[gmx-users] High Temperatures in NVT
Hello Gromacs Users. I ran an NVT simulation and i noticed that after the initial step at 300K the temperature shoots up to order of 10^3 and then suddenly comes down around 300K. Is there something wrong with the system or is this normal to see such fluctuations ? There was no warning and the equilibration ran properly.Thereafter i also ran an NPT equilibaration, in which the temperature was maintained at 300K throughout. I can't understand why do i see such high temperature and why the system didn't blow up at such a temp. Any thoughts ?? I used V-rescale and set temperature to 300K. Partial Output of the run is given below: Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 5.41e-05 Initial temperature: 300.665 K Started mdrun on node 0 Sun Mar 10 12:29:30 2013 Step Time Lambda 00.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 5.85999e+031.73773e+042.56754e+022.87887e+026.36875e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.05209e+041.35894e+05 -9.32374e+03 -1.29691e+066.02106e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.07790e+00 -1.06364e+061.72203e+05 -8.91438e+05 -8.91438e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00732e+02 -2.24892e+02 -6.01369e+034.95520e-05 Step Time Lambda 100.020000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.07859e+041.80238e+042.62454e+025.40121e+027.32982e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.09087e+041.62006e+05 -9.32374e+03 -1.25168e+066.58684e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 1.33127e+02 -9.84429e+051.42626e+064.41834e+054.42290e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.49080e+03 -2.24892e+022.15463e+042.06703e-05 Step Time Lambda 200.040000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.03629e+041.81746e+042.63472e+025.99622e+027.55735e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.14113e+041.64419e+05 -9.32374e+03 -1.25426e+066.65214e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.29278e+02 -9.83818e+058.19856e+05 -1.63962e+05 -1.63507e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.43178e+03 -2.24892e+021.20551e+041.67346e-05 Step Time Lambda 300.060000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.21495e+031.81436e+042.67028e+026.35385e+027.56268e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.15424e+041.44261e+05 -9.32374e+03 -1.23407e+066.59806e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 5.35759e+02 -9.84635e+057.90514e+05 -1.94120e+05 -1.93665e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.38054e+03 -2.24892e+021.01709e+041.65873e-05 Step Time Lambda 400.080000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.57235e+031.83147e+042.81327e+025.54864e+027.33138e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.13699e+041.36309e+05 -9.32374e+03 -1.22425e+066.51767e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 7.27259e+02 -9.82598e+057.98608e+05 -1.83990e+05 -1.83535e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.39468e+03 -2.24892e+029.60979e+031.76827e-05 Step Time Lambda 500.10.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.02210e+041.8e+042.73159e+025.94300e+027.23755e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.09596e+041.33188e+05 -9.32374e+03 -1.21864e+066.24436e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 9.17212e+02 -9.80111e+057.80934e+05 -1.99177e+05 -1.98722e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.36381e+03 -2.24892e+028.90814e+032.09207e-05
[gmx-users] RE: polymer duplicate atoms
Dear Dallas Thanks for your reply. I followed the way of you said to modify the residue number in sequence. It generated a complete sturctural file (conf.gro) without deleting the duplicate atoms. However, it denoted another strange structure which contained many seperated residue —(CH2-CF2-CF2-CF2-CFCl)— It's not the polymer structure. f2311-new.pdb http://gromacs.5086.n6.nabble.com/file/n5006333/f2311-new.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-tp5006328p5006333.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: polymer duplicate atoms
Dear Dallas Thanks for your reply. I followed the way of you said to modify the residue number in sequence. It generated a complete sturctural file (conf.gro) without deleting the duplicate atoms. However, it denoted another strange structure which contained many seperated residue —(CH2-CF2-CF2-CFCl)— It's not the polymer structure. f2311-new.pdb http://gromacs.5086.n6.nabble.com/file/n5006334/f2311-new.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-tp5006328p5006334.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] implicit solvation
hi, I am trying to simulate a 50 residue protein in implicit water.Can anyone tell me that why we usually set the cuttoff to be 0. coulombtype = Cut-off vdwtype = Cut-off nstype = grid nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0. I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain why this is being done. Also we dont need to do nvt and npt equlibration here.We dont neutralise our system too.But it keeps on showing in note: NOTE 1 [file topol.top, line 7412]: System has non-zero total charge: -2.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Correct me if I am wrong. Also while doing production run,I am getting this error:- WARNING 1 [file topol.top, line 7412]: The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG has an estimated oscillational period of 9.0e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. thankyou -- 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] High Temperatures in NVT
What happens when you take a children's swing in the playground, place it in some crazy position and push it off in some random direction? The swing will swing, but it won't look proper for a while. Apparently your initial conditions are a bit crazy, e.g. some void next to your solute where a solvent molecule couldn't quite fit... :-) Mark On Fri, Mar 15, 2013 at 7:48 AM, Abhishek Acharya aacha...@iitk.ac.inwrote: Hello Gromacs Users. I ran an NVT simulation and i noticed that after the initial step at 300K the temperature shoots up to order of 10^3 and then suddenly comes down around 300K. Is there something wrong with the system or is this normal to see such fluctuations ? There was no warning and the equilibration ran properly.Thereafter i also ran an NPT equilibaration, in which the temperature was maintained at 300K throughout. I can't understand why do i see such high temperature and why the system didn't blow up at such a temp. Any thoughts ?? I used V-rescale and set temperature to 300K. Partial Output of the run is given below: Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 5.41e-05 Initial temperature: 300.665 K Started mdrun on node 0 Sun Mar 10 12:29:30 2013 Step Time Lambda 00.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 5.85999e+031.73773e+042.56754e+022.87887e+026.36875e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.05209e+041.35894e+05 -9.32374e+03 -1.29691e+066.02106e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.07790e+00 -1.06364e+061.72203e+05 -8.91438e+05 -8.91438e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00732e+02 -2.24892e+02 -6.01369e+034.95520e-05 Step Time Lambda 100.020000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.07859e+041.80238e+042.62454e+025.40121e+027.32982e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.09087e+041.62006e+05 -9.32374e+03 -1.25168e+066.58684e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 1.33127e+02 -9.84429e+051.42626e+064.41834e+054.42290e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.49080e+03 -2.24892e+022.15463e+042.06703e-05 Step Time Lambda 200.040000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.03629e+041.81746e+042.63472e+025.99622e+027.55735e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.14113e+041.64419e+05 -9.32374e+03 -1.25426e+066.65214e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.29278e+02 -9.83818e+058.19856e+05 -1.63962e+05 -1.63507e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.43178e+03 -2.24892e+021.20551e+041.67346e-05 Step Time Lambda 300.060000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.21495e+031.81436e+042.67028e+026.35385e+027.56268e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.15424e+041.44261e+05 -9.32374e+03 -1.23407e+066.59806e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 5.35759e+02 -9.84635e+057.90514e+05 -1.94120e+05 -1.93665e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.38054e+03 -2.24892e+021.01709e+041.65873e-05 Step Time Lambda 400.080000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.57235e+031.83147e+042.81327e+025.54864e+027.33138e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.13699e+041.36309e+05 -9.32374e+03 -1.22425e+066.51767e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 7.27259e+02 -9.82598e+057.98608e+05 -1.83990e+05 -1.83535e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.39468e+03 -2.24892e+029.60979e+031.76827e-05 Step Time Lambda 500.10.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.02210e+04
Re: [gmx-users] implicit solvation
On Fri, Mar 15, 2013 at 9:28 AM, preetichoudh...@iisermohali.ac.in wrote: hi, I am trying to simulate a 50 residue protein in implicit water.Can anyone tell me that why we usually set the cuttoff to be 0. See pbc = no in chapter 7. coulombtype = Cut-off vdwtype = Cut-off nstype = grid nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0. I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain why this is being done. They think that makes for a good model physics for their objective. You need to make a decision here too. See below. Also we dont need to do nvt and npt equlibration here. You can and should treat some period of time as equilibration. Whether you need to do it in a different call to mdrun is a different question. NPT with no box wouldn't make much sense... We dont neutralise our system too. Where would you like the neutralizing atoms to go in your implicit solvent? But it keeps on showing in note: NOTE 1 [file topol.top, line 7412]: System has non-zero total charge: -2.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Check out some textbook material on implicit solvation with the model you're using and see if net charge on the solute is a problem. Likely not. Correct me if I am wrong. Also while doing production run,I am getting this error:- WARNING 1 [file topol.top, line 7412]: The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG has an estimated oscillational period of 9.0e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Like it says, the decisions about using constraints and the size of the time step are linked. See manual 6.7 for introductory discussion. 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] High Temperatures in NVT
Thanks for replying Mark So in that case, i presume a proper npt run should indicate all is well with the system. Since there was nothing wrong in the output .gro file of nvt and also the npt run was alright , should i go ahead with the production run ? Abhishek What happens when you take a children's swing in the playground, place it in some crazy position and push it off in some random direction? The swing will swing, but it won't look proper for a while. Apparently your initial conditions are a bit crazy, e.g. some void next to your solute where a solvent molecule couldn't quite fit... :-) Mark On Fri, Mar 15, 2013 at 7:48 AM, Abhishek Acharya aacha...@iitk.ac.inwrote: Hello Gromacs Users. I ran an NVT simulation and i noticed that after the initial step at 300K the temperature shoots up to order of 10^3 and then suddenly comes down around 300K. Is there something wrong with the system or is this normal to see such fluctuations ? There was no warning and the equilibration ran properly.Thereafter i also ran an NPT equilibaration, in which the temperature was maintained at 300K throughout. I can't understand why do i see such high temperature and why the system didn't blow up at such a temp. Any thoughts ?? I used V-rescale and set temperature to 300K. Partial Output of the run is given below: Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 5.41e-05 Initial temperature: 300.665 K Started mdrun on node 0 Sun Mar 10 12:29:30 2013 Step Time Lambda 00.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 5.85999e+031.73773e+042.56754e+022.87887e+02 6.36875e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.05209e+041.35894e+05 -9.32374e+03 -1.29691e+06 6.02106e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.07790e+00 -1.06364e+061.72203e+05 -8.91438e+05 -8.91438e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00732e+02 -2.24892e+02 -6.01369e+034.95520e-05 Step Time Lambda 100.020000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.07859e+041.80238e+042.62454e+025.40121e+02 7.32982e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.09087e+041.62006e+05 -9.32374e+03 -1.25168e+06 6.58684e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 1.33127e+02 -9.84429e+051.42626e+064.41834e+05 4.42290e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.49080e+03 -2.24892e+022.15463e+042.06703e-05 Step Time Lambda 200.040000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.03629e+041.81746e+042.63472e+025.99622e+02 7.55735e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.14113e+041.64419e+05 -9.32374e+03 -1.25426e+06 6.65214e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.29278e+02 -9.83818e+058.19856e+05 -1.63962e+05 -1.63507e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.43178e+03 -2.24892e+021.20551e+041.67346e-05 Step Time Lambda 300.060000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.21495e+031.81436e+042.67028e+026.35385e+02 7.56268e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.15424e+041.44261e+05 -9.32374e+03 -1.23407e+06 6.59806e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 5.35759e+02 -9.84635e+057.90514e+05 -1.94120e+05 -1.93665e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.38054e+03 -2.24892e+021.01709e+041.65873e-05 Step Time Lambda 400.080000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.57235e+031.83147e+042.81327e+025.54864e+02 7.33138e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.13699e+041.36309e+05 -9.32374e+03 -1.22425e+06 6.51767e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 7.27259e+02 -9.82598e+057.98608e+05 -1.83990e+05 -1.83535e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.39468e+03 -2.24892e+029.60979e+03
Re: [gmx-users] High Temperatures in NVT
A single frame proves very little. You should be looking at the trends in (say) average values in observables relevant to what you're going to want the simulation to sample. It's a bit of a dark art, however. Mark On Fri, Mar 15, 2013 at 11:02 AM, Abhishek Acharya aacha...@iitk.ac.inwrote: Thanks for replying Mark So in that case, i presume a proper npt run should indicate all is well with the system. Since there was nothing wrong in the output .gro file of nvt and also the npt run was alright , should i go ahead with the production run ? Abhishek What happens when you take a children's swing in the playground, place it in some crazy position and push it off in some random direction? The swing will swing, but it won't look proper for a while. Apparently your initial conditions are a bit crazy, e.g. some void next to your solute where a solvent molecule couldn't quite fit... :-) Mark On Fri, Mar 15, 2013 at 7:48 AM, Abhishek Acharya aacha...@iitk.ac.inwrote: Hello Gromacs Users. I ran an NVT simulation and i noticed that after the initial step at 300K the temperature shoots up to order of 10^3 and then suddenly comes down around 300K. Is there something wrong with the system or is this normal to see such fluctuations ? There was no warning and the equilibration ran properly.Thereafter i also ran an NPT equilibaration, in which the temperature was maintained at 300K throughout. I can't understand why do i see such high temperature and why the system didn't blow up at such a temp. Any thoughts ?? I used V-rescale and set temperature to 300K. Partial Output of the run is given below: Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 5.41e-05 Initial temperature: 300.665 K Started mdrun on node 0 Sun Mar 10 12:29:30 2013 Step Time Lambda 00.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 5.85999e+031.73773e+042.56754e+022.87887e+02 6.36875e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.05209e+041.35894e+05 -9.32374e+03 -1.29691e+06 6.02106e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.07790e+00 -1.06364e+061.72203e+05 -8.91438e+05 -8.91438e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00732e+02 -2.24892e+02 -6.01369e+034.95520e-05 Step Time Lambda 100.020000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.07859e+041.80238e+042.62454e+025.40121e+02 7.32982e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.09087e+041.62006e+05 -9.32374e+03 -1.25168e+06 6.58684e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 1.33127e+02 -9.84429e+051.42626e+064.41834e+05 4.42290e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.49080e+03 -2.24892e+022.15463e+042.06703e-05 Step Time Lambda 200.040000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.03629e+041.81746e+042.63472e+025.99622e+02 7.55735e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.14113e+041.64419e+05 -9.32374e+03 -1.25426e+06 6.65214e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 3.29278e+02 -9.83818e+058.19856e+05 -1.63962e+05 -1.63507e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.43178e+03 -2.24892e+021.20551e+041.67346e-05 Step Time Lambda 300.060000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.21495e+031.81436e+042.67028e+026.35385e+02 7.56268e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.15424e+041.44261e+05 -9.32374e+03 -1.23407e+06 6.59806e+03 Position Rest. PotentialKinetic En. Total Energy Conserved En. 5.35759e+02 -9.84635e+057.90514e+05 -1.94120e+05 -1.93665e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.38054e+03 -2.24892e+021.01709e+041.65873e-05 Step Time Lambda 400.080000.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 9.57235e+031.83147e+042.81327e+025.54864e+02 7.33138e+03
Fw: Fwd: [gmx-users] position restraints
Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- 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] Dihedral restraints in 4.6 vs 4.5.X
Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral restraint. Here's the details: Making a 4.5.5 tpr with a dihedral restraint $grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr Checking that it is there: $gmxdump -s md.tpr |grep DIHRE Reading file md.tpr, VERSION 4.5.5 (single precision) functype[166]=DIHRES, label=0, power= 1 phi= 1.2000e+02, dphi= 3.e+01, kfac= 1.e+00) Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives me an error. $ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md Reading file md.tpr, VERSION 4.5.5 (single precision) --- Program mdrun, VERSION 4.6.1 Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136 Fatal error: symtab get_symtab_handle 1051260126 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? Thanks /Per-- 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 Quick and Dirty installation
Hi, I need install gromacs 4.6.1 in Ubuntu 12.10 when I make the quick and dirty installation I have this errors: [ 1%] Performing download step (download, verify and extract) for 'gmxfftw' -- downloading... src='http://www.fftw.org/fftw-3.3.2.tar.gz' dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz' timeout='none' CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file): file DOWNLOAD MD5 mismatch for file: [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz] expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178] actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e] make[2]: *** [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1 make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2 make: *** [all] Error 2 biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo apt-get install libfftw3-devLeyendo lista de paquetes... Hecho Creando árbol de dependencias Leyendo la información de estado... Hecho libfftw3-dev ya está en su versión más reciente. 0 actualizados, 0 se instalarán, 0 para eliminar y 305 no actualizados. biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ ./configure bash: ./configure: No existe el archivo o el directorio biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make [ 1%] Performing download step (download, verify and extract) for 'gmxfftw' -- downloading... src='http://www.fftw.org/fftw-3.3.2.tar.gz' dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz' timeout='none' CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file): file DOWNLOAD MD5 mismatch for file: [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz] expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178] actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e] make[2]: *** [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1 make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2 make: *** [all] Error 2 biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make install [ 1%] Performing download step (download, verify and extract) for 'gmxfftw' -- downloading... src='http://www.fftw.org/fftw-3.3.2.tar.gz' dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz' timeout='none' CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file): file DOWNLOAD MD5 mismatch for file: [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz] expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178] actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e] make[2]: *** [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1 make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2 make: *** [all] Error 2 Please help me Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-Quick-and-Dirty-installation-tp5006348.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Timesteps don't match
Dear all, I'm receiving a timesteps don't match error, due to a wobble in the time between steps for my xtc trajectory file. The source of the wobble is mysterious. I'm running gromacs-4.5.5 with plumed patches for a very long trajectory using double precision code with a time step of 2fs and xtc frames every 200fs. The trajectory was run in 24 hour chunks, with a continuation with -append over all the chunks. The timing fit precisely the values set over many, many chunks. Unfortunately, I was trying to consolidate some disk space and lost my log file, which kept me from simply running mdrun_d with -append to continue the trajectory as I had been doing. I started a new trajectory with the checkpoint file by extending the tpr with tpbconv, and then continued appending to the output from that. The beginning time is correct, beginning right after the end of the first trajectory. However, every frame is separated from the next by 187.5 fs or 218.75 fs, repeatedly. I've checked my input files, my cpt checkpoint and my tpr run file --- there are no step values like that at all, and the xtc output time continues to be set as every 100 steps, with a step time of 2fs. Where should I look to identify the source of this wobble? Has anyone seen anything similar? Alex Peyser -- 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] Treating electrostatics and van der Waals interactions differently
Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all pairs of atoms in the electrostatics calculation but I would like to exclude 1-2 and 1-3 neighbors in the van der Waals calculation. Is this possible to do in GROMACS? If so, how might this be accomplished? Thanks in advance for your help. Jeff Woodford Assistant Professor of Chemistry Missouri Western State University -- 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 Quick and Dirty installation
That means the automatic download of FFTW did not succeed for some reason. GROMACS is not going to compile an FFTW for you unless it's sure the FFTW download was complete and the right file. Either do make clean and try again, or follow the other build instructions to prepare a suitable FFTW for yourself. Note that you should not use sudo for anything before the make install stage. That's the only time you need to consider allowing code that you have no idea about to perhaps trash your system. Mark On Fri, Mar 15, 2013 at 6:47 PM, Juando11 juando12...@gmail.com wrote: Hi, I need install gromacs 4.6.1 in Ubuntu 12.10 when I make the quick and dirty installation I have this errors: [ 1%] Performing download step (download, verify and extract) for 'gmxfftw' -- downloading... src='http://www.fftw.org/fftw-3.3.2.tar.gz' dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz' timeout='none' CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file): file DOWNLOAD MD5 mismatch for file: [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz] expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178] actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e] make[2]: *** [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1 make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2 make: *** [all] Error 2 biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo apt-get install libfftw3-devLeyendo lista de paquetes... Hecho Creando árbol de dependencias Leyendo la información de estado... Hecho libfftw3-dev ya está en su versión más reciente. 0 actualizados, 0 se instalarán, 0 para eliminar y 305 no actualizados. biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ ./configure bash: ./configure: No existe el archivo o el directorio biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make [ 1%] Performing download step (download, verify and extract) for 'gmxfftw' -- downloading... src='http://www.fftw.org/fftw-3.3.2.tar.gz' dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz' timeout='none' CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file): file DOWNLOAD MD5 mismatch for file: [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz] expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178] actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e] make[2]: *** [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1 make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2 make: *** [all] Error 2 biomedicina@biomedicina-desktop:~/gromacs/gromacs-4.6.1/build$ sudo make install [ 1%] Performing download step (download, verify and extract) for 'gmxfftw' -- downloading... src='http://www.fftw.org/fftw-3.3.2.tar.gz' dst='/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz' timeout='none' CMake Error at gmxfftw-stamp/download-gmxfftw.cmake:6 (file): file DOWNLOAD MD5 mismatch for file: [/home/biomedicina/gromacs/gromacs-4.6.1/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz] expected MD5 sum: [6977ee770ed68c85698c7168ffa6e178] actual MD5 sum: [d41d8cd98f00b204e9800998ecf8427e] make[2]: *** [src/contrib/fftw/gmxfftw-prefix/src/gmxfftw-stamp/gmxfftw-download] Error 1 make[1]: *** [src/contrib/fftw/CMakeFiles/gmxfftw.dir/all] Error 2 make: *** [all] Error 2 Please help me Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-Quick-and-Dirty-installation-tp5006348.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Treating electrostatics and van der Waals interactions differently
On 2013-03-15 19:27, Jeff Woodford wrote: Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all pairs of atoms in the electrostatics calculation but I would like to exclude 1-2 and 1-3 neighbors in the van der Waals calculation. Is this possible to do in GROMACS? If so, how might this be accomplished? Thanks in advance for your help. Jeff Woodford Assistant Professor of Chemistry Missouri Western State University In a molecular system you can do this by adding the 1-2 and 1-3 interactions as pairs, assuming the list of interactions is fixed, like in a crystal. Then you can make the LJ parameters different from the default and scale the charges down. You probably want to use PME for electrostatics. Check the manual! -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Dihedral restraints in 4.6 vs 4.5.X
On 2013-03-15 15:31, Per Larsson wrote: Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral restraint. Here's the details: Making a 4.5.5 tpr with a dihedral restraint $grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr Checking that it is there: $gmxdump -s md.tpr |grep DIHRE Reading file md.tpr, VERSION 4.5.5 (single precision) functype[166]=DIHRES, label=0, power= 1 phi= 1.2000e+02, dphi= 3.e+01, kfac= 1.e+00) Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives me an error. $ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md Reading file md.tpr, VERSION 4.5.5 (single precision) --- Program mdrun, VERSION 4.6.1 Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136 Fatal error: symtab get_symtab_handle 1051260126 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? redmine please. Thanks /Per-- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Treating electrostatics and van der Waals interactions differently
On Fri, Mar 15, 2013 at 7:27 PM, Jeff Woodford jwoodf...@missouriwestern.edu wrote: Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all pairs of atoms in the electrostatics calculation but I would like to exclude 1-2 and 1-3 neighbors in the van der Waals calculation. Is this possible to do in GROMACS? If so, how might this be accomplished? Thanks in advance for your help. Should be possible, but I don't think it's something for which GROMACS explicitly caters. I'd suggest keeping the normal exclusions for the [moleculetype] (e.g. nrexcl=3). For each 1-2 and 1-3 interaction, add [pairs] interactions that have zero VDW parameters. See manual 5.3.4, and other bits of chapter 5. You may be able to hijack the [pairtypes] mechanism here, depending whether the [pairs] mechanism is already being used by your force field for 1-4 interactions. Otherwise, I think something like [pairs] ; i j functype c6 c12 1 3 1 0 0 is the right kind of way to put a no-LJ normal-Coulomb interaction between atoms 1 and 3. Not sure offhand how to scale down the charges (which you'd probably want). You'd have to generate that list of 1-2 and 1-3 pairs yourself, but you can probably hijack the contents of the [bonds] and [angles] fields to save some legwork. 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: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 8:50 AM, Shima Arasteh wrote: Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? No, 0.2 nm is very high. With position restraints, offhand I would think around 0.05 nm or less would be indicative of proper restraints. This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Yes, using genrestr to create a suitable posre.itp file that includes only backbone atoms. -Justin Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Treating electrostatics and van der Waals interactions differently
Looking into the manual, i find under the 'energy monitor group': 'Mutual interactions between all energy monitor groups are compiled during the simulation. This is done separately for Lennard-Jones and Coulomb terms. In principle up to 256 groups could be defined, but that would lead to 256x256 items! Better use this concept sparingly. All non-bonded interactions between pairs of energy monitor groups can be excluded (see sec. 7.3). Pairs of particles from excluded pairs of energy monitor groups are not put into the pair list. This can result in a significant speedup for simulations where interactions within or between parts of the system are not required.' But i found nowhere an option to tell GROMACS to handle the exclusions for LJ and Coulomb interactions differently. Don't know if it's possible. For standard exclusions it seems that LJ and Coulomb interaction get treated equally - if one excludes one, one also excludes the other... One idea: But only possible if one can define two bonds, between the same atoms. I don't know if this is possible. One idea for a work-around would be the following (but it will slow the simulation). Exclude all 1-2 and 1-3 interactions. To get the Coulomb interacions back, construct table interactions for bonds. GMX manual 4.5.3: Look for '4.2.13 Tabulated interaction functions' and '6.7 Tabulated interaction functions' It seems that one can construct tabulated interactions also for bonds. Potential looks like: V = k * f(r) where f(r) is a cubic spline, think here one could use the values for the coulomb-interaction for the non-bonded table. For k use the product of the two charges. In the topology, one would need to write both atoms and this force-constant (our product of charges), similar to normal bonds. If two bonds between the same atoms are not possible, one could define tabulated interactions for the bonds + Coulomb interactions ... but this would be a lot of work. Probably it would be easier, to hack GMX, that it ignores Exclusions for Coulomb interactions. Or another persons has hopefully a better idea. Greetings Thomas Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all pairs of atoms in the electrostatics calculation but I would like to exclude 1-2 and 1-3 neighbors in the van der Waals calculation. Is this possible to do in GROMACS? If so, how might this be accomplished? Thanks in advance for your help. Jeff Woodford Assistant Professor of Chemistry Missouri Western State University -- 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] Parallelization performance
Hi! I have been running MD simulations on a 6 processors machine. I just got an account on a cluster. A nvt stabilization takes about 8 hours on my 6 processors machine, but it takes about 12 hours on the cluster using 16 processors. It is my understanding that the idea of running in parallel is to be more efficient, wrigth? This is the command for the run on the 6 processors machine: mdrun -v -s nvtOmpA.tpr -deffnm nvtOmpA This is the command for the run on 16 processor on the cluster: mpirun -np 16 mdrun_mpi -v -s nvtOmpA.tpr -deffnm nvtOmpA With the last command I am imaging that my process is divided in 16 processors that perform in parallel so that the wall time should be less than in the 6 processor machine. My system is a protein in oil and water, and the simulations are for FE calculations. I think it is spected that the run on the 16 processor of the cluster should be faster, but I'm getting the opposite. Am I doing something wrong? This is my mdp. I have used the same mdp for simulations in 4, 6 and 8 processor machines and everytime is faster and runs quite well. Any help will be grateful!! title= NVT equilibration ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 15; 300 ps nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxtcout= 0 xtc-precision= 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist= 1.5 ; Electrostatics coulombtype = PME rcoulomb = 1.5 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t= 1.0 ref_t= 300 ; Pressure coupling is off for NVT Pcoupl = No tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.1 delta_lambda = 0 foreign_lambda = 0.05 0.2 sc-alpha = 0 sc-power = 0 sc-sigma = 0 couple-moltype = Protein_chain_A ; name of moleculetype to decouple couple-lambda0 = vdw ; couple-lambda1 = vdw-q ; couple-intramol = yes nstdhdl = 10 ; Generate velocities to start gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Thanks in advance! Sonia Aguilera Graduate assistant -- View this message in context: http://gromacs.5086.n6.nabble.com/Parallelization-performance-tp5006357.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org 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
