[gmx-users] Error energy minimization on protein with implicit water
Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 5000; Maximum number of (minimization) steps to perform nstenergy= 1; Write energies to disk every nstenergy steps energygrps= System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type= simple ; Method to determine neighbor list (simple, grid) coulombtype= cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.0; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) I get a note as = System has non-zero total charge: -4.96e+00 then i tried using genion step as= genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log then again the grompp step and mdrun . but while doing mdrun i get an error as= Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 but here i have given nsteps as 5000 so why does it stop. -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] All-bonds vs h-bonds contraints
Hello Could you please clarify what is the reason for adopting the all-bonds constraints as a standard practice in gmx protein simulations? I mean, the argument that the time step in molecular simulations can be increased by a factor of 4 by replacing the bond vibrations by holonomic constraints' (LINCS paper) seems valid to me in the case of bonds that contain hydrogen (10 fs vibration period for a C-H bond). Why there is a need (if any) to turn ALL bonds to constraints? Furthermore, has anybody seen a difference in the ps/ns protein dynamics when switching from all-bonds to h-bonds constraints? My opinion is that if bond vibrations take place in the fs timescale AND are uncoupled to the slower degrees of freedom , the choice of constraints shouldn't matter, apart from the computation cost of course. I would really appreciate any comments on these issues. Many thanks in advance. George Patargias -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to get the block averaged MSD curve ?
Hi, I have a simulation result from 0 to 50ns after equilibration run. I want to divide this data set equally into 10blocks (10ns each) and get block averaged MSD curve (average of 10 blocks). It seems that I mange to get block MSD data by using g_msd -beginfit 0 -endfit 10, g_msd -beginfit 10 -endfit 20, Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files) My question is that how can I get averaged MSD from this outputs?? It seems that g_analyze is appropriate to do this. g_analyze -n 10 -av ?? Could anybody tell me how to get averaged MSD using g_analyze (each block data has different x values but same length) ? Another question is that what is the difference bwn g_msd and g_analyze -msd ?? Is there any reference of posting to obtain this information ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Problem with simulation of Protein-DNA complex
Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am using: Force-Field: amber99sb-ildn water model: TIP3P 40 NA ions were added in order to neutralise the complex-solvent system. Gromacs doesn't show any error up until I proceed to do nvt equilibriation. Following is nvt.mdp: title = PFV_DNA_NVT define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 100 ; 2 * 5 = 100 ps dt = 0.001 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracyi ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed It generates a tpr, but upon mpirun gives the following error: starting mdrun 'Protein in water' 100 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.027514, max 0.979682 (between atoms 3460 and 3461) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3455 3457 65.20.1542 0.2535 0.1526 3455 3456 33.30.1093 0.1322 0.1090 3457 3459 72.70.1105 0.1739 0.1090 3457 3458 65.70.1105 0.1588 0.1090 3460 3469 78.60.1409 0.2693 0.1400 3460 3461 78.80.1409 0.2772 0.1400 3461 3463 75.10.1406 0.1489 0.1400 3463 3465 37.20.1403 0.1756 0.1400 3463 3464 40.70.1083 0.1408 0.1080 3465 3467 35.50.1403 0.1733 0.1400 3467 3469 74.00.1405 0.1373 0.1400 3467 3468 42.90.1083 0.1433 0.1080 Wrote pdb files with previous and current coordinates Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3475 3495 110.80.1526 20544.7148 0.1522 3475 3477 111.60.1529 20544.4336 0.1526 3475 3476 108.10.1094 20543.1309 0.1090 3477 3480 62.80.1527 4.6441 0.1526 3477 3479 57.50.1091 4.5683 0.1090 3477 3478 93.60.1091 4.6160 0.1090 3495 3497 138.10.1336 4.9133 0.1335 3495 3496 69.60.1230 4.9085 0.1229 3497 3499 40.20.1449 0.2036 0.1449 3497 3498 43.80.1010 0.1527 0.1010 3480 3483 35.60.1526 0.1902 0.1526 3480 3482 42.20.1090 0.1501 0.1090 3480 3481 41.70.1090 0.1485 0.1090 3453 3455 88.70.1701 117322.3672 0.1449 3453 3454 88.30.1035 65066.2227 0.1010 3455 3471 48.90.1763 171383.6562 0.1522 3455 3457 134.60.2535 572521.2500 0.1526 3455 3456 66.70.1322 143042. 0.1090 3457 3460 67.5
Re: [gmx-users] Problem with simulation of Protein-DNA complex
On Thu, Feb 9, 2012 at 8:44 PM, rar...@ens-cachan.fr wrote: Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am using: Force-Field: amber99sb-ildn water model: TIP3P 40 NA ions were added in order to neutralise the complex-solvent system. Gromacs doesn't show any error up until I proceed to do nvt equilibriation. Before the NVT, you may do some energy minimization. Following is nvt.mdp: title = PFV_DNA_NVT define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100 ; 2 * 5 = 100 ps dt = 0.001 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracyi ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed It generates a tpr, but upon mpirun gives the following error: starting mdrun 'Protein in water' 100 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.027514, max 0.979682 (between atoms 3460 and 3461) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3455 3457 65.2 0.1542 0.2535 0.1526 3455 3456 33.3 0.1093 0.1322 0.1090 3457 3459 72.7 0.1105 0.1739 0.1090 3457 3458 65.7 0.1105 0.1588 0.1090 3460 3469 78.6 0.1409 0.2693 0.1400 3460 3461 78.8 0.1409 0.2772 0.1400 3461 3463 75.1 0.1406 0.1489 0.1400 3463 3465 37.2 0.1403 0.1756 0.1400 3463 3464 40.7 0.1083 0.1408 0.1080 3465 3467 35.5 0.1403 0.1733 0.1400 3467 3469 74.0 0.1405 0.1373 0.1400 3467 3468 42.9 0.1083 0.1433 0.1080 Wrote pdb files with previous and current coordinates Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3475 3495 110.8 0.1526 20544.7148 0.1522 3475 3477 111.6 0.1529 20544.4336 0.1526 3475 3476 108.1 0.1094 20543.1309 0.1090 3477 3480 62.8 0.1527 4.6441 0.1526 3477 3479 57.5 0.1091 4.5683 0.1090 3477 3478 93.6 0.1091 4.6160 0.1090 3495 3497 138.1 0.1336 4.9133 0.1335 3495 3496 69.6 0.1230 4.9085 0.1229 3497 3499 40.2 0.1449 0.2036 0.1449 3497 3498 43.8 0.1010 0.1527 0.1010 3480 3483 35.6 0.1526 0.1902 0.1526 3480 3482 42.2 0.1090 0.1501 0.1090 3480 3481 41.7 0.1090 0.1485 0.1090 3453 3455 88.7 0.1701 117322.3672 0.1449 3453 3454 88.3 0.1035 65066.2227 0.1010 3455 3471 48.9
Re: [gmx-users] how to get the block averaged MSD curve ?
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim ilmare...@gmail.com wrote: Hi, I have a simulation result from 0 to 50ns after equilibration run. I want to divide this data set equally into 10blocks (10ns each) and get block averaged MSD curve (average of 10 blocks). I would try some external software. excel. It seems that I mange to get block MSD data by using g_msd -beginfit 0 -endfit 10, g_msd -beginfit 10 -endfit 20, Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files) My question is that how can I get averaged MSD from this outputs?? It seems that g_analyze is appropriate to do this. g_analyze -n 10 -av ?? Could anybody tell me how to get averaged MSD using g_analyze (each block data has different x values but same length) ? Another question is that what is the difference bwn g_msd and g_analyze -msd ?? Is there any reference of posting to obtain this information ? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error energy minimization on protein with implicit water
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 emtol = 1.0 kJ/mol nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple ; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = no ; Periodic Boundary Conditions (yes/no) I get a note as = System has non-zero total charge: -4.96e+00 then i tried using genion step as= genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log then again the grompp step and mdrun . but while doing mdrun i get an error as= Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 but here i have given nsteps as 5000 so why does it stop. -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error energy minimization on protein with implicit water
Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 5000; Maximum number of (minimization) steps to perform nstenergy= 1; Write energies to disk every nstenergy steps energygrps= System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type= simple ; Method to determine neighbor list (simple, grid) coulombtype= cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.0; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) I get a note as = System has non-zero total charge: -4.96e+00 then i tried using genion step as= genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log then again the grompp step and mdrun . but while doing mdrun i get an error as= Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 but here i have given nsteps as 5000 so why does it stop. -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Error energy minimization on protein with implicit water
lina wrote: On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1.0 emtol = 1.0 If mdrun could not converge to 1000, setting a target of 1 will not solve anything. The OP should refer to: http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation
vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with simulation of Protein-DNA complex
Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NVT. I was so engrossed in other details that I forgot to mention it! Quoting lina lina.lastn...@gmail.com: On Thu, Feb 9, 2012 at 8:44 PM, rar...@ens-cachan.fr wrote: Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am using: Force-Field: amber99sb-ildn water model: TIP3P 40 NA ions were added in order to neutralise the complex-solvent system. Gromacs doesn't show any error up until I proceed to do nvt equilibriation. Before the NVT, you may do some energy minimization. Following is nvt.mdp: title = PFV_DNA_NVT define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100 ; 2 * 5 = 100 ps dt = 0.001 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracyi ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed It generates a tpr, but upon mpirun gives the following error: starting mdrun 'Protein in water' 100 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.027514, max 0.979682 (between atoms 3460 and 3461) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3455 3457 65.2 0.1542 0.2535 0.1526 3455 3456 33.3 0.1093 0.1322 0.1090 3457 3459 72.7 0.1105 0.1739 0.1090 3457 3458 65.7 0.1105 0.1588 0.1090 3460 3469 78.6 0.1409 0.2693 0.1400 3460 3461 78.8 0.1409 0.2772 0.1400 3461 3463 75.1 0.1406 0.1489 0.1400 3463 3465 37.2 0.1403 0.1756 0.1400 3463 3464 40.7 0.1083 0.1408 0.1080 3465 3467 35.5 0.1403 0.1733 0.1400 3467 3469 74.0 0.1405 0.1373 0.1400 3467 3468 42.9 0.1083 0.1433 0.1080 Wrote pdb files with previous and current coordinates Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3475 3495 110.8 0.1526 20544.7148 0.1522 3475 3477 111.6 0.1529 20544.4336 0.1526 3475 3476 108.1 0.1094 20543.1309 0.1090 3477 3480 62.8 0.1527 4.6441 0.1526 3477 3479 57.5 0.1091 4.5683 0.1090 3477 3478 93.6 0.1091 4.6160 0.1090 3495 3497 138.1 0.1336 4.9133 0.1335 3495 3496 69.6 0.1230 4.9085 0.1229 3497 3499 40.2 0.1449 0.2036 0.1449 3497 3498 43.8 0.1010 0.1527 0.1010 3480 3483 35.6 0.1526 0.1902 0.1526 3480 3482 42.2 0.1090 0.1501 0.1090 3480 3481 41.7 0.1090
Re: [gmx-users] Error energy minimization on protein with implicit water
By setting the emtol to 1.0, didnt work. Anyother way i could figure out. On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1.0 emtol = 1.0 If mdrun could not converge to 1000, setting a target of 1 will not solve anything. The OP should refer to: http://www.gromacs.org/**Documentation/Errors#Stepsize_** too_small.2c_or_no_change_in_**energy._Converged_to_machine_** precision.2c_but_not_to_the_**requested_precisionhttp://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Energy minimization Error
Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ;Include restraints on water #ifdef POSRES_WAT #include posre_wat.itp #endif ; Include generic topology for ions #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 ;SOL 390842 SOL 390820 NA+22 while this is the posre_wat.itp file I generated with genrestr ; position restraints for non-Protein of Protein in water [ position_restraints ] ; i funct fcxfcyfcz 152311 1000 1000 1000 152321 1000 1000 1000 152331 1000 1000 1000 152341 1000 1000 1000 152351 1000 1000 1000 152361 1000 1000 1000 152371 1000 1000 1000 152381 1000 1000 1000 152391 1000 1000 1000 152401 1000 1000 1000 152411 1000 1000 1000 152421 1000 1000 1000 152431 1000 1000 1000 152441 1000 1000 1000 152451 1000 1000 1000 152461 1000 1000 1000 152471 1000 1000 1000 152481 1000 1000 1000 152491 1000 1000 1000 152501 1000 1000 1000 152511 1000 1000 1000 .. 1877121 1000 1000 1000
Re: [gmx-users] Energy minimization Error
francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision. http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ;Include restraints on water #ifdef POSRES_WAT #include posre_wat.itp #endif ; Include generic topology for ions #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 ;SOL 390842 SOL 390820 NA+22 while this is the posre_wat.itp file I generated with genrestr ; position restraints for non-Protein of Protein in water [ position_restraints ] ; i funct fcxfcyfcz 152311 1000 1000 1000 152321 1000 1000 1000 152331 1000 1000 1000 152341 1000 1000 1000 152351 1000 1000 1000 152361 1000 1000 1000 152371 1000 1000 1000 152381 1000 1000 1000 152391 1000 1000 1000 152401 1000 1000 1000 152411 1000 1000 1000 152421 1000 1000 1000 152431
Re: [gmx-users] Using groups in the mdp file
--- On Mon, 6/2/12, Ignacio Fernández Galván jel...@yahoo.com wrote: The .gro file does not contain any mention to ACX, but I believe it's not needed, as long as it's in the .top, right? It seems that default group names are generated not from moleculetype names, but from residue names. At least that's what it says in http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx: default index groups are already generated (entire system, 9 groups for proteins, and one for every other *residue name*). In my case, if I use GLC (residue) for energygrps instead of ACX (molecule), it works fine. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Energy minimization Error
Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? 2012/2/9 Justin A. Lemkul jalem...@vt.edu francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision. http://www.gromacs.org/**Documentation/Errors#Stepsize_** too_small.2c_or_no_change_in_**energy._Converged_to_machine_** precision.2c_but_not_to_the_**requested_precisionhttp://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/**gromacs_special/share/gromacs/** top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology #include /home/cocktail/vitalini/**gromacs_special/share/gromacs/** top/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ;Include restraints on water #ifdef POSRES_WAT #include posre_wat.itp #endif ; Include generic topology for ions #include /home/cocktail/vitalini/**gromacs_special/share/gromacs/** top/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 ;SOL 390842 SOL 390820 NA+22 while this is the posre_wat.itp file I generated with genrestr ; position restraints for non-Protein of Protein in water [ position_restraints ] ; i funct fcxfcyfcz 152311 1000 1000 1000 152321 1000 1000
[gmx-users] how does gromacs handle the force on the virtual site of the TIP4P model
Hi, ALL We are writing our own MD program to simulate water and the TIP4P model is being considered. I am wondering that how does GROMACS program handle the force on the massless M site of the TIP4P model? It would be better to be informed the algorithm(or the code in GROMACS). Thanks. Guozhen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Energy minimization Error
francesca vitalini wrote: Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? What is the Fmax you achieve, and what are your intents for this process? Minimizing very low is only strictly necessary for certain types of very sensitive calculations. For normal MD, convergence below 100-1000 kJ/mol-nm is typical. Other algorithms are listed in the manual. They may or may not be necessary. -Justin 2012/2/9 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision. http://www.gromacs.org/__Documentation/Errors#Stepsize___too_small.2c_or_no_change_in___energy._Converged_to_machine___precision.2c_but_not_to_the___requested_precision http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/__gromacs_special/share/gromacs/__top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology
[gmx-users] Equilibration of polymer chains- gauche defects
Hi all, Can you please guide me how one can calculate fraction of gauche+ and gauche- defects in the center of a polymer chain? Appreciate you help. Juliete -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: REMD tutorial
Hi, I am planning to carry out a REMD study on a 12 residue beta-hairpin peptide. I have read the gromacs tutorial for that . I have certain doubts regarding the tutorial :- 1. Step. 4 says that run short simulations to have an estimate of the exchange rate (can get a good estimate within ~100 ps) and modify the temperatures if it does not correspond to the wished exchange. Do I have to run short MD of 100 ps for each replica . I am not able to understand this step ?? 2. I have currently 24 processors available for REMD. The temperature range that I have obtained from tgenerator server has 69 different values (300K-600K). I want to know how to calculate the no. of processors required for carrying out REMD for a certain temperature range ?? Kindly clarify these doubts Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with simulation of Protein-DNA complex
Hi Rohit, Have you checked the atoms around 3460? It seems there's something wrong with your starting structure. Cheers, Tsjerk On Feb 9, 2012 2:09 PM, rar...@ens-cachan.fr wrote: Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NVT. I was so engrossed in other details that I forgot to mention it! Quoting lina lina.lastn...@gmail.com: On Thu, Feb 9, 2012 at 8:44 PM, rarora@ens-cachan.f... Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] LINCS warning and segmentation fault for methane in 1-octanol simulation
Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished successfully. Can you comment on this? As par the tutorial I am using simple vdW transformation only as mentioned below - couple-moltype = Methane ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW - Thanks, Vivek On 09/02/2012, Justin A. Lemkul jalem...@vt.edu wrote: vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Check out my photos on Facebook
Hi Wara, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Wara To sign up for Facebook, follow the link below: http://www.facebook.com/p.php?i=1020183564k=AQC3bZ5tnu7NXnKTF-2onHidqZyvDmXKiSyIJp4zzVGRyh3KdS4hNRyNwXV5brp-6YQHsLR5SI029gVUr Already have an account? Add this email address to your account: http://www.facebook.com/n/?merge_accounts.phpe=gmx-users%40gromacs.orgc=AQAO8pJDBNtoEj303KSWwt29XyvBfrJXJZAnXy1fgMAeGQ === This message was sent to gmx-users@gromacs.org. If you don't want to receive these emails from Facebook in the future, please follow the link below to unsubscribe. http://www.facebook.com/o.php?k=7c1955u=11958234951mid=59eb311G5af385328b47G0G8 Facebook, Inc. Attention: Department 415 P.O Box 10005 Palo Alto CA 94303 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] LINCS warning and segmentation fault for methane in 1-octanol simulation
On 10/02/2012 4:41 PM, vivek sharma wrote: Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished successfully. Can you comment on this? I suggest you read the manual section on pressure coupling, which likely explains this observation. Mark As par the tutorial I am using simple vdW transformation only as mentioned below - couple-moltype = Methane ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW - Thanks, Vivek On 09/02/2012, Justin A. Lemkuljalem...@vt.edu wrote: vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD tutorial
On 10/02/2012 1:20 PM, bharat gupta wrote: Hi, I am planning to carry out a REMD study on a 12 residue beta-hairpin peptide. I have read the gromacs tutorial for that . I have certain doubts regarding the tutorial :- 1. Step. 4 says that run short simulations to have an estimate of the exchange rate (can get a good estimate within ~100 ps) and modify the temperatures if it does not correspond to the wished exchange. Do I have to run short MD of 100 ps for each replica . I am not able to understand this step ?? You want to obtain an real estimate of the exchange acceptance frequency before you commit large resources. So do a short REMD simulation to see what that frequency is. 2. I have currently 24 processors available for REMD. The temperature range that I have obtained from tgenerator server has 69 different values (300K-600K). I want to know how to calculate the no. of processors required for carrying out REMD for a certain temperature range ?? Your system size, number of replicas, temperature range and exchange acceptance frequency are interlinked. You can only choose three of them independently. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how does gromacs handle the force on the virtual site of the TIP4P model
On 10/02/2012 5:11 AM, GZ Zhang wrote: Hi, ALL We are writing our own MD program to simulate water and the TIP4P model is being considered. I am wondering that how does GROMACS program handle the force on the massless M site of the TIP4P model? It would be better to be informed the algorithm(or the code in GROMACS). Thanks. It's a virtual site. The forces get projected onto the real sites from which it is constructed. See manual section 4.7 Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
