Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM
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.comwrote: 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 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 -- 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
Re: [gmx-users] help about ibi
Hi, Something went wrong earlier in your workflow. Check your log files, etc. Mark On Nov 13, 2013 3:57 AM, guozhicheng222 guozhicheng...@126.com wrote: Hi: When I am running the ibi procedure, I get the following error message: A coordinate in file conf.gro does not contain a '.' Additionally, I check the coordinate file of confout.gro in step_001. It showed that 'nan' symbol appeared in confout.gro. What is wrong with this? How can I fix it? I am very appreciating for anyone's help. Best Wishes! Zhicheng Guo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: 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)
[gmx-users] Invalid order for directive defaults
Dear Justin Very thanks for your reply. I created a new topol.top file as below: 1) I used once default directive. 2) I put cnt.itp file in working directory. 3) I copied pr.top and renamed it to topol.top. I added #include cnt.itp in the end of topol.top file. I modified [ molecules ] directive. -- begining of topol.top file is as follows: ; Include forcefield parameters #include charmm27.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] . . . . end of com.top file is as follows: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif #include cnt.itp ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 CNT 1 SOL 1388 --- Previous error (Invalid order for directive defaults) was solved, but When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with this error: ERROR1 [file cnt.itp, line 2861]: No default Angle types . . . . . . ERROR 1218 [file cnt.itp, line 4078]: No default Angle types Fatal error: There were 1218 errors in input file(s). Lines 2861-4078 are related to [ angles ] directive in cnt.itp file. How to solve this issue? Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error while running pdb2gmx
Hello GROMACS users, I have phosphorylated Serine residue in my protein (140 residues) of interest, now when I run pdb2gmx I get this following error Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms while sorting atoms. I checked aminoacid.rtp, there is no separate entry for OXT there.When I did the simulation for the same protein prior phosphorylation I did not get this error. What is the reason for this and how should I rectify this error? Please help me with this regard Regards, Hasthi -- 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] Invalid order for directive defaults
Dear Justin My cnt is infinite. I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp. For obtaining cnt.top, I used following files: --- ffcnt.atp: CA 12.01100 ; aromatic C --- ffcnt.n2t: CCA0.0012.011 3C 0.141 C 0.141 C 0.141 CCA0.0012.011 2C 0.141 C 0.141 --- ffcntbon.itp: [ bondtypes ] ; i j funcb0 kb CA CA 3 0.1418 47890.0 21.867 [ angletypes ] ; i j k functh0 cth ub0 cub CA CA CA 2 120.00 562.20 [ dihedraltypes ] ; i j k l funcphi0cp mult CA CA CA CA 5 0.00 25.12 0.00 0.00 --- ffcntnonbon.itp: [ atomtypes ] ;name at.num masscharge ptype sigma epsi CA 6 12.011000.00A 0.385 0.4396 --- In cnt.itp file, angle section of file is as follows: [ angles ] ; aiajak functc0c1c2c3 2 1 8 1 2 1 287 1 8 1 287 1 1 2 3 1 1 210 1 3 210 1 2 3 289 1 2 3 406 1 289 3 406 1 5 417 1 5 4 320 1 17 4 320 1 4 5 6 1 . . . . . . I saw system.gro file by VMD, there are all angles defined above in [angle] directive. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about my single point calculation
Hello Mark, I don't get any informing of your reply by e-mail, but get your reply searched by google. Anyway thanks very much for your reply! Yeah, I used two totally different mdp files for the single point calculation because I thought that gromcs would report the potential energy of my system if I used the option -rerun, no matter what mdp files I used. Gromacs-4.5.5 was used in the calculations. Some time later, I also tried as you mentioned in the e-mail below. Problem was the same. I used this mdp (attached minim.mdp) file for both 0-step minimization and single point calculation with rerun: The only difference is the integrator, steep for 0-step minimization while md for single point calculation. And the following lines are the output I got: Single point calculation with rerun : Step Time Lambda 00.00.0 Energies (kJ/mol) G96Bond G96Angle Improper Dih. LJ-14 Coulomb-14 3.97878e+051.44370e+041.06677e+043.93431e+01 9.36593e+01 LJ (SR)Coulomb (SR) Potential Kinetic En. Total Energy 2.77574e+015.17380e+024.23661e+050.0e+00 4.23661e+05 Temperature Pressure (bar) 0.0e+000.0e+00 0-step minimization: Step Time Lambda 00.00.0 Energies (kJ/mol) G96Bond G96AngleImproper Dih. LJ-14 Coulomb-14 5.75700e+011.78703e+018.25973e-02 -9.22001e+00 5.93500e+01 LJ (SR)Coulomb (SR) Potential Pressure (bar) -1.96671e+013.75963e+024.81949e+020.0e+00 Later, I also used the mdp file which was pasted on the forum (attached sp.mdp) to do single point calculation with rerun, The following is what I got: Step Time Lambda 00.00.0 Energies (kJ/mol) G96BondG96Angle Improper Dih. LJ-14 Coulomb-14 3.97878e+051.44370e+041.06677e+043.93431e+01 9.36593e+01 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 2.77575e+015.17379e+024.23661e+056.54617e+01 4.23726e+05 Conserved En.Temperature Pressure (bar) 4.23726e+051.45800e+020.0e+00 I found that those energies are pretty much the same as the one mentioned above. The differences between corresponding energies are huge, I still don't understand the difference. My system only contains 37 atom, the energies generated from the 0-step minimization seem more reasonable than those from single point calculation with rerun. Do you know the possible reasons which could result in the huge difference? Or I made some mistake? Thanks very much! All the best, Qinghua On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl fantastic...@gmail.com wrote: Dear Justin, I am sorry for the late reply. I still can't figure it out. It isn't rocket science - your two .mdp files describe totally different model physics. To compare things, change as few things as necessary to generate the comparison. So use the same input .mdp file for the MD vs EM single-point comparison, just changing the integrator line, and maybe unconstrained-start (I forget the details). And be aware of http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark Could you please send me the mdp file which was used for your single point calculations. I want to do some comparison and then solve the problem. Thanks very much! All the best, Qinghua -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012295.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? Readhttp://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? Readhttp://www.gromacs.org/Support/Mailing_Lists define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002; time step in ps nsteps = 2; number of steps for 1000ns run emtol = 100; convergence criterion emstep
[gmx-users] How to construct mixed lipid bilayer
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
[gmx-users] Recompile Gromacs 4.6.3
Hello, all I intend to make some modification on minimize.c in mdlib. Do I need to do cmake make make install all over again? Or is there a quick way for recompiling? Thanks for any tips. JhengWei Li Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan -- 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] Calculating diffusion coefficient in three dimension
On 11/13/13 12:20 AM, Venkat Reddy wrote: Dear Justin and Piggot, Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle by placing lipids in random conformation in a simulation box. My lipid system is heterogeneous, i.e., it has different types of lipids (POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of vesicle (POPC), and some stay in the intermediate region (CHOL). So, I want to calculate the diffusion rates of these lipids. Since POPC forms the surface (polar heads interacting with water and their tails points to the core), I suppose we have to calculate 2D diffusion for POPC. For the lipids in the core, they can diffuse in 3-dimension. So, it requires a 3D diffusion coefficient for these core lipids. How to calculate 2D and 3D diffusion coeff.? Hope I am clear. 2D diffusion coefficients are what the -lateral option does. I really don't understand why you want a 2D value for anything with spherical symmetry. If there is an outer layer of a vesicle, that's as much a sphere as anything inside it. -Justin On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot t.pig...@soton.ac.ukwrote: Hi Venkat, Can you make it a bit clearer what you actually want? If it is the diffusion of the lipids along the curved surface of the vesicle, rather than simply the overall 3D diffusion, this is not trivial to calculate as I don't believe g_msd will do this for you. This property has been studied before though, so I suggest you search the literature for papers simulating vesicles to see how the lipid diffusion was calculated. Cheers Tom On 11/12/2013 06:35 PM, Justin Lemkul wrote: On 11/12/13 1:33 PM, Venkat Reddy wrote: Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? If you just want the overall diffusion constant, that's what g_msd does without any additional options. -Justin On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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 -- == Justin A. Lemkul,
Re: [gmx-users] Invalid order for directive defaults
On 11/13/13 5:51 AM, Atila Petrosian wrote: Dear Justin Very thanks for your reply. I created a new topol.top file as below: 1) I used once default directive. 2) I put cnt.itp file in working directory. 3) I copied pr.top and renamed it to topol.top. I added #include cnt.itp in the end of topol.top file. I modified [ molecules ] directive. -- begining of topol.top file is as follows: ; Include forcefield parameters #include charmm27.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] . . . . end of com.top file is as follows: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif #include cnt.itp ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 CNT 1 SOL 1388 --- Previous error (Invalid order for directive defaults) was solved, but When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with this error: ERROR1 [file cnt.itp, line 2861]: No default Angle types . . . . . . ERROR 1218 [file cnt.itp, line 4078]: No default Angle types Fatal error: There were 1218 errors in input file(s). Lines 2861-4078 are related to [ angles ] directive in cnt.itp file. How to solve this issue? In your previous setup, you were effectively trying to use CHARMM27 + some other force field related to the CNT. You can't do that. What you can do (and need to do) is incorporate the nonbonded and bonded parameters related to the CNT into the parent force field. You may be able to simply #include the ffnonbonded.itp and ffbonded.itp files in the topology. Your current approach has simply deleted necessary information. -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 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
Re: [gmx-users] error while running pdb2gmx
On 11/13/13 6:02 AM, hasthi wrote: Hello GROMACS users, I have phosphorylated Serine residue in my protein (140 residues) of interest, now when I run pdb2gmx I get this following error Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms while sorting atoms. I checked aminoacid.rtp, there is no separate entry for OXT there.When I did the simulation for the same protein prior phosphorylation I did not get this error. What is the reason for this and how should I rectify this error? Please help me with this regard Presumably you have modified the force field to include the phosphorylated residue, correct? Have you followed every one of the steps shown at http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue? If you need further help, we will need more information, which will include (at minimum): 1. Snippet of the PDB file containing the problematic residue 2. Your exact pdb2gmx command 3. The screen output of pdb2gmx (all of it, not just the error message) -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 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
Re: [gmx-users] How to construct mixed lipid bilayer
Start with packmol if you want to start from scratch. Or else get a pretty equilibrated mixed lipid bilayer if available somewhere on web. On Nov 13, 2013 6:45 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote: 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 -- 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 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
Re: [gmx-users] How to construct mixed lipid bilayer
Let me correct myself :). Its pre-equilibrated. Not pretty equilibrated. :) On Nov 13, 2013 7:23 PM, Arun kumar V arun.tar...@gmail.com wrote: Start with packmol if you want to start from scratch. Or else get a pretty equilibrated mixed lipid bilayer if available somewhere on web. On Nov 13, 2013 6:45 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote: 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 -- 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] Recompile Gromacs 4.6.3
For just modifying a file, just doing make is sufficient. I would recommend not installing the modified version (since you can run the build/src/kernel/mdrun directly), or if you must install, to use the suffixing options available in the ccmake advanced mode. Mark On Nov 13, 2013 2:48 PM, Jheng Wei Li lijheng...@gmail.com wrote: Hello, all I intend to make some modification on minimize.c in mdlib. Do I need to do cmake make make install all over again? Or is there a quick way for recompiling? Thanks for any tips. JhengWei Li Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error while running pdb2gmx
Probably the default behaviour of pdb2gmx for termini is not appropriate for your input. Use pdb2gmx -ter and choose wisely Mark On Nov 13, 2013 12:03 PM, hasthi durgs7kr...@gmail.com wrote: Hello GROMACS users, I have phosphorylated Serine residue in my protein (140 residues) of interest, now when I run pdb2gmx I get this following error Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms while sorting atoms. I checked aminoacid.rtp, there is no separate entry for OXT there.When I did the simulation for the same protein prior phosphorylation I did not get this error. What is the reason for this and how should I rectify this error? Please help me with this regard Regards, Hasthi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Dear Justin, I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A, Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Comput Biol 6(10): e1000964. doi:10.1371/journal.pcbi.1000964), where the authors have clearly described the fitting of 2D diffusion coefficient to the surface lipids (diffusion along the lipid-water interface ) and 3D diffusion coefficient to the core lipids. On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/13/13 12:20 AM, Venkat Reddy wrote: Dear Justin and Piggot, Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle by placing lipids in random conformation in a simulation box. My lipid system is heterogeneous, i.e., it has different types of lipids (POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of vesicle (POPC), and some stay in the intermediate region (CHOL). So, I want to calculate the diffusion rates of these lipids. Since POPC forms the surface (polar heads interacting with water and their tails points to the core), I suppose we have to calculate 2D diffusion for POPC. For the lipids in the core, they can diffuse in 3-dimension. So, it requires a 3D diffusion coefficient for these core lipids. How to calculate 2D and 3D diffusion coeff.? Hope I am clear. 2D diffusion coefficients are what the -lateral option does. I really don't understand why you want a 2D value for anything with spherical symmetry. If there is an outer layer of a vesicle, that's as much a sphere as anything inside it. -Justin On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot t.pig...@soton.ac.uk wrote: Hi Venkat, Can you make it a bit clearer what you actually want? If it is the diffusion of the lipids along the curved surface of the vesicle, rather than simply the overall 3D diffusion, this is not trivial to calculate as I don't believe g_msd will do this for you. This property has been studied before though, so I suggest you search the literature for papers simulating vesicles to see how the lipid diffusion was calculated. Cheers Tom On 11/12/2013 06:35 PM, Justin Lemkul wrote: On 11/12/13 1:33 PM, Venkat Reddy wrote: Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? If you just want the overall diffusion constant, that's what g_msd does without any additional options. -Justin On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
On 11/13/13 9:41 AM, Venkat Reddy wrote: Dear Justin, I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A, Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Comput Biol 6(10): e1000964. doi:10.1371/journal.pcbi.1000964), where the authors have clearly described the fitting of 2D diffusion coefficient to the surface lipids (diffusion along the lipid-water interface Diffusion along a lipid-water interface is one thing. Trying to use g_msd do to it is another, because I don't think it will. It looks for a plane in the configuration and calculates relative to it. I suspect you will need to modify the code to implement a custom algorithm. -Justin ) and 3D diffusion coefficient to the core lipids. On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/13/13 12:20 AM, Venkat Reddy wrote: Dear Justin and Piggot, Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle by placing lipids in random conformation in a simulation box. My lipid system is heterogeneous, i.e., it has different types of lipids (POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of vesicle (POPC), and some stay in the intermediate region (CHOL). So, I want to calculate the diffusion rates of these lipids. Since POPC forms the surface (polar heads interacting with water and their tails points to the core), I suppose we have to calculate 2D diffusion for POPC. For the lipids in the core, they can diffuse in 3-dimension. So, it requires a 3D diffusion coefficient for these core lipids. How to calculate 2D and 3D diffusion coeff.? Hope I am clear. 2D diffusion coefficients are what the -lateral option does. I really don't understand why you want a 2D value for anything with spherical symmetry. If there is an outer layer of a vesicle, that's as much a sphere as anything inside it. -Justin On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot t.pig...@soton.ac.uk wrote: Hi Venkat, Can you make it a bit clearer what you actually want? If it is the diffusion of the lipids along the curved surface of the vesicle, rather than simply the overall 3D diffusion, this is not trivial to calculate as I don't believe g_msd will do this for you. This property has been studied before though, so I suggest you search the literature for papers simulating vesicles to see how the lipid diffusion was calculated. Cheers Tom On 11/12/2013 06:35 PM, Justin Lemkul wrote: On 11/12/13 1:33 PM, Venkat Reddy wrote: Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? If you just want the overall diffusion constant, that's what g_msd does without any additional options. -Justin On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? The options for the -type flag are x, y, or z. You said you wanted the diffusion coefficient in each spatial dimension. That is precisely what this option will do. and I have recently gone through Justin's membrane protein tutorial, where You mean my tutorial :) he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. Yes, a representative atom is usually what is passed to g_msd. -Justin On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention to the -type flag. -Justin On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 8:55 AM, Venkat Reddy wrote: Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? No. The system is a sphere, so what use is it to calculate motion perpendicular to z when you have lipids moving in all three spatial dimensions? A vesicle is very different from a membrane, in which the lipids move in a plane, thus making -lateral z useful. -Justin On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: MSD is 3D by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy
[gmx-users] Invalid order for directive defaults
Dear Justin Thanks for your reply. In your previous setup, you were effectively trying to use CHARMM27 + some other force field related to the CNT. You can't do that. Thus, Gromacs is not appropriate for systems containing cnt. Is my deduction true? In my case, peptid + cnt + water molecules, what is your suggestion? Please guide me and explain more. How to do MD simulation of my system by gromacs? Any help will highly appreciated. -- 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] Invalid order for directive defaults
On 11/13/13 10:39 AM, Atila Petrosian wrote: Dear Justin Thanks for your reply. In your previous setup, you were effectively trying to use CHARMM27 + some other force field related to the CNT. You can't do that. Thus, Gromacs is not appropriate for systems containing cnt. Is my deduction true? Of course not. People simulate CNTs with Gromacs all the time. You just didn't construct the force field properly. In my case, peptid + cnt + water molecules, what is your suggestion? Please guide me and explain more. How to do MD simulation of my system by gromacs? You have missing parameters in the .top/.itp file. You have those parameters already in ffbonded.itp for the CNT. As long as those parameters are compatible with the peptide force field (CHARMM27), then you just need to add those parameters. Again, that may be as simple as adding #include cntffbonded.itp of whatever it is to the .top file after the #include statement for the parent force field. Your only problem was #including another force field that re-defined a [defaults] directive. That is syntactically illegal. Nothing else was inherently problematic, unless you're mixing incompatible force fields, but I haven't seen any evidence of that. -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 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
[gmx-users] Invalid order for directive defaults
Dear Justin Thanks for your quick reply. I was confused. If I add #include ffcntbon.itp after #include cnt.itp in .top file, my problem was solved and error was solved? -- 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] Invalid order for directive defaults
On 11/13/13 11:53 AM, Atila Petrosian wrote: Dear Justin Thanks for your quick reply. I was confused. If I add #include ffcntbon.itp after #include cnt.itp in .top file, my problem was solved and error was solved? No. The parameters are at the force field level and thus have to be #included before any [moleculetype] is introduced (see Chapter 5 of the manual for required order of directives). If you do: #include charmm27.ff/forcefield.itp #include ffcntbon.itp you should be fine. -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 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
[gmx-users] GROMACS 4.6.4 is released
Hi GROMACS users, GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and some noteworthy simulation performance enhancements (particularly with GPUs!). We encourage all users to upgrade their installations from earlier 4.6-era releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that some tests have been added, and the manual has changed only in chapter 7 and appendix D. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.4.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.4.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.4 http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.4.tar.gz Happy simulating! The GROMACS team -- 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 4.6.4 is released
Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4? Hi GROMACS users, GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and some noteworthy simulation performance enhancements (particularly with GPUs!). We encourage all users to upgrade their installations from earlier 4.6-era releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that some tests have been added, and the manual has changed only in chapter 7 and appendix D. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.4.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.4.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.4 http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.4.tar.gz Happy simulating! The GROMACS team -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs
Hello, I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 12 cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch job GROMCAS is using only GPUs on first node come across and failing to use GPUs on other nodes. The command I used for two gpu enable nodes was, mpirun -np 2 mdrun -v -deffnm $configfile I tried with many other options but none of them worked. The one thing needs to remember here is that on all the nodes, GPUs got id 0 and 1 so -gpu_id option also didn't work. This old thread gave me some idea but I didn't understand it completely. http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html Please suggests me the possible solutions for this issue. Thank you --Jignesh -- 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] (no subject)
sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- 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] remd
sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- 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] shear viscosity
Dear users, g_energy -f *.edr -vis I have two questions about the results of eviscoi.xvg ( derivative of Einstein relation): 1.) I dont understand the unit of y-axis. It is kg.m^(-1).s^(-1).10^(-3) in B.Hess 2002 In eviscoi.xvg @yaxis label (kg m\S-1\N s\S-1\N ps) That is The unit of y-axis:kg.m^(-1).s^(-1).ps What is that? kg.m^(-1).s^(-1).ps equals to kg.m^(-1).s^(-1).10^(-3)? 2.) There are 5 columns in eviscoi.xvg. 1th is time. What are the rest? By the way, there is 216 water molecules in spc216.gro. But I want to calculate the shear viscosity of 512 water molecules. How can I get/derive 512 water molecules from spc216.gro? Can anyone give me some hint of this? Thanks in advance -- Ahmet Yıldırım -- 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
