NODEID=3 argc=13 [localhost:17514] *** Process received signal *** [localhost:17514] Signal: Segmentation fault (11) [localhost:17514] Signal code: Address not mapped (1) [localhost:17514] Failing at address: 0x134 [localhost:17514] [ 0] /lib64/libpthread.so.0 [0x38dec0f0f0] [localhost:17514] [ 1] /lib64/libc.so.6(memcpy+0x15b) [0x38de08432b] [localhost:17514] [ 2] /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(ompi_convertor_pack+0x152) [0x3886e45392] [localhost:17514] [ 3] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0x13d) [0x7f39dd118a4d] [localhost:17514] [ 4] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_rndv+0x140) [0x7f39dd735230] [localhost:17514] [ 5] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x748) [0x7f39dd72e508] [localhost:17514] [ 6] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_split_bintree+0x91c) [0x7f39dc6f735c] [localhost:17514] [ 7] /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(MPI_Bcast+0x15c) [0x3886e4c40c] [localhost:17514] [ 8] mdrun_mpi(bcast_state+0x26c) [0x56d59c] [localhost:17514] [ 9] mdrun_mpi(mdrunner+0x1067) [0x42b807] [localhost:17514] [10] mdrun_mpi(main+0x3b4) [0x431c34] [localhost:17514] [11] /lib64/libc.so.6(__libc_start_main+0xe6) [0x38de01e576] [localhost:17514] [12] mdrun_mpi [0x413339] [localhost:17514] *** End of error message *** mpirun noticed that job rank 0 with PID 17514 on node localhost.localdomain exited on signal 11 (Segmentation fault). 3 additional processes aborted (not shown) On Wed, Jun 24, 2009 at 6:04 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> >> I just replaced the old gmx 4.0 version with the 4.0.5 version and still >> the same problem >> >> NOTE: atoms involved in distance restraints should be within the longest >> cut-off distance, if this is not the case mdrun generates a fatal error, in >> that case use particle decomposition (mdrun option -pd) >> > > Well, does it work with -pd? It looks like your distance restraints are > indeed quite long, so this looks like it is your only option. > > -Justin > > > >> WARNING: Can not write distance restraint data to energy file with domain >> decomposition >> >> >> >> On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>jayant james wrote: >> >>Hi! >>I am performing an mpi MD (on a quad core system) run with >>distance restraints. When I execute this command below without >>position restraints the MD run is distributed over 4 nodes >>perfectly well. But when I incorporate the distance restraints I >>hit a road block >> mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro >> & >> I get this error message (below). My pr.mdp and distance >>restraints files are given below the error message >>. * >>Question.* How do I handle this sitation? Do I increase the long >>range cut off in the pr.mdp file? If you see my distance >>restraints file, my upper range of distances are close to 9nm!! >> >> >>Upgrade to the latest version (4.0.5), since there have been >>numerous improvements to domain decomposition throughout the >>development of version 4.0. >> >>-Justin >> >>Please guide. >>Thanks >>JJ >> >> >> -- >>Back Off! I just backed up md.log to ./#md.log.6# >>Reading file pr.tpr, VERSION 4.0 (single precision) >> >>NOTE: atoms involved in distance restraints should be within the >>longest cut-off distance, if this is not the case mdrun >>generates a fatal error, in that case use particle decomposition >>(mdrun option -pd) >> >> >>WARNING: Can not write distance restraint data to energy file >>with domain decomposition >> >>
Re: [gmx-users] handling particle decomposition with distance restraints
I just replaced the old gmx 4.0 version with the 4.0.5 version and still the same problem NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) WARNING: Can not write distance restraint data to energy file with domain decomposition On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi! >> I am performing an mpi MD (on a quad core system) run with distance >> restraints. When I execute this command below without position restraints >> the MD run is distributed over 4 nodes perfectly well. But when I >> incorporate the distance restraints I hit a road block >> mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro & >> I get this error message (below). My pr.mdp and distance restraints files >> are given below the error message >> . * >> Question.* How do I handle this sitation? Do I increase the long range cut >> off in the pr.mdp file? If you see my distance restraints file, my upper >> range of distances are close to 9nm!! >> > > Upgrade to the latest version (4.0.5), since there have been numerous > improvements to domain decomposition throughout the development of version > 4.0. > > -Justin > > Please guide. >> Thanks >> JJ >> >> -- >> Back Off! I just backed up md.log to ./#md.log.6# >> Reading file pr.tpr, VERSION 4.0 (single precision) >> >> NOTE: atoms involved in distance restraints should be within the longest >> cut-off distance, if this is not the case mdrun generates a fatal error, in >> that case use particle decomposition (mdrun option -pd) >> >> >> >> >> WARNING: Can not write distance restraint data to energy file with domain >> decomposition >> >> --- >> Program mdrun_mpi, VERSION 4.0.2 Source code file: >> domdec.c, line: 5842 >> Fatal error: >> There is no domain decomposition for 4 nodes that is compatible with the >> given box and a minimum cell size of 9.85926 nm >> Change the number of nodes or mdrun option -rdd or -dds >> Look in the log file for >> details on the domain decomposition >> >> --- >> >> *pr.mdp* >> >> ; User spoel (236) >> ; Wed Nov 3 17:12:44 1993 >> ; Input file >> ; >> title = Yo >> cpp = /usr/bin/cpp >> define = -DDISRES >> constraints = none >> ;constraint_algorithm = lincs >> ;lincs_order = 4 >> integrator = md >> dt = 0.001; ps ! >> nsteps = 400 ; total 2.0ns. >> nstcomm = 1 >> nstxout = 5 >> nstvout = 5 >> nstfout = 5 >> nstlog = 5 >> nstenergy = 500 >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> coulombtype = PME >> rcoulomb= 1.0 >> vdwtype = cut-off >> rvdw= 1.4 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft= yes >> disre = simple >> disre_weighting = equal >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = V-rescale >> tc-grps = Protein Non-Protein >> tau_t = 0.1 0.1 >> ref_t = 300 300 >> ; Energy monitoring >> energygrps = Protein Non-Protein >> ;tnc Non-Protein tnt NMR tni >> ; Pressure coupling is not on >> Pcoupl = parrinello-rahman >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ;simulated annealing >> ;Type of annealing form each temperature group (no/single/periodic) >> ;annealing = no, no, no, single, no >> ; >> ;Number of annealing points to use for specifying annealing in each group &
[gmx-users] handling particle decomposition with distance restraints
Hi! I am performing an mpi MD (on a quad core system) run with distance restraints. When I execute this command below without position restraints the MD run is distributed over 4 nodes perfectly well. But when I incorporate the distance restraints I hit a road block mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro & I get this error message (below). My pr.mdp and distance restraints files are given below the error message . * Question.* How do I handle this sitation? Do I increase the long range cut off in the pr.mdp file? If you see my distance restraints file, my upper range of distances are close to 9nm!! Please guide. Thanks JJ -- Back Off! I just backed up md.log to ./#md.log.6# Reading file pr.tpr, VERSION 4.0 (single precision) NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) WARNING: Can not write distance restraint data to energy file with domain decomposition --- Program mdrun_mpi, VERSION 4.0.2 Source code file: domdec.c, line: 5842 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 9.85926 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- *pr.mdp* ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DDISRES constraints = none ;constraint_algorithm = lincs ;lincs_order = 4 integrator = md dt = 0.001; ps ! nsteps = 400 ; total 2.0ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 5 nstlog = 5 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes disre = simple disre_weighting = equal ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ;tnc Non-Protein tnt NMR tni ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ;simulated annealing ;Type of annealing form each temperature group (no/single/periodic) ;annealing = no, no, no, single, no ; ;Number of annealing points to use for specifying annealing in each group ;annealing_npoints = 0, 0, 0, 9, 0 ; ; List of times at the annealing points for each group ;annealing_time = 0 25 50 75 100 125 150 175 200 ; Temp.at each annealing point, for each group. ;annealing_temp = 300 350 400 450 500 450 400 350 300 * distance restraints file* distance_restraints ] ; ai aj typeindex type' low up1 up2 fac ;TnT240-TnI131, 145, 151, 160, 167 (ca+-7) 201938891 1 1 3.913.915.31 0.574679 201940561 2 1 4.864.866.26 0.409911 201941331 3 1 5.695.697.09 0.457947 201942071 4 1 6.636.638.03 0.323852 201942731 5 1 7.147.148.54 0.294559 ;TnT276- Tni 131,145,151,160,167,5,17,27,40 243438891 6 1 1.341.342.74 4.884769 243440561 7 1 2.132.133.53 0.523368 243441331 8 1 3.663.665.06 0.409911 243442071 9 1 4.484.485.88 0.547825 243442731 10 1 5.435.436.83 0.285938 243426281 11 1 5.895.897.29 0.241333 243427191 12 1 4.764.766.16 0.366358 243428241 13 1 3.813.815.21 0.644145 243429721 14 1 3.103.104.50 0.431009 ;TnT288- Tni 131,145,151,160,167,5,17,27,40 25573889
Re: [gmx-users] mpi mdrun
Hi! After installing GMX without the mpi Igive the following commands make clean ./configure --enable-mpi --disable-nice --program-suffix="_mpi" I am getting this problem when I give the --enable-mpi option checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/local/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /usr/local/bin/grep checking for egrep... /usr/local/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi mdrun
Hi! Thanks for your reply. So I suppose I need to have a hostfile in my directory and call it during the mpirun command. I have one clarification, since I am using a quad core how am I to list the processors on the host file? would it need to open a file name \d hostfile and have a list for example like some thing below? processor1 processor 2 processor 3 processor 4 or is getting to the hostfile an automated process (i.e.,) results from executing a program? I just put a search for host file and saw a folder by that name in the directory below ~/software/open-mpi-1.2.8/orte/mca/rds/hostfile Thanks JJ On Wed, Jun 17, 2009 at 9:42 PM, Mark Abraham wrote: > jayant james wrote: > >> Hi! >> Oh!! I see that nnodes: 1. So does that mean that the job I gave is not >> running on four processors? If so how am I to solve this problem? >> > > You haven't configured your MPI system with a suitable hostfile/whatever > for your machine, probably. > > > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi mdrun
Hi! Oh!! I see that nnodes: 1. So does that mean that the job I gave is not running on four processors? If so how am I to solve this problem? thanks JJ On Wed, Jun 17, 2009 at 9:10 PM, Mark Abraham wrote: > jayant james wrote: > >> Hi Mark! >> Thanks for the tip I got it the mpi mdrun running on my quad core machine. >> I just have one small clarification. In the output file md.log I see this >> message >> >> "Started mdrun at node (0)" >> >> I monitor my processor's load using gkrellm to see how many are running. >> When I started the mdrun ( mpirun -np 4 mdrun ) I specified 4 processors >> and gkrellm displays the four processors running to full capacity but why >> does the output in md.log give the above message. I am wondering if I missed >> out some thing !! >> > > Well that's all fairly normal. The top of your .log file will indicate how > many MPI processes are running. > > > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi mdrun
Hi Mark! Thanks for the tip I got it the mpi mdrun running on my quad core machine. I just have one small clarification. In the output file md.log I see this message "Started mdrun at node (0)" I monitor my processor's load using gkrellm to see how many are running. When I started the mdrun ( mpirun -np 4 mdrun ) I specified 4 processors and gkrellm displays the four processors running to full capacity but why does the output in md.log give the above message. I am wondering if I missed out some thing !! Thanks JJ On Tue, Jun 16, 2009 at 2:47 PM, Mark Abraham wrote: > jayant james wrote: > >> Hi !! >> I am attempting to install mpi mdrun such that I can use all four >> processors of my quad core system. But I keep running into this problem!! My >> operating system is Suse 10.1. >> >> (cd .libs && rm -f libgmxpreprocess_mpi.la < >> http://libgmxpreprocess_mpi.la> && ln -s ../libgmxpreprocess_mpi.la < >> http://libgmxpreprocess_mpi.la> libgmxpreprocess_mpi.la < >> http://libgmxpreprocess_mpi.la>) >> make[1]: *** No rule to make target `../mdlib/libmd_mpi.la < >> http://libmd_mpi.la>', needed by `mdrun'. Stop. >> make[1]: Leaving directory `/usr/local/gromacs-4.0.3/src/kernel' >> >> I would appreciate help/suggestions in my installation. >> > > Don't install in root filespace. Unpack the distribution in your own home > directory, configure, make, and then switch to root for "make install". > Also, why bother installing a version that's months old? > > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi mdrun
Hi !! I am attempting to install mpi mdrun such that I can use all four processors of my quad core system. But I keep running into this problem!! My operating system is Suse 10.1. (cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la) make[1]: *** No rule to make target `../mdlib/libmd_mpi.la', needed by `mdrun'. Stop. make[1]: Leaving directory `/usr/local/gromacs-4.0.3/src/kernel' I would appreciate help/suggestions in my installation. Thanks JJ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] essential dynamics analysis
Hi! I have a 7ns MD run of a protein and the RMSD of the protein had stabilized after 3ns. I am about to performed essential dynamics (ED) analysis (using the commands g_covar and g_anaeig) on the trajectory and I have a few questions/clarifications. 1) Should ED analysis be performed only on the segment of trajectory wherein the protein's RMSD has equilibrated, am I right? Because I have the notion that harmonic analysis of a trajectory can only be performed when the protein is undergoing fluctuations about a minimum. In other words once rmsd stabilizes, then one can perform a harmonic analysis. 2) Which would be a better marker to see if the protein has equilibrated to the simulation environment the RMSD of the protein or the projection of motion along Eigen vectors? 3) When I plot the root mean square fluctuation (r.m.s.f.) of the amino acids am I plotting the motions (of c-alphas) orthogonal to the principal component, Eigen vector 1? and would I wrong in saying that these regions of the protein which have large fluctuations, (say greater than 2 angstroms), do experience anharmonic fluctuation? If so how can I pick up anharmonic fluctuations? Thank you JJ -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy
Hi! Thanks for your mail. I used two different operating systems and in both I found this problem of the energy file recurring!! Well I will go ahead and use the tpdconv to extend the simulations. Thanks JJ On Sun, Apr 5, 2009 at 4:38 PM, Mark Abraham wrote: > jayant james wrote: > >> >> Hi! >> I ran a simulation for 1ns and I find that the energy file has been >> written only till 627 ps. I am wondering how to extend my simulations as I >> need the energy file (simulated with 1bar pressure)!!! >> I wonder why this is happening on a consistent basis. I cannot think of >> the energy file being large nor the operating system not being able to write >> it, because the .trr file is much larger than this file and is being written >> down succedfully till 1000ps. I am using GMX 4.0. >> I welcome any suggestions on how to extend the MD run and to overcome this >> energy file problem. >> > > You should be running version 4.0.4, and either way using checkpoints for > your restarts. There's no GROMACS-related reason why your energy file should > stop being written. It's rather more likely you or your filesystem have done > something to cause the observations, but we can't tell what on this > information. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy
Hi! I ran a simulation for 1ns and I find that the energy file has been written only till 627 ps. I am wondering how to extend my simulations as I need the energy file (simulated with 1bar pressure)!!! I wonder why this is happening on a consistent basis. I cannot think of the energy file being large nor the operating system not being able to write it, because the .trr file is much larger than this file and is being written down succedfully till 1000ps. I am using GMX 4.0. I welcome any suggestions on how to extend the MD run and to overcome this energy file problem. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulated annealing
Hi! I have two phosphorylated serines which form part of peptide that I want to perform simulated annealing. But the catch is the SEP group is read as a Non-Protein and so it is present in two T-coupling groups, the Non-Potein and the protein group I want to heat. I need to remove this group (SEP-phosphorylated serine) from the Non-Protein group. The Non-Protein group contains about 20,000 atoms (water, counterions and also the SEP group). So how can I remove this group from the Non-Protein group? Welcoming your suggestions Jayant James On Sat, Mar 21, 2009 at 4:52 AM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi ! >> I am attempting to do a simulated annealing and running into problem. >> Let me give a introduction to my system. I have a segment of a protein >> that was not crystallographyically resolved, but was later resolved by NMR. >> So I ligated the NMR structure to the crystal structure and in an attempt >> to find the correct orientation of the NMR segment in the crystal structure >> I planned to do a simulated annealing run specifically to this ligated NMR >> segment. Having ligated this NMR segment to the crystal structure I gave the >> pdb2gmx command, then created a box, filled it with water and performed a >> distance restrained energy minimization (wherein I input some FRET distances >> as distance restraints). Its all fine till this step. Now I create an index >> group that has the NMR group as the third group in the temperature coupling, >> the other two are Protein and Non-Protein. when I run the grompp to start a >> simulated annealing run I get a message stating that the NMR group's atoms >> are also found in the Protein group. Gromacs is right in detecting this >> problem. As I cannot have the same amino acids in 2 different groups which >> are coupled to two different temperatures. So how am I to attempt this >> simulated annealing because the program does not want to have the NMR group >> present in the Protein group? >> > > You will need to make special index groups, i.e.: > > r 1-x (for the appended segment) > r x-y (the rest of the protein) > > These groups can be used as your tc-grps. > > -Justin > > So say I delete the NMR segment that was appended to the crystal >> structure how and which stage do I integrate the NMR group that I wanted to >> perform the simulated annealing on, into the system? >> Thanks >> Jayant >> *The pr.mdp file is as below* >> >> ; Berendsen temperature coupling is on in two groups >> >> Tcoupl = Berendsen >> >> tc-grps = Protein Non-Protein NMR-group >> tau_t = 0.1 0.1 0.1 >> >> ref_t = 300 300 300 >> >> ; Energy monitoring >> >> energygrps = Protein Non-ProteinNMR-group >> ; Pressure coupling is not on >> >> Pcoupl = parrinello-rahman >> >> tau_p = 0.5 >> >> compressibility = 4.5e-5 >> >> ref_p = 1.0 >> >> ; Generate velocites is on at 300 K. >> >> gen_vel = yes >> >> gen_temp= 300.0 >> >> gen_seed= 173529 >> >> ; >> >> ; >> >> ; >> >> ;simulated annealing >> >> ;Type of annealing form each temperature group (no/single/periodic) >> >> annealing = nono single >> >> ; >> >> ;Number of annealing points to use for specifying annealing in each group >> >> annealing_npoints 0 0 9 >> >> ; >> >> ; List of times at the annealing points for each group >> >> annealing_time = 0 25 50 75 100 125 150 175 200 >> >> ; Temp.at each annealing point, for each group. >> >> annealing_temp = 300 350 400 450 500 450 400 350 300 >> *The error messge is given below* >> >> >> creating statusfile for 1 node... >> >> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14# >> >> checking input for internal consistency... >> >> calling /usr/bin/cpp... >> >> processing topology... >> >> Generated 279 of the 1225 non-bonded parameter combinations >> >> Excluding 3 bonded neighbours for Protein_D 1 >> >> Excluding 2 bonded neighbours for SOL 72948 >> >> Excluding 1 bonded neighbours for NA+ 214 >> >> Excluding 1 bonded neighbours for CL- 207 >> >> processing coordinates... >> >> double-checking input for internal consistency...
[gmx-users] Simulated annealing
ning MD. grompp -f pr.mdp -c em.gro -o pr.tpr -p new.top -n index #mdrun -s pr -e pr -g md -o traj.trr -c pr.gro & #extending #tpbconv -s ../pr.tpr -f 300.xtc -e ../ener.edr -o 1ns.tpr -until 1000 #mdrun -s 1ns.tpr -o 1ns.trr & -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulated annealing
Hi! So the part of my pr.mdp files that handles pressure and temperature looks like as below and if I were to create an index file by name "N-extension" an type it next in the tc-grps as N-extension along with the existing Protein Non-Protein groups is this how I get to handle the simulated annealing for the appended NMR group? Thanks Jayant James ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 On Sat, Mar 7, 2009 at 4:33 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi! >> I have appended the NMR structure to a part of the protein that was not >> resolved to the protein and now I want to perform simulated annealing of the >> 40 amino acids (NMR structure had 33 amino acids and to link I needed >> another 7 aa) that have been thrown into the crystal structure. I am new to >> this simulated annealing procedure. So please help me out as how to write >> out a typical pr.mdp file. I am thinking of increasing the temp of the >> appended piece protein piece to about 1K (while the rest of the protein, >> solvent, Na+ and Cl- are at 300K) and slowly bring the temperature down to >> 300K, say, in about 100 ps and then continue to perform MD simulations. >> > > Running a protein segment at 1 K with solvent at 300 K will probably > lead to some wild behavior of that protein segment, clashes with the > solvent, and possibly an explosion of your system. Just thinking ahead... > > 1) So would it be the wise time to apply distance constraints from the >> protein at 300K to the appended peptide while performing simulated >> annealing? >> > > If you have actual NMR data, perhaps. But attempting to simulate at 1 > K while simultaneously applying distance restraints might be a difficult > task (consider a lower temperature). > > 2) If so what would be a good temperature to set it to kick in? I am really >> confused as to how I am going to specify these 40 residues to be the group >> that needs to be heated up. >> > > Warm it up from some low temperature. There is an example at: > > http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#sa > > If you want a separate temperature coupling group, make a special index > group for it. No idea if that will actually work, but that's how you treat > components of your system differently, in general. > > 3) Usually I have tc-grps specified in pr.mdp as Protein and Non-Protein. >> So how would I go about setting up the temperature groups during the >> simulated annealing protocol? >> > > With the special index group. See #2. > > -Justin > > Thanks >> JJ >> >> >> On Thu, Feb 26, 2009 at 4:47 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>jayant james wrote: >> >>Hi! >>I have a question with regard to a system that I am attempting >>to model. >>The N-terminal of chain of the protein was not resolved >>crystallographically but was later solved by NMR. >>Now my plan is to append the NMR structure on to chain A of the >>protein and perform simulated annealing only for the appended >>NMR fragment. To help it find it biologically relevent >>orientation in the system I could also apply distance restraints >>that I have. >>Is this possible in Gromacs? >> >> >>All except that actual construction part (modeling the two segments >>together), yes. >> >>-Justin >> >>thanks >>JJ >> >> >> >> >> >>___ >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search >>before 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/mailing_lists/users.php >> >> >>-- &g
Re: [gmx-users] Simulated annealing
Hi! I have appended the NMR structure to a part of the protein that was not resolved to the protein and now I want to perform simulated annealing of the 40 amino acids (NMR structure had 33 amino acids and to link I needed another 7 aa) that have been thrown into the crystal structure. I am new to this simulated annealing procedure. So please help me out as how to write out a typical pr.mdp file. I am thinking of increasing the temp of the appended piece protein piece to about 1K (while the rest of the protein, solvent, Na+ and Cl- are at 300K) and slowly bring the temperature down to 300K, say, in about 100 ps and then continue to perform MD simulations. 1) So would it be the wise time to apply distance constraints from the protein at 300K to the appended peptide while performing simulated annealing? 2) If so what would be a good temperature to set it to kick in? I am really confused as to how I am going to specify these 40 residues to be the group that needs to be heated up. 3) Usually I have tc-grps specified in pr.mdp as Protein and Non-Protein. So how would I go about setting up the temperature groups during the simulated annealing protocol? Thanks JJ On Thu, Feb 26, 2009 at 4:47 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi! >> I have a question with regard to a system that I am attempting to model. >> The N-terminal of chain of the protein was not resolved >> crystallographically but was later solved by NMR. >> Now my plan is to append the NMR structure on to chain A of the protein >> and perform simulated annealing only for the appended NMR fragment. To help >> it find it biologically relevent orientation in the system I could also >> apply distance restraints that I have. >> Is this possible in Gromacs? >> > > All except that actual construction part (modeling the two segments > together), yes. > > -Justin > > thanks >> JJ >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulated annealing
Hi! I have a question with regard to a system that I am attempting to model. The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR. Now my plan is to append the NMR structure on to chain A of the protein and perform simulated annealing only for the appended NMR fragment. To help it find it biologically relevent orientation in the system I could also apply distance restraints that I have. Is this possible in Gromacs? thanks JJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy file
Hi! Thanks for your reply. I am having an on going simulation the md.log file states that it has written 875ps but the energy file data for only 662 ps!! this is brand new machine and is so there is no problem of running out of space. I am appending my pr.mdp file please take a look if its some thing to do with parameters and kindly suggest modifications if needed. Thanks JJ title = Yo cpp = /usr/bin/cpp define = -DDISRES constraints = none ;constraint_algorithm = lincs ;lincs_order = 4 integrator = md dt = 0.001; ps ! nsteps = 100 ; total 1.0ns. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes disre = simple disre_weighting = equal ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = ProteinNon-Protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 "pr.mdp" 52L, 1481C 38,1 Top On Wed, Feb 25, 2009 at 11:03 PM, Mark Abraham wrote: > jayant james wrote: > >> Hi! >> I ran a simulation for 1ns (it was a continious run) and when I analyse >> the system energy, I find that the energy file has input till only 500pico >> seconds. Now that I want to extend my simulations I am in a fix!! What could >> be going wrong? I am using GMX version 3.3.3. >> > > Maybe your file system became full, or your cluster file system was no > longer accessible to the simulation node, or the simulation was interrupted > before it completed flushing the buffers. Whatever happened, GROMACS did not > terminate normally, because if there were any relevant .edr parameters to > save at simulation end, it would have done so. > > If you consult the wiki, you will see some strategies for recovering from > here. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy file
Hi! I ran a simulation for 1ns (it was a continious run) and when I analyse the system energy, I find that the energy file has input till only 500pico seconds. Now that I want to extend my simulations I am in a fix!! What could be going wrong? I am using GMX version 3.3.3. Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] checkpoint
Hi! I recently installed GROMACS 4.0 and in the md.log file (pasted below) I found the "writing check point" statement. This was not there in the previous versions of GROMACS. Is this to be expected or is this an indication that some thing is going wrong? Thanks JJ Writing checkpoint, step 58060 at Thu Feb 12 09:09:31 2009 Writing checkpoint, step 59140 at Thu Feb 12 09:24:32 2009 Step Time Lambda 6 60.00.0 Writing checkpoint, step 6 at Thu Feb 12 09:36:31 2009 Energies (kJ/mol) G96Bond G96AngleProper Dih. Improper Dih. LJ-14 5.97995e+037.39308e+033.31574e+032.12446e+031.21354e+03 "md.log" 634L, 23758C550,0-1 87% -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS warning
Hi! I am getting a message in the MD log file as below with respect ro LINCS mentioning deviations. I have constrained all bonds but this problem seems to pertain to a water molecule. Please suggest a way to oversome this issue. Thanks Jayant James Initializing LINear Constraint Solver number of constraints is 4539 average number of constraints coupled to one constraint is 2.9 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.048807 517 518 0.006284 After LINCS 0.000551 520 522 0.000113 Going to use C-settle (72211 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074 rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.064202 1746 1747 0.008456 After LINCS 0.000134 2867 2869 0.18 Started mdrun on node 0 Fri Jan 9 12:43:22 2009 Initial temperature: 299.944 K Step Time Lambda 0 0.0 0.0 Grid: 13 x 20 x 22 cells Configuring nonbonded kernels... Testing x86_64 SSE support... present. Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.015569 675 676 0.001354 After LINCS 0.80 520 522 0.14 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 2.96794e+03 2.64964e+03 9.36791e+02 1.39165e+03 4.77210e+04 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest. 6.48697e+05 -9.38928e+03 -4.00822e+06 -4.30837e+05 2.74831e+03 D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature 1.27022e+01 -3.74134e+06 5.53033e+05 -3.18830e+06 2.99966e+02 Pressure (bar) -2.82027e+03 Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Step Time Lambda 5000 5.0 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.014423 4388 4389 0.001377 After LINCS 0.26 3409 3410 0.06 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.22704e+03 3.55030e+03 2.16248e+03 1.62198e+03 4.75481e+04 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest. 5.11526e+05 -9.27329e+03 -3.36888e+06 -4.42423e+05 3.30945e+02 D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature 4.61447e+00 -3.24661e+06 5.52683e+05 -2.69393e+06 2.99776e+02 Pressure (bar) 2.28435e+01 Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Step Time Lambda 1 10.0 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.016397 3336 3337 0.001453 After LINCS 0.25 2689 2691 0.06 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.09757e+03 3.64033e+03 2.11140e+03 1.63821e+03 4.76074e+04 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest. 5.13273e+05 -9.28148e+03 -3.37251e+06 -4.42402e+05 2.78608e+02 D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature 4.20109e+00 -3.24855e+06 5.53775e+05 -2.69477e+06 3.00369e+02 Pressure (bar) 1.19419e+02 Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Step Time Lambda 15000 15.0 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.016405 2451 2452 0.001466 After LINCS 0.30 520 522 0.06 -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restraining Ca2+ ion
Hi! Thanks for the reply. So would Gromos96 53a6 be available in the latest version of GROMACS? I am currently using Gromacs version 3.3.3. Thanks JJ On Wed, Jan 7, 2009 at 4:28 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi! >> Thanks for the reply. >> I am using the option 0 of pdb2gmx which corresponds to GROMOS96 43a1 >> force field. But earlier today I was linked to a thesis which used GROMACS >> force field so I am still wondering if it would be right for me to go to the >> *.top file and change the charges to amino acids for simulations in GROMOS96 >> force field found in GROMACS package. >> > > I tend to opt for the most recent revision of a modern force field, > something like Gromos96 53a6, unless there is a specific basis for a choice > like 43a1 (i.e., consistency with previous work, parameters that have been > specifically developed for use with that parameter set, etc.) Otherwise, > blindly choosing a force field with no basis for the choice is not a good > idea. > > If you are considering making ad hoc changes to your .top to force a > certain behavior, I think you are asking for trouble, especially if it comes > to peer review. Force fields aren't designed to be tinkered with according > to the whim of a user. If you are willing to expend a great deal of effort > in developing new parameters to accurately replicate real-life behavior, > then by all means do so. Otherwise, I would be very suspicious of results > that come from untested modifications. > > -Justin > > Thanks >> JJ >> >> On Wed, Jan 7, 2009 at 3:07 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>jayant james wrote: >> >>Hi! >>In the protein of my interest I find that oxygen atoms of Thr, >>Tyr and Ser are close to the bound Ca2+. So is there any >>information on charge modifications that need to be made for the >>specified amino acids in the gromacs force field, such that the >>Ca2+ would stay and not stray! >> >> >>I should hope you're not using the "Gromacs force field" (ffgmx), it >>has long been deprecated. You are better off with a more modern >>Gromos96 parameter set. >> >>I think the best procedure would first to refer to the citation you >>were provided earlier today, then proceed with a further literature >>search. Has anyone simulated a similar protein with any success? >> You may be in for some parameterization if you find the existing >>parameters inadequate. Beware, such work is very difficult. >> >>-Justin >> >>Thanks >>Jayant James >> >> >> >> On Wed, Jan 7, 2009 at 10:36 AM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> jayant james wrote: >> >> Hi! >> Thanks for your suggestions. In my protein there are two >> phosphorylated serines (-vely charged) adjacent to each >>other on >> chain A and these serines start to move towards the Ca2+ >>ion in >> chain B. It is only after a while of them being close to >> each >> other that the Ca2+ starts popping off. Also to modify the >> charges of the residues adjoining the Ca2+ ion, what file >>should >> I be looking for to make these changes? would it be the >>topology >> file? >> >> >> Well, that behavior may not be entirely unexpected. Two >> adjacent >> phosphates would likely repel each other, making it difficult to >> bind ions at that location. Is there some basis to suggest that >> Ca2+ should even bind there? >> >> Yes, charges are in your topology. If you generated your >>.top with >> pdb2gmx, then obviously there are entries in the appropriate >> .rtp >> file that can be modified to generate future topologies with the >> same charges. >> >> >> As per your suggestions I would be going with the PME so >>should >> the mdp file modified to incorporate the parameters below be >> sufficient?!! >> >> Well, assuming those are the appropriate cutoff's for your force >> field, and the res
Re: [gmx-users] restraining Ca2+ ion
Hi! Thanks for the reply. I am using the option 0 of pdb2gmx which corresponds to GROMOS96 43a1 force field. But earlier today I was linked to a thesis which used GROMACS force field so I am still wondering if it would be right for me to go to the *.top file and change the charges to amino acids for simulations in GROMOS96 force field found in GROMACS package. Thanks JJ On Wed, Jan 7, 2009 at 3:07 PM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi! >> In the protein of my interest I find that oxygen atoms of Thr, Tyr and Ser >> are close to the bound Ca2+. So is there any information on charge >> modifications that need to be made for the specified amino acids in the >> gromacs force field, such that the Ca2+ would stay and not stray! >> > > I should hope you're not using the "Gromacs force field" (ffgmx), it has > long been deprecated. You are better off with a more modern Gromos96 > parameter set. > > I think the best procedure would first to refer to the citation you were > provided earlier today, then proceed with a further literature search. Has > anyone simulated a similar protein with any success? You may be in for some > parameterization if you find the existing parameters inadequate. Beware, > such work is very difficult. > > -Justin > > Thanks >> Jayant James >> >> >> >> On Wed, Jan 7, 2009 at 10:36 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>jayant james wrote: >> >>Hi! >>Thanks for your suggestions. In my protein there are two >>phosphorylated serines (-vely charged) adjacent to each other on >>chain A and these serines start to move towards the Ca2+ ion in >>chain B. It is only after a while of them being close to each >>other that the Ca2+ starts popping off. Also to modify the >>charges of the residues adjoining the Ca2+ ion, what file should >>I be looking for to make these changes? would it be the topology >>file? >> >> >>Well, that behavior may not be entirely unexpected. Two adjacent >>phosphates would likely repel each other, making it difficult to >>bind ions at that location. Is there some basis to suggest that >>Ca2+ should even bind there? >> >>Yes, charges are in your topology. If you generated your .top with >>pdb2gmx, then obviously there are entries in the appropriate .rtp >>file that can be modified to generate future topologies with the >>same charges. >> >> >>As per your suggestions I would be going with the PME so should >>the mdp file modified to incorporate the parameters below be >>sufficient?!! >> >> >>Well, assuming those are the appropriate cutoff's for your force >>field, and the rest of your .mdp file is satisfactory (and you >>actually specify PME), then it is probably reasonable enough. >> >>-Justin >> >>ns_type= grid >>rlist = 1.0 >>rcoulomb = 1.0 >>rvdw = 1.4 >>vdwtype= cut-off >>fourierspacing = 0.12 >>fourier_nx = 0 >>fourier_ny = 0 >>fourier_nx = 0 >>pme_order = 4 >>ewald_rtol = 1e-5 >>optimize_fft = yes >>disre= simple >>disre_weighting = equal >> Thanks >>Jayant James >> >> >> >> >> >> >> >>___ >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search >>before 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/mailing_lists/users.php >> >> >>-- >> >>Justin A. Lemkul >>Graduate Research Assistant >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >>http://www.bevanlab.b
Re: [gmx-users] restraining Ca2+ ion
Hi! In the protein of my interest I find that oxygen atoms of Thr, Tyr and Ser are close to the bound Ca2+. So is there any information on charge modifications that need to be made for the specified amino acids in the gromacs force field, such that the Ca2+ would stay and not stray! Thanks Jayant James On Wed, Jan 7, 2009 at 10:36 AM, Justin A. Lemkul wrote: > > > jayant james wrote: > >> Hi! >> Thanks for your suggestions. In my protein there are two phosphorylated >> serines (-vely charged) adjacent to each other on chain A and these serines >> start to move towards the Ca2+ ion in chain B. It is only after a while of >> them being close to each other that the Ca2+ starts popping off. Also to >> modify the charges of the residues adjoining the Ca2+ ion, what file should >> I be looking for to make these changes? would it be the topology file? >> > > Well, that behavior may not be entirely unexpected. Two adjacent > phosphates would likely repel each other, making it difficult to bind ions > at that location. Is there some basis to suggest that Ca2+ should even bind > there? > > Yes, charges are in your topology. If you generated your .top with > pdb2gmx, then obviously there are entries in the appropriate .rtp file that > can be modified to generate future topologies with the same charges. > > As per your suggestions I would be going with the PME so should the mdp >> file modified to incorporate the parameters below be sufficient?!! >> >> > > Well, assuming those are the appropriate cutoff's for your force field, and > the rest of your .mdp file is satisfactory (and you actually specify PME), > then it is probably reasonable enough. > > -Justin > > ns_type= grid >> rlist = 1.0 >> rcoulomb = 1.0 >> rvdw = 1.4 >> vdwtype= cut-off >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nx = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> disre= simple >> disre_weighting = equal >> Thanks >> Jayant James >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restraining Ca2+ ion
Hi! Thanks for your suggestions. In my protein there are two phosphorylated serines (-vely charged) adjacent to each other on chain A and these serines start to move towards the Ca2+ ion in chain B. It is only after a while of them being close to each other that the Ca2+ starts popping off. Also to modify the charges of the residues adjoining the Ca2+ ion, what file should I be looking for to make these changes? would it be the topology file? As per your suggestions I would be going with the PME so should the mdp file modified to incorporate the parameters below be sufficient?!! ns_type= grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 vdwtype= cut-off fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nx = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes disre= simple disre_weighting = equal Thanks Jayant James ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restraining Ca2+ ion
Hi, Thanks for your suggestions. Please take a look at the mdp file that I am using. Please suggest any changes that you feel would be adequate if the electrostatic treatment is poor. Thanks Jayant James ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DDISRES -DPOSRES constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 100 ; total 0.5ns. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 disre = simple disre_weighting = conservative ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps= ProteinNon-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 On Tue, Jan 6, 2009 at 2:43 PM, Mark Abraham wrote: > jayant james wrote: > >> Hi! >> I have been performing MD simulations of a protein which has 3 ca2+ ions. >> I find that after 3ns of simulations the ca2+ ions start to drift away. So >> what would be a good strategy to have the ca2+ in place during the >> simulations. I would prefer not to use position restraining as this would >> pin the ca2+ in space hindering the spacial movement of that particular >> area!! but I am wondering if distance restraining of the ca2+ to the >> adjacent residues would be fine? or is there any other/better strategy? >> Awaiting your suggestions. >> > > This is one of the purposes of distance restraints. Better would be a > proper model for protein-bound calcium ions. Also, a poor-quality > electrostatic treatment could be the source of the problem (e.g. a cut-off > shorter than the distances to nearby negative (partial) charges). > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] restraining Ca2+ ion
Hi! I have been performing MD simulations of a protein which has 3 ca2+ ions. I find that after 3ns of simulations the ca2+ ions start to drift away. So what would be a good strategy to have the ca2+ in place during the simulations. I would prefer not to use position restraining as this would pin the ca2+ in space hindering the spacial movement of that particular area!! but I am wondering if distance restraining of the ca2+ to the adjacent residues would be fine? or is there any other/better strategy? Awaiting your suggestions. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] phi/psi
Hi ! I am using the gromos 96 force field to simulate a protein. Is there an option that which I can turn on during a MD run that would constrain side chain motion to within the ramachandran phi/psi values? In insight II there is a switch that a user needs to click and it takes care of the issue. Is there some thing like this in GMX which I can specify in the *.mdp file? Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RMSD between
hi ! I am interested in plotting the RMSD between two amino acids to see if they come close or move away during simulations. Any suggestions would be helpful. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to distancing the counter ions from the protein?
well it seems to be on the protein's surface is it OK? On Mon, Jun 9, 2008 at 6:08 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > jayant james wrote: > >> Hi! >> I had to incorporate a salt conc of 0.15M NaCl and once I have them in put >> in the the box,via genion, I find that they are in close proximity to the >> protein. Is it possible to keep them away from the protein because I do not >> want them so close !! >> > > What about your system makes "close proximity" seem wrong? > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to distancing the counter ions from the protein?
Hi! I had to incorporate a salt conc of 0.15M NaCl and once I have them in put in the the box,via genion, I find that they are in close proximity to the protein. Is it possible to keep them away from the protein because I do not want them so close !! Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] calculating ionic strength
Hi all !! I want to add 150mM KCl into a cubic box that contains a protein in an aqueous environment. How am I to calculate as to how? many Ions of K and Cl, I need to add to bring to the above said salt conc? Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein molecule fragmenting after addition of counter ions
Hi all! I am attempting to counter a charge of -13 in a simulation, where the protein is solvated in water. I use the genion option and choose to replace 13 solvent (water) atoms. Upon visualizing the genion output structure, I find that some atoms from three of the eight cys ( a Hydrogen and two sulphur atoms ) have be yanked out of the protein! I wonder why this is happening!! Is there a way to rectify this? Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] distance restrained energy minimisation
Hi! I am attempting DISRES energy minimization. I'd like to turn ur attention to the 2nd & 5th line below. these contain a common atom 2711 and the distance in the PDB file to its counterpart (2444 or 2575) is 55 angstroms well within the specified range. But still I get a system explode warning!!! The distances given is between SG of CYS to another SG of a Cys. I suppose GMX is pushing/pulling and the SG comes off ; ai aj typeindex type' low up1 up2 fac 25752620 1 1 1 60 60.185 1.0 25752711 1 2 1 40 40 70 1.0 ; 25752824 1 3 1 40 40.160 1.0 24442620 1 4 1 62 62.05 100.00 1.0 24442711 1 5 1 40 40.180 1.0 ; 24442824 1 6 1 47 47.157 1.0 ~ Any tips to overcome this problem is welcome. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ngmx crash
Hi! I am trying to get the intermediate structures from a 2ns simulation and I use ngmx for the same. I am able to open the visualizer using the command ngmx -f trj.trr -s pr.tpr But when I try to get the coordinate file (say 50ps) I get an error as given below. How am I to overcome this problem ? I am using the latest version og GMX! thanks Jayant --- Program ngmx, VERSION 3.3.3 Source code file: confio.c, line: 1130 Software inconsistency error: Not supported in write_sto_conf --- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] position and distance restraining
Hi! During simulations for distance restraints to kick in, is it necessary to specify disre = simple even after it is defined as DDISRES in the pr.mdp file? Thanks Jayant Ititle = cpp = /usr/bin/cpp define = -DDISRES -DPOSRES . . . . . . -.- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] recognising phos group
Hi! It is actually a phosphorylated serine!! So I am wondering if GMX has any special building block for handling such special cases? Jayant On Wed, Apr 9, 2008 at 12:26 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Darn, forget that post, I wasn't reading clearly. Too early here. It's > part of a phosphorylated residue, you could've at least mentioned the > residue to go with it. There's some stuff on the contributions pages > of the gromacs site about phosphorylated residues. Have a look there. > > Sorry for the previous babbling... The reference to the wiki still goes > though > > Cheers, > > Tsjerk > > > > On Wed, Apr 9, 2008 at 9:24 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> > wrote: > > Hi Jayant, > > > > PO3 seems to me the anion of metaphosphoric acid, not much to do with > > phosphoric acid. The latter could be sort of extracted from phosphoric > > acid containing residues, although that doesn't give guarantees for > > good behaviour. Also, I wouldn't count on the PO4 parameters thus > > extracted to have much to do with PO3. Very likely that the atomic > > charges are quite different, but maybe LJ parameters too. > > > > Have a look at > > > > http://wiki.gromacs.org/index.php/Parameterization > > > > Cheers, > > > > Tsjerk > > > > > > > > On Wed, Apr 9, 2008 at 3:44 AM, jayant james <[EMAIL PROTECTED]> > wrote: > > > Hi ! > > > I am attempting to simulate a protein that is phosphorylated below is > a part > > > of the PDF file > > > HETATM 460 P PO3 A 200 14.995 1.523 4.011 1.00 0.89 > > > P > > > HETATM 461 O1 PO3 A 200 14.287 1.882 5.272 1.00 1.16 > > > O > > > HETATM 462 O2 PO3 A 200 15.841 0.179 4.048 1.00 0.77 > > > O > > > HETATM 463 O3 PO3 A 200 14.134 1.500 2.694 1.00 0.97 > > > O > > > HETATM 464 P PO3 A 201 13.207 -1.138 -1.342 1.00 1.31 > > > P > > > HETATM 465 O1 PO3 A 201 12.997 -2.551 -0.914 1.00 1.43 > > > O > > > HETATM 466 O2 PO3 A 201 11.918 -0.211 -1.324 1.00 1.47 > > > O > > > HETATM 467 O3 PO3 A 201 13.927 -0.914 -2.727 1.00 1.41 > > > O > > > > > > but upon executing pdb2gmx of the PDB file I get an error > > > ----- > > > Fatal error: > > > Residue 'PO3' not found in residue topology database > > > -- > > > > > > I do know that DNA can be simulated in GROMOS (option 0 of pdb2gmx). > So I am > > > wondering how to overcome the above error. > > > > > > Awaiting suggestions > > > Thanks > > > Jayant > > > > > > > > > -- > > > Jayasundar Jayant James > > > > > > www.chick.com/reading/tracts/0096/0096_01.asp) > > > Residence -24935864, cell-9841042164 > > > ___ > > > gmx-users mailing listgmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > Junior UD (post-doc) > > Biomolecular NMR, Bijvoet Center > > Utrecht University > > Padualaan 8 > > 3584 CH Utrecht > > The Netherlands > > P: +31-30-2539931 > > F: +31-30-2537623 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] recognising phos group
Hi ! I am attempting to simulate a protein that is phosphorylated below is a part of the PDF file HETATM 460 P PO3 A 200 14.995 1.523 4.011 1.00 0.89 P HETATM 461 O1 PO3 A 200 14.287 1.882 5.272 1.00 1.16 O HETATM 462 O2 PO3 A 200 15.841 0.179 4.048 1.00 0.77 O HETATM 463 O3 PO3 A 200 14.134 1.500 2.694 1.00 0.97 O HETATM 464 P PO3 A 201 13.207 -1.138 -1.342 1.00 1.31 P HETATM 465 O1 PO3 A 201 12.997 -2.551 -0.914 1.00 1.43 O HETATM 466 O2 PO3 A 201 11.918 -0.211 -1.324 1.00 1.47 O HETATM 467 O3 PO3 A 201 13.927 -0.914 -2.727 1.00 1.41 O but upon executing pdb2gmx of the PDB file I get an error - Fatal error: Residue 'PO3' not found in residue topology database -- I do know that DNA can be simulated in GROMOS (option 0 of pdb2gmx). So I am wondering how to overcome the above error. Awaiting suggestions Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] To the GMX developers-distance restraints
To the GMX developers. Hi! I am attempting to perform distance restrained energy minimization and I have a specific doubt regarding the "define" parameter in em.mdp. To specify distance restraints I include disre= simple in the em.mdp file. Do I need to specify some thing like "define = -DDISRES"? I have not seen some thing like this in the gromacs manual but I was going thro the GMX discussion list and seen some folks define distance restraints as "define = -DDISRES". I am under the impression that by specifying disre=simple I automatically turn on distance restraints. Also I saw one person had "gen_vel=yes" in em.mdp is this option possible . Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] table-extension
*hi ! I am getting this error with regard to table extensions. Any suggestions to overcome this would be greatly appreciated! Thanks Jayant James * Warning: 1-4 interaction between 429 and 434 at distance 1.002 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file On Fri, Mar 28, 2008 at 11:42 AM, Yang Ye <[EMAIL PROTECTED]> wrote: > jayant james wrote: > > *hi! > I am attempting to run a distance & position restrained simulation in > water. The **distance and position restraining files are called from the > *.top file as posres.itp and disres.itp. After a 200ps run I do not see > the distance nor position restraining kicking in. I am not sure if I have > specified every thing correctly. I have pasted essential parts of the > topology file, em.mdp, pr.mdp, disres.itp and posres.itp. Awaiting your > feedback > Thanks > Jayant James > * > *TOP FILE* > > ; Include Position restraint file > #ifdef POSRES > ;include "posre.itp" > #endif > > ;include"disres.itp" > > Putting semicolon in front of the line effectively turns off that line. > > Regards, > Yang Ye > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Position restraint and distance restraints
*hi! I am attempting to run a distance & position restrained simulation in water. The **distance and position restraining files are called from the *.top file as posres.itp and disres.itp. After a 200ps run I do not see the distance nor position restraining kicking in. I am not sure if I have specified every thing correctly. I have pasted essential parts of the topology file, em.mdp, pr.mdp, disres.itp and posres.itp. Awaiting your feedback Thanks Jayant James * *TOP FILE* ; Include Position restraint file #ifdef POSRES ;include "posre.itp" #endif ;include"disres.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_D 1 SOL 70360 NA+ 14 *em.mdp *; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEXIBLE -DPOSRES constraints = none integrator = steep nsteps = 10 disre = simple ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no *pr.mdp* title = Nterm of TnC free (1-19) and TnT fully constrained cpp = /usr/bin/cpp define = -DPOSRES -DFLEXIBLE constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 10 ; total 200 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 disres = simple ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 *disres.itp *[ distance_restraints ]* *; ai aj typeindex type' low up1 up2 fac 973 926 1 1 1 20.721.730.51.0 842 926 1 1 1 16.317.320.91.0 429 926 1 1 1 40.15 41.15 52.85 1.0 973 10791 1 1 39.45 30.45 48.75 1.0 842 10791 1 1 21.85 22.85 33.55 1.0 429 10791 1 1 40 42 65.31.0 973 11481 1 1 38 39 61.21.0 842 11481 1 1 32 33.75 53.71.0 429 11481 1 1 52 54.972.91.0 973 12161 1 1 42 46.35 69.25 1.0 842 12161 1 1 43 43.85 64.55 1.0 429 12161 1 1 57 59.881.61.0 973 12841 1 1 48 50.05 76.35 1.0 842 12841 1 1 45 47.476.91.0 429 12841 1 1 55 58.95 94.45 1.0 * posres.itp* [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 10 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 14 1 1000 1000 1000 15 1 1000 1000 1000 . . . . . . . . . . . . -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Distance constrained energy minimization and MD
Hi all! The protein that I am trying to simulate has 3 chains. My aim is to apply harmonic constraints to certain parts of the protein and (based on FRET derived distances) I am attempting to incorporate distance constraint between certain amino acids of different chains during EM and MD. *Harmonic Constraints* I figured, that for the harmonic constraining the input is in the file "posres_D.itp" and I specify define = -DFLEXIBLE -DPOSRES in the em.mdp *Distance constraints * I would also like to have amino acids contrained, not by a fixed distance but within a range(say 45-75 angstroms). How do I go about doing this? thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] enabling threads in GROMACS
hi all IS it possible to enable threads in gromacs during configuration? Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] binutils error msg x86_64-unknown-linux-gnu
hi friends, I am installing GMX on a 2xdual core opteron processor system running on linux 10.0 I install lam by disabling the fortran as ./configure -without-fc make make install I configure fftw ./configure --enable-floats --enable-mpi make make install distclean ./configure --enable-mpi make make install but during the installation of binutils2.16.1 I get the following output message. I am not sure whether to go forward or not with the gromacs installation. linux:/usr/local/binutils-2.16.1 # ./configure loading cache ./config.cache checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking build system type... x86_64-unknown-linux-gnu checking for a BSD compatible install... (cached) /usr/bin/install -c checking whether ln works... (cached) yes checking whether ln -s works... (cached) yes checking for gcc... (cached) gcc checking whether the C compiler (gcc ) works... yes checking whether the C compiler (gcc ) is a cross-compiler... no checking whether we are using GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gnatbind... no checking whether compiler driver understands Ada... (cached) no checking how to compare bootstrapped objects... (cached) cmp --ignore-initial=16 $$f1 $$f2 checking for correct version of gmp.h... yes checking for MPFR... yes checking for bison... (cached) bison checking for bison... (cached) bison -y checking for gm4... (cached) m4 checking for flex... (cached) flex checking for flex... (cached) flex checking for makeinfo... no checking for x86_64-unknown-linux-gnu-ar... no checking for ar... (cached) ar checking for x86_64-unknown-linux-gnu-as... no checking for as... (cached) as checking for x86_64-unknown-linux-gnu-dlltool... no checking for dlltool... (cached) dlltool checking for x86_64-unknown-linux-gnu-ld... (cached) /usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld checking for x86_64-unknown-linux-gnu-nm... no checking for nm... (cached) nm checking for x86_64-unknown-linux-gnu-ranlib... no checking for ranlib... (cached) ranlib checking for x86_64-unknown-linux-gnu-windres... no checking for windres... (cached) windres checking for x86_64-unknown-linux-gnu-objcopy... no checking for objcopy... (cached) objcopy checking for x86_64-unknown-linux-gnu-objdump... no checking for objdump... (cached) objdump checking for x86_64-unknown-linux-gnu-ar... no checking for ar... (cached) ar checking for x86_64-unknown-linux-gnu-as... no checking for as... (cached) as checking for x86_64-unknown-linux-gnu-dlltool... no checking for dlltool... (cached) dlltool checking for x86_64-unknown-linux-gnu-ld... no checking for ld... (cached) ld checking for x86_64-unknown-linux-gnu-nm... no checking for nm... (cached) nm checking for x86_64-unknown-linux-gnu-ranlib... no checking for ranlib... (cached) ranlib checking for x86_64-unknown-linux-gnu-windres... no checking for windres... (cached) windres checking whether to enable maintainer-specific portions of Makefiles... no checking if symbolic links between directories work... (cached) yes creating ./config.status creating Makefile Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] position restrained energy minimization
Hello gmx-users! 1. Is it possible to perform position restrained energy minimisation? 2. If so what are the parameter that I need to incorporate in the em.mdp file. By just changing the define = -DFLEX_SPC in the em.mdp to define = -DPOSRES will it mean that I am now entering into position restrained energy minimisation? Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] failed dependencies
hi ! I am trying to install GMX on a opteron 2xdual core processor. OS- Suse Linux10.0. I actually installed the intel fortran compiler as I was just not able to get the Suse fortran compiler. I downloaded the suse 10 from opensuse.org. I get this message while trying to install lam error: Failed dependencies: gcc-g77 is needed by lam-7.0.6-5 openssh-clients is needed by lam-7.0.6-5 openssh-server is needed by lam-7.0.6-5 Suggestions to overcome this problem will be greatly appreciated. Thanks Jayant Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GMX on 2xopteron Dual core
Hello friends! After reviewing the chart for GMX performance I purchased this 2x dual core opteron ,2.6GHz procesors and installed Fedora Core 4 (K8N-DL mother board). On booting up, the OS gives the message 'MP system not assigned by PSB bios structure". how do I overcome this problem? Would installation of another OS overcome the proble, like say example would installing SuSe 10.0 solve the problem. Your suggestions/response will be greatly appreciated. processor specifications: -- 1. AMD opteron Model 285, 2.6 GHz, Dual core 2mb Cache Qty-2 2. Motherboard Asus K8N-DL supports Dual opteron , 8-channel sound, Serial ATA, USB2.0 3. Memory, PC 3200, 1024, ECC resistered, total : 4 GB. 4. Sea gate Hard drive SATA,3.5", 300GB, 8MB cache,Native command Queing, model ST3300831AS During Installation I give - /boot- 10 GB /home-10GB /swap- 8GB Thanks Jayant ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulations to corroborate FRET data
Hi all! I am performing simulations to corraborate with FRET data. I have performed mutations on a few residues and made them cys. To these cys AEDANS needs to be attached. The pdb O/P was got from PRODRG. Now my worry is how am I gonna build the .top file for this flour and how to attach it to the Cys of interest. Looking forward to your suggestions. Thanks Jayant Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] missing residues
Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Please suggest suggestions on how? I go about building these missing residues and integrating with the crystallographically resolved structure such that I can proceed with MD simulations. Thanks Jayant Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] opteron 2xdual core for MD
Ok. THanks! On Tue, 28 Mar 2006 Mark Abraham wrote : >Jayant James Jayasundar wrote: >>OK. So which one would perform better! > >> >There's probably nothing meaningful different between these two with respect to performance and maintenance. > >Like I said, there'd be no meaningful difference in performance. I understand EL might get some phone support or something that might be worth the money to you. Otherwise read the Redhat promo material for their comparison of the two. > >Mark >___ >gmx-users mailing list gmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] opteron 2xdual core for MD
OK. So which one would perform better! thanks Jayant On Tue, 28 Mar 2006 Mark Abraham wrote : >Jayant James Jayasundar wrote: >>hello friends, >>Based on the benchmarking of gromacs on various processors I am planning to buy a opteron 2xdual core system to perform MD simulation. I am giving the configuration below please give your comments on the operating system that is best suited. Whether to use Fedora core4 or Enterprise Linux. > >There's probably nothing meaningful different between these two with respect to performance and maintenance. > >Mark >___ >gmx-users mailing list gmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] opteron 2xdual core for MD
hello friends, Based on the benchmarking of gromacs on various processors I am planning to buy a opteron 2xdual core system to perform MD simulation. I am giving the configuration below please give your comments on the operating system that is best suited. Whether to use Fedora core4 or Enterprise Linux. CPU - 2 AMD Opteron model 285 Dual-Core 2.6Ghz x2 Memory - 4gb Memory DDR-400 ECC Registered (4x1024mb, 2 for each processor) x4 Hard Drive(s) - Seagate 300 Gb SATA (NCQ) Video - XFX 7800GT 256mb Dual DVI Operating System - ? Thanking you Jayant James Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
