Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM
Hi Tsjerk, That was very sage advice! Thank you. I will try regenerating velocities and see if the motion goes away... On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajat, If you remove comm on the bilayer, there may be relative comm between leaflets. If that relative motion is significant and you switch to removing comm per leaflet, the program suddenly finds itself resetting the com over a large distance. About equilibration, you equilibrated with comm_grps = SOL DMPC, the system is not equilibrated for another scheme. You can solve this issue by regenerating velocities, or by running short cycles with the time step increasing from very small to normal. Hope it helps, Tsjerk On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, Any suggestions? Thanks, On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I am experiencing a few problems in membrane simulations wrt COM removal. I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the accompanying files. I then carried out the following steps: 1) energy minimization 2) NVT Eq - 100 ps 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) Then I used g_select to select the upper and lower DMPC leaflets. The then carried out a 250 ps NPT eq again. The only change was: comm-grps= SOL DMPC == comm-grps= SOL upper lower On every step in log file, I get the following message: *Step Time Lambda 124000 248.00.0 Large VCM(group lower): -0.00051, -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 -1.45245e+05 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 -5.84134e+05 -8.87497e+04 PotentialKinetic En. Total Energy Temperature Pres. DC (bar)-6.76497e+051.76468e+05 -5.00029e+05 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 6.42934e-06* *Large VCM(group lower): -0.00187, -0.00369, 0.00032, Temp-cm: 2.02076e+29 Large VCM(group lower): -0.00725, -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large VCM(group lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29 Large VCM(group lower): -0.00220, 0.00362, -0.00741, Temp-cm: 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, -0.00293, -0.00364, Temp-cm: 2.59422e+29 Large VCM(group lower): -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large VCM(group lower): 0.00252, 0.00594, 0.00068, Temp-cm: 4.93342e+29* *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme mesh/force 0.636* I do not know what to make of it. There are no issues when I remove COM for the entire system. I have seen this issue come up a few times in the archives too, but I didn't find a satisfactory solution since the bilayer was very well equilibrated. I would appreciate any suggestions. Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please
Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM
An update to anyone interested: Regenerating velocities by itself did not solve the problem. I had to regenerate velocities and couple the upper and lower leaflets separately to the thermostat to equilibrate the system. To smoothen the equilibration process further, I used a 0.5 fs timestep instead of 2 fs (though this is probably unnecessary). Thank you once more, Tsjerk. Old .mdp: comm-grps= SOL DMPC tcoupl = v-rescale; Thermostat tc-grps = DMPC SOL ; Couple lipids and SOL separately tau-t= 0.1 0.1 ; Time constant for temperature coupling ref-t= 310 310 ; Desired temperature (K) New .mdp: comm-grps= SOL upper lower tcoupl = v-rescale; Thermostat, v-rescale is also fine tc-grps = upper lower SOL ; Couple lipid leaflets and SOL separately tau-t= 0.1 0.1 0.1 ; Time constant for temperature coupling ref-t= 310 310 310 ; Desired temperature (K) On Wed, Nov 13, 2013 at 4:07 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Tsjerk, That was very sage advice! Thank you. I will try regenerating velocities and see if the motion goes away... On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Rajat, If you remove comm on the bilayer, there may be relative comm between leaflets. If that relative motion is significant and you switch to removing comm per leaflet, the program suddenly finds itself resetting the com over a large distance. About equilibration, you equilibrated with comm_grps = SOL DMPC, the system is not equilibrated for another scheme. You can solve this issue by regenerating velocities, or by running short cycles with the time step increasing from very small to normal. Hope it helps, Tsjerk On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, Any suggestions? Thanks, On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I am experiencing a few problems in membrane simulations wrt COM removal. I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the accompanying files. I then carried out the following steps: 1) energy minimization 2) NVT Eq - 100 ps 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) Then I used g_select to select the upper and lower DMPC leaflets. The then carried out a 250 ps NPT eq again. The only change was: comm-grps= SOL DMPC == comm-grps= SOL upper lower On every step in log file, I get the following message: *Step Time Lambda 124000 248.00.0 Large VCM(group lower): -0.00051, -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 -1.45245e+05 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 -5.84134e+05 -8.87497e+04 PotentialKinetic En. Total Energy Temperature Pres. DC (bar)-6.76497e+051.76468e+05 -5.00029e+05 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 6.42934e-06* *Large VCM(group lower): -0.00187, -0.00369, 0.00032, Temp-cm: 2.02076e+29 Large VCM(group lower): -0.00725, -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large VCM(group lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29 Large VCM(group lower): -0.00220, 0.00362, -0.00741, Temp-cm: 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, -0.00293, -0.00364, Temp-cm: 2.59422e+29 Large VCM(group lower): -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large VCM(group lower): 0.00252, 0.00594, 0.00068, Temp-cm: 4.93342e+29* *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme mesh/force 0.636* I do not know what to make of it. There are no issues when I remove COM for the entire system. I have seen this issue come up a few times in the archives too, but I didn't find a satisfactory solution since the bilayer was very well equilibrated. I would appreciate any suggestions. Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof
Re: [gmx-users] How to construct mixed lipid bilayer
Hi Nikhil, The first step would be to determine what forcefield you are going to use for the lipids. If you are going to use Charmm or Slipids, you can use charmmgui (just google it). If you are planning to use the Gromos forcefields, you can check Prof. Tieleman's website or lipidbook for pure bilayers and then build your own from scratch using packmol... Hope this helps... On Wed, Nov 13, 2013 at 6:44 PM, Nikhil Agrawal nikhil.08...@gmail.comwrote: Dear All, can anyone tell me how to construct mixed lipid bilayer in gromacs id possible also provide me the command to construct the mixed bilayer Thanks in advance Nikhil -- -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: Bilayer COM removal issue: Large VCM
Hi All, Any suggestions? Thanks, On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I am experiencing a few problems in membrane simulations wrt COM removal. I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the accompanying files. I then carried out the following steps: 1) energy minimization 2) NVT Eq - 100 ps 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) Then I used g_select to select the upper and lower DMPC leaflets. The then carried out a 250 ps NPT eq again. The only change was: comm-grps= SOL DMPC == comm-grps= SOL upper lower On every step in log file, I get the following message: *Step Time Lambda 124000 248.00.0 Large VCM(group lower): -0.00051, -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 -1.45245e+05 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 -5.84134e+05 -8.87497e+04 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar)-6.76497e+051.76468e+05 -5.00029e+05 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 6.42934e-06* *Large VCM(group lower): -0.00187, -0.00369, 0.00032, Temp-cm: 2.02076e+29 Large VCM(group lower): -0.00725, -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large VCM(group lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29 Large VCM(group lower): -0.00220, 0.00362, -0.00741, Temp-cm: 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, -0.00293, -0.00364, Temp-cm: 2.59422e+29 Large VCM(group lower): -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large VCM(group lower): 0.00252, 0.00594, 0.00068, Temp-cm: 4.93342e+29* *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme mesh/force 0.636* I do not know what to make of it. There are no issues when I remove COM for the entire system. I have seen this issue come up a few times in the archives too, but I didn't find a satisfactory solution since the bilayer was very well equilibrated. I would appreciate any suggestions. Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Bilayer COM removal issue: Large VCM
Hi All, I am experiencing a few problems in membrane simulations wrt COM removal. I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the accompanying files. I then carried out the following steps: 1) energy minimization 2) NVT Eq - 100 ps 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) Then I used g_select to select the upper and lower DMPC leaflets. The then carried out a 250 ps NPT eq again. The only change was: comm-grps= SOL DMPC ==comm-grps = SOL upper lower On every step in log file, I get the following message: *Step Time Lambda 124000 248.00.0Large VCM(group lower): -0.00051, -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 -1.45245e+05LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 -5.84134e+05 -8.87497e+04 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) -6.76497e+051.76468e+05 -5.00029e+05 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 6.42934e-06* *Large VCM(group lower): -0.00187, -0.00369, 0.00032, Temp-cm: 2.02076e+29Large VCM(group lower): -0.00725, -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large VCM(group lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29Large VCM(group lower): -0.00220, 0.00362, -0.00741, Temp-cm: 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, -0.00293, -0.00364, Temp-cm: 2.59422e+29Large VCM(group lower): -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large VCM(group lower): 0.00252, 0.00594, 0.00068, Temp-cm: 4.93342e+29* *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme mesh/force 0.636* I do not know what to make of it. There are no issues when I remove COM for the entire system. I have seen this issue come up a few times in the archives too, but I didn't find a satisfactory solution since the bilayer was very well equilibrated. I would appreciate any suggestions. Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi Justin, Thanks for your time. I think I will use g_traj to spit out the P8 coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD routine :) On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... What you did looks reasonable to me. Seg faults are frustrating, but can only really be addressed by recompiling in debug mode and running the command through a debugger to see which function is failing. -Justin On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: CHARMM .mdp settings for GPU
Hi Justin, I take it that both the sets of parameters should produce identical macroscopic quantities. For the GPU, is this a decent .mdp? cutoff-scheme= Verlet vdwtype = switch rlist= 1.2 ;rlistlong = 1.4 NOT USED IN GPU...IS THIS OK? rvdw = 1.2 ;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK? coulombtype = pme DispCorr = EnerPres rcoulomb= 1.2 On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5012351...@n6.nabble.com wrote: On 11/7/13 11:32 PM, Rajat Desikan wrote: Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their .mdp parameters for a membrane-protein system? Justin's recommendation is highly valued since I am using his forcefield. Justin, your comments please Careful now, it's not my forcefield. I derived only a very small part of it :) To summarize: Klauda et al., suggest rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombtype = pme DispCorr= EnerPres ;only usefull with reaction-field and pme or pppm rcoulomb = 1.0 rcoulomb_switch= 0.0 rvdw = 1.2 Justin's recommendation (per mail above) vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 The differences between these two sets of run parameters are very small, dealing mostly with Coulomb and neighbor searching cutoffs. I would suspect that any difference between simulations run with these two settings would be similarly small or nonexistent, given that rcoulomb is a bit flexible when using PME. The value of rlist is rarely mentioned in papers, so it is good that the authors have provided the actual input file. Previous interpretation of CHARMM usage generally advised setting rcoulomb = 1.2 to remain consistent with the original switching/shifting functions. That setting becomes a bit less stringent when using PME. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012351i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012351.html To unsubscribe from CHARMM .mdp settings for GPU, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012267code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: CHARMM .mdp settings for GPU
Dear All, Any suggestions? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: CHARMM .mdp settings for GPU
Thank you, Mark. I think that running it on CPUs is a safer choice at present. On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Hi, It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the original paper's coulomb settings can be taken with a grain of salt for use with PME - others' success in practice should be a guideline here. The good news is that the default GROMACS PME settings are pretty good for at least some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU auto-tuning of parameters in 4.6 is designed to preserve the right sorts of things. LJ is harder because it would make good sense to preserve the way CHARMM did it, but IIRC you can't use something equivalent to the CHARMM LJ shift with the Verlet kernels, either natively or with a table. We hope to fix that in 5.0, but code is not written yet. I would probably use vdwtype = cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2, but I don't run CHARMM simulations for a living ;-) Mark On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.com wrote: Dear All, Any suggestions? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: CHARMM .mdp settings for GPU
Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their .mdp parameters for a membrane-protein system? Justin's recommendation is highly valued since I am using his forcefield. Justin, your comments please To summarize: Klauda et al., suggest rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombtype = pme DispCorr= EnerPres ;only usefull with reaction-field and pme or pppm rcoulomb = 1.0 rcoulomb_switch= 0.0 rvdw = 1.2 Justin's recommendation (per mail above) vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 On Fri, Nov 8, 2013 at 2:20 AM, Gianluca Interlandi [via GROMACS] ml-node+s5086n5012329...@n6.nabble.com wrote: Hi Mark! I think that this is the paper that you are referring to: dx.doi.org/10.1021/ct900549r Also for your reference, these are the settings that Justin recommended using with CHARMM in gromacs: vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 As you mention the switch function in gromacs is different than in CHARMM but it appears that the difference is very small. Gianluca On Thu, 7 Nov 2013, Mark Abraham wrote: Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM switch differs from the GROMACS switch (Justin linked a paper here with the CHARMM switch description a month or so back, but I don't have that link to hand). Mark On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan [hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=0wrote: Thank you, Mark. I think that running it on CPUs is a safer choice at present. On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham [hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=1 wrote: Hi, It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the original paper's coulomb settings can be taken with a grain of salt for use with PME - others' success in practice should be a guideline here. The good news is that the default GROMACS PME settings are pretty good for at least some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU auto-tuning of parameters in 4.6 is designed to preserve the right sorts of things. LJ is harder because it would make good sense to preserve the way CHARMM did it, but IIRC you can't use something equivalent to the CHARMM LJ shift with the Verlet kernels, either natively or with a table. We hope to fix that in 5.0, but code is not written yet. I would probably use vdwtype = cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2, but I don't run CHARMM simulations for a living ;-) Mark On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan [hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=2 wrote: Dear All, Any suggestions? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=3 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=4. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=5 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=6. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=7 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012329i=8. * Can't
[gmx-users] CHARMM .mdp settings for GPU
Dear All, I intend to run a membrane-protein system in GPU. I am slightly confused about the .mdp settings Non-gpu settings (according to original CHARMM FF paper): rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombtype = pme DispCorr= EnerPres ;only usefull with reaction-field and pme or pppm rcoulomb = 1.0 rcoulomb_switch= 0.0 rvdw = 1.2 For cutoff-scheme = Verlet , shouldn't rvdw=rcoulomb? How should the above settings be modified? Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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 using CHARMM36
Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] All-bonds vs. H-bonds using CHARMM36
Thank you, Justin! I did intend to use h-bonds for the CHARMM36 simulations and all-bonds elsewhere (depending on the FF). I just wanted some clarity before I proceeded. On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 2:21 PM, rajat desikan wrote: Hi, In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds are constrained for the lipid simulations using SHAKE (excerpt from the paper below) Consistent for all of these simulations was the use of a 1 fs time step and constraining of the hydrogen atoms using the SHAKE algorithm. For a membrane-protein system, is constraining all-bonds via LINCS the right option while using CHARMM36? Normally, as the paper states, only bonds involving H are constrained with CHARMM. LINCS is a suitable replacement for SHAKE, though you can use SHAKE in Gromacs if you want. LINCS is generally more robust. There was a mention somewhere (I forgot) that constraining all-bonds probably prevents alkane isomerisations in membranes, which could lower the melting temperature. I intend to simulate a POPC bilayer. Can someone with experience please shed some light on this? Can't comment on this, but I doubt there is any issue if you don't constrain all bonds. P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.**uk/uploads/package/CHARMM36/** 48-POPE-wurl/v1/charmm_npt.mdphttp://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp It is very uncommon that such input files exist without specifically requesting them; if this is exactly what the authors used, I see no reason to deviate from it unless you have a demonstrably superior protocol. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Gromos54a8
Thank you so much, Djurre. I will do some tests with protein-membrane systems in mind and share it with the community. I will see if I can reproduce the results in the 54A8 paper. On Fri, Oct 25, 2013 at 1:01 PM, Djurre de Jong-Bruinink djurredej...@yahoo.com wrote: Dear Rajat Desikan, I recently ported the 54A8 to Gromacs format. However I did not have the time yet to extensively test it or compare it to published results. I did the porting by hand (the differences between 54A7 and 54A8 are modest), which is of course more error prone. I'll send you the files off list. If you would want to check and test them, that would be of great value for me too. And after that the force field could of course be shared with the greater Gromacs community. Groetnis, Djurre H. de Jong, PhD Theory of complex systems group Westfällische Wilhelms-Universität Münster On Thursday, 24 October 2013, 15:18, rajat desikan rajatdesi...@gmail.com wrote: Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgz http://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://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_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==** Justin
[gmx-users] Gromos54a8
Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgzin the user contributions, I do not see any other relevant scripts. Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Gromos54a8
Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp**://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Gromos54a8
Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org
Re: [gmx-users] Continuing runs from 4.5.4 in 4.6.3
Thank you, Mark! On Wed, Oct 23, 2013 at 2:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? This is not recommended. Even if it works, the trajectory is discontinuous, and the years of accumulated bug fixes, and complete re-implementation of the kernels in 4.6.3, are likely to make the discontinuity observable. Upgrading within a minor release (4.5.4 - 4.5.7, 4.6 - 4.6.3) is intended to work (modulo relevant bug fixes), but would still tend to make your reviewer nervous. Mark I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Continuing runs from 4.5.4 in 4.6.3
Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] CHARMM36 force field available for GROMACS
Superb stuff, Justin. Thank you so much. Is it asking too much for a brief list of the test systems that you used? Thanks again. On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul jalem...@vt.edu wrote: All, I am pleased to announce the immediate availability of the latest CHARMM36 force field in GROMACS format. You can obtain the archive from our lab's website at http://mackerell.umaryland.**edu/CHARMM_ff_params.htmlhttp://mackerell.umaryland.edu/CHARMM_ff_params.html . The present version contains up-to-date parameters for proteins, nucleic acids, lipids, some carbohydrates, CGenFF version 2b7, and a variety of of other small molecules. Please refer to forcefield.doc, which contains a list of citations that describe the parameters, as well as the CHARMM force field files that were used to generate the distribution. We have validated the parameters by comparing energies of a wide variety of molecules within CHARMM and GROMACS and have found excellent agreement between the two. If anyone has any issues or questions, please feel free to post them to this list or directly to me at the email address below. Happy simulating! -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] CHARMM36 force field available for GROMACS
Thank you, Justin. I am particularly interested in the lipid simulations. Can you upload the final results on dropbox? Sorry for the trouble...I intend to simulate a membrane-protein system using charmm36. I will let you know how that goes. Thanks. On Wed, Oct 9, 2013 at 5:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/9/13 7:03 AM, rajat desikan wrote: Superb stuff, Justin. Thank you so much. Is it asking too much for a brief list of the test systems that you used? Thanks again. We tested everything, at least in terms of representative examples. Single amino acids, full proteins in vacuo, single nucleotides, full-length ssRNA and dsDNA, individual lipids with and without water and ions, proteins in solution with ions, and a wide variety of small molecules interacting with each other. Everything came out in agreement between the two programs, including everything that utilized NBFIX terms. -Justin On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul jalem...@vt.edu wrote: All, I am pleased to announce the immediate availability of the latest CHARMM36 force field in GROMACS format. You can obtain the archive from our lab's website at http://mackerell.umaryland.edu/CHARMM_ff_params.htmlhttp **://mackerell.umaryland.edu/**CHARMM_ff_params.htmlhttp://mackerell.umaryland.edu/CHARMM_ff_params.html . The present version contains up-to-date parameters for proteins, nucleic acids, lipids, some carbohydrates, CGenFF version 2b7, and a variety of of other small molecules. Please refer to forcefield.doc, which contains a list of citations that describe the parameters, as well as the CHARMM force field files that were used to generate the distribution. We have validated the parameters by comparing energies of a wide variety of molecules within CHARMM and GROMACS and have found excellent agreement between the two. If anyone has any issues or questions, please feel free to post them to this list or directly to me at the email address below. Happy simulating! -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] how to calculate kinetic constant?
Hi Chris, The activation energy is obtained from the PMF well depth. So that leaves two variables k and A. If we get K at say 5 temepratures, and plot ln(k) vs. 1/T, the intercept will give us A. From that, at the temperature of interest, we can back out k. I will dig up the paper I saw this in. It was a really long time ago though. On Sun, Oct 6, 2013 at 2:33 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Dear Rajat: I just checked the first two papers that you mentioned and they both get kinetics from standard equilibrium simulations. As for the Arrhenius law, with k, A, and the energy of activation (Ea) all unknown for each T, how do you obtain a unique solution for k given T ? Even if you assume that Ea is some function of the maximum of your PMF (which is not always true), I presume that you can only then get the relationship between k and A, not the absolute value of k, even with information from many temperatures. However, I've never worked on this directly. Can you provide a reference so that I can take a look? Thank you, Chris. -- original message -- Hi Chris, I have never done this and I may be missing something. But here is what I think. I have seen a few papers use the Arrhenius law, k=A*exp (-deltaG/kB*T)...-deltaG/kB*T can be obtained from the PMF...Now, if you do this for different temperatures, you can back out the activation energy and hence the rate constant. I would love to learn more about this. Any inputs will be welcome. Regards, On Sat, Oct 5, 2013 at 11:44 PM, Christopher Neale chris.neale at mail.utoronto.ca wrote: If you want K_on and K_off, then I think you need to look at long-time equilibrium simulations or massively repeated simulations connected with a MSM. Beyond that, I believe that you will need to understand all of the important free energy barriers in all degrees of freedom (hard, to say the least). Rajat: how are you going to compute kinetics from a PMF? Barriers in orthogonal degrees of freedom don't show up on your PMF but can greatly affect the kinetics. Even relatively minor roughness of the multidimensional free energy surface and off-pathway kinetic traps are going to affect the kinetics but not the PMF. Some people have tried to circumvent this limitation by using the PMF in addition to computing the local diffusion at each small section of the order parameter (e.g., http://www.nature.com/nnano/journal/v3/n6/full/nnano.2008.130.html ) but unless there is excellent sampling overlap and lots of transitions between all relevant states, I see this as a way to calculate an upper bound of rates that I think could easily be much slower. See, for example, http://pubs.acs.org/doi/abs/10.1021/jp045544s . Finally, I am not sure how rates can be usefully extracted from a non-equilibrium method like REMD. Unless I missed it, the paper that David cites: http://pubs.acs.org/doi/abs/10.1021/ct400404q doesn't compute kinetics. Perhaps the OP can provide more information on what they are trying to obtain, exactly. Chris. -- original message -- If you are looking at binding/unbinding as a function of temperature (hopefully with REMD), you can use g_kinetics. If you are looking at unbinding/binding events in a single simulation with temperature, etc constant (no annealing), you will need to calculate binding probabilities, from which you can back out a rate constant. A simple google search gave me these papers (http://www.pnas.org/content/90/20/9547.full.pdf, http://pubs.acs.org/doi/abs/10.1021/jp037422q) Of course, the best approach is to calculate the PMF and back out the rate constant from the free energy. Hope that helps. -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] how to calculate kinetic constant?
Hi Chris, I have never done this and I may be missing something. But here is what I think. I have seen a few papers use the Arrhenius law, k=A*exp (-deltaG/kB*T)...-deltaG/kB*T can be obtained from the PMF...Now, if you do this for different temperatures, you can back out the activation energy and hence the rate constant. I would love to learn more about this. Any inputs will be welcome. Regards, On Sat, Oct 5, 2013 at 11:44 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: If you want K_on and K_off, then I think you need to look at long-time equilibrium simulations or massively repeated simulations connected with a MSM. Beyond that, I believe that you will need to understand all of the important free energy barriers in all degrees of freedom (hard, to say the least). Rajat: how are you going to compute kinetics from a PMF? Barriers in orthogonal degrees of freedom don't show up on your PMF but can greatly affect the kinetics. Even relatively minor roughness of the multidimensional free energy surface and off-pathway kinetic traps are going to affect the kinetics but not the PMF. Some people have tried to circumvent this limitation by using the PMF in addition to computing the local diffusion at each small section of the order parameter (e.g., http://www.nature.com/nnano/journal/v3/n6/full/nnano.2008.130.html ) but unless there is excellent sampling overlap and lots of transitions between all relevant states, I see this as a way to calculate an upper bound of rates that I think could easily be much slower. See, for example, http://pubs.acs.org/doi/abs/10.1021/jp045544s . Finally, I am not sure how rates can be usefully extracted from a non-equilibrium method like REMD. Unless I missed it, the paper that David cites: http://pubs.acs.org/doi/abs/10.1021/ct400404q doesn't compute kinetics. Perhaps the OP can provide more information on what they are trying to obtain, exactly. Chris. -- original message -- If you are looking at binding/unbinding as a function of temperature (hopefully with REMD), you can use g_kinetics. If you are looking at unbinding/binding events in a single simulation with temperature, etc constant (no annealing), you will need to calculate binding probabilities, from which you can back out a rate constant. A simple google search gave me these papers (http://www.pnas.org/content/90/20/9547.full.pdf, http://pubs.acs.org/doi/abs/10.1021/jp037422q) Of course, the best approach is to calculate the PMF and back out the rate constant from the free energy. Hope that helps. -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] g_select problem
Hi, I am not sure, but try resname SOL or something similar. Also, your first line has waterO and second line has water0. On Sat, Sep 28, 2013 at 1:00 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to analyze the water density along Z direction of my protein. Here is my g_select command: g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf select.dat and here is my select.dat: waterO = water and name OW and z30 and z70; close = water0 and within 0.4 of group Protein; close it failed with messages: Reading file ../md.tpr, VERSION 4.6.3 (single precision) Reading file ../md.tpr, VERSION 4.6.3 (single precision) selection parser: syntax error selection parser: invalid selection 'waterO = water and name OW and z30 and z70' I am just wondering, is there anything wrong with my syntax? thank you very much. best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: Force Field for peptides and proteins
I found this list useful: http://md.chem.rug.nl/cgmartini/index.php/blog/265-comparingforcefields http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2 On Wed, Sep 25, 2013 at 4:16 PM, fcarb frac...@myopera.com wrote: If it may be of help this paper ( http://www.ncbi.nlm.nih.gov/pubmed/?term=Systematic+Validation+of+Protein+Force+Fields+against+Experimental+Data ) compares several force field with experimental data. It was useful to me at the time I read it. cheers Fra -- View this message in context: http://gromacs.5086.x6.nabble.com/Force-Field-for-peptides-and-proteins-tp5010461p5011442.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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] g_select help
Hi All, I have a dopc+50% cholesterol bilayer. I want to selectively choose the upper and lower leaflets. I used g_select the following way g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol and z6' (6 is the COM of my box) I am getting the following error. Possible bug: one of the values for comparison missing g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol' works perfectly fine. What is the problem? Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] g_select help
Thank you very much. My bilayers were initially built with packmol which is probably why z6 worked. I will keep this in mind. On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote: Hello, On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.com wrote: I have a dopc+50% cholesterol bilayer. I want to selectively choose the upper and lower leaflets. I used g_select the following way g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol and z6' (6 is the COM of my box) I am getting the following error. Possible bug: one of the values for comparison missing g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol' works perfectly fine. What is the problem? Your problem is that 'resname DOPC and resname Cholesterol' by definition selects zero atoms. Try 'resname DOPC Cholesterol' instead. I will fix the error message, but most likely not in any upcoming 4.6.x releases. You may also find that unless you bilayer is very flat and static, you don't get exactly the atoms you want. Try 'resname DOPC Cholesterol and res_com z 6'. Best regards, Teemu -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] g_select help
Basic question: How do I verify that the right atoms were chosen in the index file? There are a lot of atoms. On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan rajatdesi...@gmail.comwrote: Thank you very much. My bilayers were initially built with packmol which is probably why z6 worked. I will keep this in mind. On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote: Hello, On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.com wrote: I have a dopc+50% cholesterol bilayer. I want to selectively choose the upper and lower leaflets. I used g_select the following way g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol and z6' (6 is the COM of my box) I am getting the following error. Possible bug: one of the values for comparison missing g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol' works perfectly fine. What is the problem? Your problem is that 'resname DOPC and resname Cholesterol' by definition selects zero atoms. Try 'resname DOPC Cholesterol' instead. I will fix the error message, but most likely not in any upcoming 4.6.x releases. You may also find that unless you bilayer is very flat and static, you don't get exactly the atoms you want. Try 'resname DOPC Cholesterol and res_com z 6'. Best regards, Teemu -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Long range Lennard Jones
Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] rvdw, rlist and rcoulomb for Amber03
Hi Justin, In a recent post (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944) you commented that: Unless you can demonstrate that your changes in cutoffs do not produce artifacts or lead to other inaccuracies using robust test systems, I wouldn't recommend any deviations. I have the habit of reading the original forcefield papers and using their parameters directly. In this regard, I use rlist=rvdw=rcoulomb=0.8 nm for Amber03 (same parameters are used in the following tutorial: http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) ). My system is a protein in a water box with counter-ions and 0.1M NaCl. It is a NVT simulation at 310 K. My queries are the following 1) Are my parameters appropriate for Amber03? 2) How would I go about constructing robust test systems to demonstrate the validity of my parameters for a protein in a water box? What parameters do I measure? Energies? Any structural parameters in particular? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/rvdw-rlist-and-rcoulomb-for-Amber03-tp5010711.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] #coordinates do not match
Hi, In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I don't think the ions are written into your .top . Please check and see if grompp works. On Sun, Aug 25, 2013 at 9:34 AM, The One And Only chappybo...@gmail.comwrote: I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Early registration period ending for 2013 GROMACS USA Workshop and Conference
Hi Prof. Shirts, I am sure that I speak for a lot of GROMACS users when I say that I want to attend the workshop, but I cannot. I would be willing to pay the whole workshop fee (and more) if you could kindly video the whole workshop and make it available to us. Thank you. On Tue, Aug 20, 2013 at 10:50 AM, Michael Shirts michael.shi...@virginia.edu wrote: Dear GROMACS users- I'd like to remind you all about the 2013 GROMACS USA Workshop and Conference at the University of Virginia Sept 13th-15th. There are still registration slots available, but the early registration deadline of Aug 22nd is coming up in just a few days; after the 22nd, the registration price will rise from the very low $60 for the two day conference to the moderately-low-but-why-pay-more $95. As mentioned in previous emails to the list, the workshop and conference will consist of two days of tutorials, discussions of future plans for GROMACS, face time with many of the main GROMACS developers, plenary software and application sessions, and an optional last day of development planning to which attendees are also invited to help influence the future directions of GROMACS. Please visit http://faculty.virginia.edu/gromacsworkshop for registration and for much more information about the workshop, including travel logistics. The website was also recently has been updated with more specifics about the program. For specific questions about registering or logistics after visiting the website, please write to gromacsworkshop-registrat...@virginia.edu. Sincerely, The 2013 GROMACS USA Workshop and Conference Steering Committee Michael Shirts (chair) Angel Garcia Berk Hess Yu-Shan Lin Erik Lindahl Peter Kasson -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] plans for mdrun features to deprecate in GROMACS 5.0
I am interested in Generalized Born. My coding skills are limited, but I would like to help to whatever extent I can. I am also interested in helping towards revamping the tutorials if the need should arise. On Wed, Aug 14, 2013 at 8:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Hi gmx-users and gmx-developers, There are a number of features of GROMACS that we plan to drop for 5.0 (scheduled for early 2014). We don’t like doing this, but if things are broken or cause developers pain, then they will go unless there is manpower to support them. We’d like to keep you informed and hear how much pain any of this might cause. Some features will be dropped entirely, and others are likely to be reduced to explicit support only for some cases. Some discussion has already occurred here http://redmine.gromacs.org/issues/1292. Things we plan to drop entirely: * particle decomposition (see below) * current QM support (this will be dropped, work on a replacement is underway, planned for 5.0) * writing of pair distance and/or time-averaged pair distance to energy files during simulations with position/orientation restraints * reaction-field-nec * Encad-shift * mdrun -ionize * GCT * mdrun -seppot * mdrun -ffscan * OpenMM support There are several algorithms (e.g. fancy kinds of restraints) that have only ever worked with particle decomposition (if they work at all...). We plan to support these only in serial. Things that will likely only work in serial (ie. single-domain DD): * ensemble- and time-averaged distance restraints * L-BFGS energy minimization * Generalized Born In some cases, “in serial” might mean “in parallel (with DD) with an extra communication stage that will make it work, but might scale poorly.” Or “in parallel but if things diffuse too far, the simulation will crash.” If you have working examples of any of the above in parallel, we would be most interested to hear from you. We’d like to construct test cases that show what works now, so that later if we are able to support some kind of parallelism, we can show that it still works. Things that won’t support constraints (because the implementations are broken or missing): * L-BFGS energy minimization * MTTK pressure coupling As always, what goes into GROMACS depends on people putting the work in. If something above would affect you, then do speak up. Contributions of working test cases are particularly valuable, but in the end you might have to be the one to write the code to make the test pass. You will have the option of continuing to use old code, too! Cheers, 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Force Field for peptides and proteins
On this note, I wanted to ask about simulated unfolding of proteins. I have a primarily alpha-helical-protein ( about 300 amino acids, 5 alpha helices, no beta strands) and 3 of its single point mutants. Now, to answer the question of relative stability, I want to place them in a water bath and heat them until they unfold. The temperature at which they unfold should qualitatively tell me which is more stable (the most stable unfolding at the highest temperature). I have been wondering which forcefield would be more suitable. I intend to use simulated heating at a constant rate (simulated annealing option in .mdp file). Any answers will be greatly appreciated. Thank you. On Mon, Aug 12, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/12/13 8:19 AM, Maria Astón Serrano wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Interestingly, this same question was just asked on the development list, although the discussion indeed belongs here. http://lists.gromacs.org/**pipermail/gmx-developers/2013-** August/007016.htmlhttp://lists.gromacs.org/pipermail/gmx-developers/2013-August/007016.html There is a wide body of literature on this topic, and it is very educational to read through as much of it as you can. Some force fields, like AMBER94 and CHARMM22+CMAP are decidedly too helical, while others (Gromos96 53A6 being a good example) tend to understate helices and overstate extended configurations. New parameter sets like AMBER99SB-ILDN and CHARMM22* are often used in protein folding studies and seem to do quite well. I think, in the end, it depends to some extent about the scope of what you are doing and the protein(s) to be studied. Even high quality force fields that perform well for folded proteins do not necessarily perform well on intrinsically disordered proteins or model peptides. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
Hi, are you referring to the MSD of the protein? I am not sure which of the MSDs are right, or why there is a difference between the two versions. But, both of the MSDs are plausible. There is no obvious wrong answer. Complex molecules have a long time relaxation and may exhibit glassy behavior and thus an MSD like the blue line. Look at this reference which shows that lipids exhibit sub-diffusive behavior till 30 ns. Protein dynamics are never straightforward. http://pre.aps.org/abstract/PRE/v79/i1/e011907 There is a valid issue about the discrepancy between the two versions. Others may be able to help you here. I suggest longer simulations. On Fri, Aug 2, 2013 at 9:20 PM, Guillaume Chevrot gchev...@cnrs-orleans.frwrote: Hi, I performed 2 simulations of a lysozyme in water: one with the version 4.5 of Gromacs and another with the version 4.6.1 (I used the exact same inputs). Then I calculated the MSD and I obtained a complete different behavior with the version 4.6.1 of Gromacs and this MSD is obviously wrong. http://gromacs.5086.x6.nabble.com/file/n5010317/MSD_gmxList.jpg Do you have any ideas what I am doing wrong or did you encounter such a behavior? Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317.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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Using the checkpoint file to restore corrupt trajectory.
Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. Thanks. -- View this message in context: http://gromacs.5086.x6.nabble.com/Using-the-checkpoint-file-to-restore-corrupt-trajectory-tp5009851.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.
Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Using the checkpoint file to restore corrupt trajectory.
I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Using the checkpoint file to restore corrupt trajectory.
Thank you! On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:56 AM, rajat desikan wrote: I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. It does not. Checkpoints are recycled every -cpt minutes. You can keep all checkpoints by using the mdrun -cpnum option, but I suspect that will use up a lot of disk space. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. Or just re-run the simulation from the same .tpr file you used before. -Justin On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] nvt T coupling group problem
If the rest of your system is just water and ions, couple them separately into another group and include it in your .mdp file. On Sat, Jun 1, 2013 at 2:23 PM, neshat haq neshat...@gmail.com wrote: Hello everyone I have a protein with covalently attached prosthetic group. Now while trying use thermostat I grouped the protein and prosthetic group though an index file asProtein_pro my Tc group is astc-grps= Protein_pro Non-Protein Now issuing the grompp for nvt step, following error is appearing Atom 1076 in multiple T-Coupling groups (1 and 2) This is very obvious that the prosthetic group will be in nonprotein index. The how to couple the prosthetic group and protein together with non protein. Or is it fine to couple a part of protein (prostheic group) with nonprotein. Any suggestion will be highly regarded. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] GROMACS 4.6.2 released
Excellent work. Thank you all for working so hard! On Thu, May 30, 2013 at 9:24 PM, Albert mailmd2...@gmail.com wrote: it seems that Gromacs update quite frequently these days.. On 05/30/2013 05:42 PM, Mark Abraham wrote: Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to upgrade their installations from 4.6 and 4.6.1. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/**gromacs/gromacs-4.6.2.tar.gzftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz ftp://ftp.gromacs.org/pub/**manual/manual-4.6.2.pdfftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf http://www.gromacs.org/About_**Gromacs/Release_Notes/**Versions_4.6.2.xhttp://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x http://www.gromacs.org/**Documentation/Installation_**Instructionshttp://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/**files/regressiontests-4.6.2.**tar.gzhttp://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz Happy simulating! The GROMACS development team -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] arrange the atoms in sphere
Use packmol. On Wed, May 29, 2013 at 1:32 AM, dariush d.mohammady...@gmail.com wrote: Hello All, Does anybody have any script to arrange the molecules in the sphere? Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC around). Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: MSD and frequency of writing trajectories
Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: MSD and frequency of writing trajectories
Thanks for the reply, trjconv does not have any bugs in removing pbc, right? We can just feed the -nojump output to g_msd. I am going to output the coordinates and velocities with g_traj and run it through my own code :) On Wed, May 22, 2013 at 11:19 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Along the lines of take a trajectory, and look through it for a frame where it crosses the periodic boundary of the original cell. Look for artefacts in the analysis at that time. Or take that frame and use it as a reference state for whatever trjconv-based PBC-massaging workflow you previously used before your analysis. How best to test depends exactly what you're measuring. There are too many combinations in most GROMACS tools for one test to prove the whole tool works correctly (or even agrees with how you think it works), so you need to think about the context that matters to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] g_msd problem
I have experienced something similar with large trajectories. This command got killed by 42 ns, with the same error. It is a 60 ns trajectory of a large membrane-protein system (approx 45 particles, Gromos 54A7 ff) with data stored every ps. g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tpr -o msd_popc_overall.xvg -lateral z -n index.ndx On Sun, May 19, 2013 at 1:57 AM, Yutian Yang yyan...@syr.edu wrote: Dear all, I am using g_msd to calculate diffusion coefficient of the centre of mass of single polymer chain with the following command: g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit 40 However, it often get killed for number of beads larger than 37, as shown below: Reading file eqm.tpr, VERSION 4.0.3 (single precision) Reading file eqm.tpr, VERSION 4.0.3 (single precision) Select a group to calculate mean squared displacement for: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' Now select a group for center of mass removal: Group 0 ( System) has 13042 elements Group 1 (PEO) has37 elements Group 2 ( WF) has 1301 elements Group 3 ( W) has 11704 elements Group 4 ( WF_W) has 13005 elements Select a group: 1 Selected 1: 'PEO' trn version: GMX_trn_file (single precision) Reading frame 24000 time 24.000 Killed. Is it also a bug in the program or have I done something wrong on the command? Thank you! Best Regards Yutian Yang -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Gromos 54A8 forcefield
Hi All, I just read the paper pertaining to Gromos 54A8. I was wondering if the force field files were available somewhere? Thanks. -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromos-54A8-forcefield-tp5007713.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] G54a7 compatibility with G53a6?
Hi All I have a membrane protein with a lot of alpha helices in it. I want to use the 54a7 parameters for the protein and Kukol parameters (modified 53a6) for the POPC membrane. Is this feasible? I know that there are issues with combining widely different ffs, but these forcefields seem very similar. Thanks, -- View this message in context: http://gromacs.5086.n6.nabble.com/G54a7-compatibility-with-G53a6-tp5006619.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: g_density fails after calculating for the last snapshot
-7fb120708000 rw-p 00:00 0 7fb120708000-7fb1207f3000 r-xp 08:06 4099652 /usr/lib/libmd.so.6 7fb1207f3000-7fb1209f3000 ---p 000eb000 08:06 4099652 /usr/lib/libmd.so.6 7fb1209f3000-7fb1209f4000 r--p 000eb000 08:06 4099652 /usr/lib/libmd.so.6 7fb1209f4000-7fb1209f5000 rw-p 000ec000 08:06 4099652 /usr/lib/libmd.so.6 7fb1209f5000-7fb120baa000 r-xp 08:06 3014908 /lib/x86_64-linux-gnu/libc-2.15.so 7fb120baa000-7fb120da9000 ---p 001b5000 08:06 3014908 /lib/x86_64-linux-gnu/libc-2.15.so 7fb120da9000-7fb120dad000 r--p 001b4000 08:06 3014908 /lib/x86_64-linux-gnu/libc-2.15.so 7fb120dad000-7fb120daf000 rw-p 001b8000 08:06 3014908 /lib/x86_64-linux-gnu/libc-2.15.so 7fb120daf000-7fb120db4000 rw-p 00:00 0 7fb120db4000-7fb120f38000 r-xp 08:06 4099654 /usr/lib/libgmxana.so.6 7fb120f38000-7fb121138000 ---p 00184000 08:06 4099654 /usr/lib/libgmxana.so.6 7fb121138000-7fb121139000 r--p 00184000 08:06 4099654 /usr/lib/libgmxana.so.6 7fb121139000-7fb121144000 rw-p 00185000 08:06 4099654 /usr/lib/libgmxana.so.6 7fb121144000-7fb121146000 rw-p 00:00 0 7fb121146000-7fb121168000 r-xp 08:06 3014922 /lib/x86_64-linux-gnu/ld-2.15.so 7fb12118-7fb1211c5000 rw-p 00:00 0 7fb1211cd000-7fb1211ef000 rw-p 00:00 0 7fb1211ef000-7fb121288000 rw-p 00:00 0 7fb12129f000-7fb1212c1000 rw-p 00:00 0 7fb1212c1000-7fb12131 rw-p 00:00 0 7fb12131d000-7fb121346000 rw-p 00:00 0 7fb121362000-7fb121368000 rw-p 00:00 0 7fb121368000-7fb121369000 r--p 00022000 08:06 3014922 /lib/x86_64-linux-gnu/ld-2.15.so 7fb121369000-7fb12136b000 rw-p 00023000 08:06 3014922 /lib/x86_64-linux-gnu/ld-2.15.so 7fff7be01000-7fff7be21000 rwxp 00:00 0 [stack] 7fff7be21000-7fff7be22000 rw-p 00:00 0 7fff7bf39000-7fff7bf3a000 r-xp 00:00 0 [vdso] ff60-ff601000 r-xp 00:00 0 [vsyscall] Aborted (core dumped) I reinstalled gromacs on my system, but the problem persists. Can somebody please help? Thanks. -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5006228i=0 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5006228i=1. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.n6.nabble.com/g-density-fails-after-calculating-for-the-last-snapshot-tp5006217p5006228.html To unsubscribe from g_density fails after calculating for the last snapshot, click herehttp://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5006217code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDA2MjE3fDM0NzUwNzcwNA== . NAMLhttp://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- View this message in context: http://gromacs.5086.n6.nabble.com/g-density-fails-after-calculating-for-the-last-snapshot-tp5006217p5006249.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] g_density fails after calculating for the last snapshot
Hi All I have a 100 ns lipid simulation for which I want the density profile. I issued the following command g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5 The program fails with the following message Selected 3: 'Water' Last frame 25000 time 10.000 *** glibc detected *** g_density: munmap_chunk(): invalid pointer: 0x00d655d0 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fb120a73b96] /usr/lib/libgmxana.so.6(calc_density+0x30c)[0x7fb120e14bec] /usr/lib/libgmxana.so.6(gmx_density+0x42b)[0x7fb120e1541b] g_density(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fb120a1676d] g_density[0x400659] === Memory map: 0040-00401000 r-xp 08:06 4099695 /usr/bin/g_density 0060-00601000 r--p 08:06 4099695 /usr/bin/g_density 00601000-00602000 rw-p 1000 08:06 4099695 /usr/bin/g_density 00d57000-00e57000 rw-p 00:00 0 [heap] 7fb11f003000-7fb11f018000 r-xp 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f018000-7fb11f217000 ---p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f217000-7fb11f218000 r--p 00014000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f218000-7fb11f219000 rw-p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f239000-7fb11f26c000 rw-p 00:00 0 7fb11f26c000-7fb11f282000 r-xp 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f282000-7fb11f481000 ---p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f481000-7fb11f482000 r--p 00015000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f482000-7fb11f483000 rw-p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f483000-7fb11f485000 r-xp 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f485000-7fb11f685000 ---p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f685000-7fb11f686000 r--p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f686000-7fb11f687000 rw-p 3000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f687000-7fb11f7d8000 r-xp 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f7d8000-7fb11f9d7000 ---p 00151000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9d7000-7fb11f9df000 r--p 0015 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9df000-7fb11f9e1000 rw-p 00158000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9e1000-7fb11f9e2000 rw-p 00:00 0 7fb11f9e2000-7fb11fb46000 r-xp 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fb46000-7fb11fd45000 ---p 00164000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd45000-7fb11fd51000 r--p 00163000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd51000-7fb11fd52000 rw-p 0016f000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd52000-7fb11fe4d000 r-xp 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb11fe4d000-7fb12004c000 ---p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004c000-7fb12004d000 r--p 000fa000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004d000-7fb12004e000 rw-p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004e000-7fb120066000 r-xp 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120066000-7fb120265000 ---p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120265000-7fb120266000 r--p 00017000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120266000-7fb120267000 rw-p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120267000-7fb12026b000 rw-p 00:00 0 7fb12026b000-7fb1204f9000 r-xp 08:06 4099651 /usr/lib/libgmx.so.6 7fb1204f9000-7fb1206f8000 ---p 0028e000 08:06 4099651 /usr/lib/libgmx.so.6 7fb1206f8000-7fb1206fe000 r--p 0028d000 08:06 4099651 /usr/lib/libgmx.so.6 7fb1206fe000-7fb120707000 rw-p 00293000 08:06 4099651 /usr/lib/libgmx.so.6 7fb120707000-7fb120708000 rw-p 00:00 0 7fb120708000-7fb1207f3000 r-xp 08:06 4099652 /usr/lib/libmd.so.6 7fb1207f3000-7fb1209f3000 ---p 000eb000 08:06 4099652 /usr/lib/libmd.so.6 7fb1209f3000-7fb1209f4000
[gmx-users] Selectively choose the upper and lower leaflets of a DPPC bilayer.
Hi All, Is there a convenient method to selectively make an index file containing the upper leaflet and the lower leaflet of a DPPC bilayer? Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/Selectively-choose-the-upper-and-lower-leaflets-of-a-DPPC-bilayer-tp5005134.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_bundle: angle with x or y axis.
Why don't you try rotating your simulation box using editconf (.gro) or trjconv (.xtc) On Sat, Jan 19, 2013 at 5:39 AM, Mortuza Munna mortuza...@yahoo.com wrote: Dear gromacs user, I have found that g_bundle can measure the angle between a group from index file and z-axis with the option -z. Is it possible to measure the angle of that group from index file with y-axis/x-axis? Any suggestion will be appreciable. Regards, Mortuza -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Re: Can i construct a solid wall in gromacs?
I once constructed a solid hydrophilic wall by applying large constraints on an equilibrated slab of spce water. Just construct a simulation box of the size of the wall needed (don't make it too thin), equilibrate it, use genrestr in all 3 dimensions to construct a restraints file, and then genconf to place it in the final simulation box (after matching box sizes, etc). It worked pretty well for me. On Tue, Dec 4, 2012 at 3:31 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Dear All users Can i construct a solid wall in gromacs? -- Sincerely Ali Alizadeh Yes, you can. Atom-by-atom, until your castle is ready. If you start with 1-atom unit cell, you can then genconf -f unitcell.gro -o wall.gro -nbox $many $many $many Afterwards, the only challenge is to place this wall correctly into your [final] box. Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] Gromacs 54a7 force field
Hi all... I heard that gromos 54a7 ff is much better for simulations than 53a6. i have a membrane protein system. To simulate it, should I include the berger lipid parameters manually as shown in justin Lemkul's membrane protein tutorial? Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538.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 * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
54A7 also introduced changes to the Gromos96 lipid parameters How will this change my inclusion of the berger lipid parameters? Any thing that I should pay special attention to? Are there other lipid parameters more compatible? I heard from a faculty member at our Institute that the 53a6 is a bad ff for a protein with a lot of alpha helices for longer simulations. She apparently saw the helices unravel when they were supposed to be stable. -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999540.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 * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
Thanks for the quick and detailed replies Justin :) This helped clear some doubts I had. I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you referring to? -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999542.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 * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
So CHARMM36 would be the best ff for a long membrane protein simulation? Is it possible to integrate CHARMM36 into Gromacs? -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999544.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 * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
I got the answer to whether we can implement CHARMM36 into gromacs...:) thanks http://www.gromacs.org/Downloads/User_contributions/Force_fields I still want your opinion on whether it is the best ff for simulating a membrane-protein system, and if any modifications to the ff are necessary? Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999545.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 * Only plain text messages are allowed! * 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] Simulation of the pure lipid bilayer
Justin,I have a question. If we download files from Peter Tieleman's website, all you get are .gro files, and no cpt files. Then what should one do? Continue using the velocities in the .gro file? On Fri, Apr 13, 2012 at 5:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: James Starlight wrote: Dear Gromacs Users! I want to perform simulation of the pure bilayer surrounded by water. I'm using already pre-equilibrated bilayers as the initial structure. During conversion pdb- gro - pdb the velocities from initial equilibration runs of the structure were lost. Should I start generating Relying on a .gro file to maintain velocities is a bad idea. The values contained therein lack sufficient precision to be reliable. You should be using .cpt files to continue runs to preserve the previous ensemble, thus making the choice of coordinate file format irrelevant. this velocities in my production run ( gen_Vel= yes) or i must do equilibration instead first to generate velocities? Finally what length A production run should not start with newly generated velocities. Doing so destroys the initial equilibration, and if you haven't taken care to preserve that anyway, you should probably just start over and make proper use of .cpt files. should this equilibration be to provide reasonable velocities for futrher MD run if I would avoild long equilibration period because of suitability of my initial model? There is no universal answer to this question. It depends on your criteria for convergence and contents of the system, among other considerations. -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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] g_wham error
Justin, Should i turn off charges on the methane molecules? I have left them on. On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com**__ wrote: Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this? With 15 windows, you should have 15 histograms. Plot with: xmgrace -nxy histo.xvg It will show you where the lack of sampling is. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**__ vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_ vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org ** http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org
Re: [gmx-users] g_wham error
Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increasing and decreasing it's position, sort of going back and forth. Also, one more thing. Originally, I had given the option for pull_dim as Y N N (x direction). But the second methane moved in all 3 directions. So I position restrained the second methane to the x axis (Fcx=0, Fcy=1000 and Fcz=1000)...does this have any bearing on my simulations? On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** __ mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** wrote: Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct
[gmx-users] g_wham error
Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this? Thanks -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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] g_wham error
Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this? With 15 windows, you should have 15 histograms. Plot with: xmgrace -nxy histo.xvg It will show you where the lack of sampling is. -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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, 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
