[gmx-users] NPT and NVT eqquilibruim - membrane simulation
Hi all, I'd like to know if it is necessary to run NVT and NPT equilibrium on a membrane-water system? Would only the NPT be sufficient? How can I understand it? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction energy..
Hi justin, the out put of g_energy are like - 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:energy-energy 51 LJ-SR:energy-energy 52 LJ-LR:energy-energy 53 Coul-14:energy-energy 54 LJ-14:energy-energy 55 Coul-SR:energy-extra34 56 LJ-SR:energy-extra34 57 LJ-LR:energy-extra3458 Coul-14:energy-extra34 59 LJ-14:energy-extra3460 Coul-SR:energy-rest 61 LJ-SR:energy-rest 62 LJ-LR:energy-rest 63 Coul-14:energy-rest 64 LJ-14:energy-rest 65 Coul-SR:extra34-extra34 66 LJ-SR:extra34-extra34 67 LJ-LR:extra34-extra34 68 Coul-14:extra34-extra34 69 LJ-14:extra34-extra34 70 Coul-SR:extra34-rest 71 LJ-SR:extra34-rest 72 LJ-LR:extra34-rest 73 Coul-14:extra34-rest74 LJ-14:extra34-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein When I used g_enemat with the groups.dat file like these 2 extra34 energy I got the output roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) Now When I changed the groups.dat like 2 energy extra34 ( change in the order of the index groups ) I got the following output, Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames Segmentation fault (core dumped) So What is wrong ?? Is I am doing any wrong ?? 2. I am using the temp 310 so the reference temp by default is 300 Should I have to change it to 310 (-tempreal 300 reference temperature for free energy calculation ) Any suggestion on these topic, is helpful to me. Thank you in advance, With best wishes and regards, Rama david. -- 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] NPT and NVT eqquilibruim - membrane simulation
The answer depends on what you are doing and where you got your starting structure. Please provide more information. Generally, if you are in doubt, then do NVT prior to NPT. Nevertheless, going straight to NPT is often ok. -- original message -- I'd like to know if it is necessary to run NVT and NPT equilibrium on a membrane-water system? Would only the NPT be sufficient? How can I understand it? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation
In my own, I want to simulate POPC-water and then insert a protein in it. Then run a new simulation for my new system. I got the starting structure from Prof.Klauda website. Then dear Peter provides this link to get some useful files: http://uab.hyperfine.info/~pcl/files/popc36/ Regarding to the pblished paper, written by Peter, NPT equilibration had been done. I also followed them and did the NPT. But now, I'm wondering when NPT is needed to be done and when NPT NVT are both needed? Thanks for your suggestions. Sincerely, Shima - Original Message - From: Christopher Neale chris.ne...@mail.utoronto.ca To: gmx-users@gromacs.org gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 10:24 AM Subject: [gmx-users] NPT and NVT eqquilibruim - membrane simulation The answer depends on what you are doing and where you got your starting structure. Please provide more information. Generally, if you are in doubt, then do NVT prior to NPT. Nevertheless, going straight to NPT is often ok. -- original message -- I'd like to know if it is necessary to run NVT and NPT equilibrium on a membrane-water system? Would only the NPT be sufficient? How can I understand it? Thanks in advance. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Model of water
Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to center to molecule in pbc box?
hello: I am using the following command for md production in gromacs: grompp -f md.mdp -p md.top -o md.tpr mpirun -np 64 mdrun -s md.tpr -x md.xtc -g md.log However, I found that the md.xtc file need command: trjconv -f md.xtc -o convert.xtc -pbc mol to put the molecule in the centre of pbc box, otherwise it is messy when we visualize in VMD. I am wondering, is it possible to ask mdrun generate the .xtc file cetering the molecule in PBC box automatically and we no longer need to use trjconv command to convert it. 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
Re: [gmx-users] Model of water
I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About pritein Lipid Bilayer Simulation
On 10/6/12 1:35 AM, vidhya sankar wrote: Dear Justin , Thank you for your Previous reply using Genbox I have Successfully Solvated Energy Minimized System_shrink.gro file It adds 84266 water molecules . Then Tutorial How to Check Existence of Water Molecules within HydroPhobic core of Bilayer it is Difficult to see and detect in VMD Solvation should only be done at the very end, after a few dozen rounds of shrinking. Are you working through the tutorial or a system of your own? If you're doing the tutorial, the amount of water molecules is far too high. Water molecules within the hydrophobic core of the membrane should be obvious upon visualization (there should only be a few, at most, if the system is constructed properly). Methods for dealing with these stray molecules are described in the tutorial. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation
On 10/6/12 3:15 AM, Shima Arasteh wrote: In my own, I want to simulate POPC-water and then insert a protein in it. Then run a new simulation for my new system. I got the starting structure from Prof.Klauda website. Then dear Peter provides this link to get some useful files: http://uab.hyperfine.info/~pcl/files/popc36/ Regarding to the pblished paper, written by Peter, NPT equilibration had been done. I also followed them and did the NPT. But now, I'm wondering when NPT is needed to be done and when NPT NVT are both needed? As long as the system is stable and you obtain converged observables, then there's nothing wrong with doing NPT as your only equilibration. Not all systems are very well behaved and do require NVT first before switching on pressure coupling, so it is often advisable. There are no hard and fast rules for equilibration, however. Every system is different, so a universal recipe is not really possible. If your method worked, then you're fine. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to center to molecule in pbc box?
On 10/6/12 4:08 AM, Albert wrote: hello: I am using the following command for md production in gromacs: grompp -f md.mdp -p md.top -o md.tpr mpirun -np 64 mdrun -s md.tpr -x md.xtc -g md.log However, I found that the md.xtc file need command: trjconv -f md.xtc -o convert.xtc -pbc mol to put the molecule in the centre of pbc box, otherwise it is messy when we visualize in VMD. I am wondering, is it possible to ask mdrun generate the .xtc file cetering the molecule in PBC box automatically and we no longer need to use trjconv command to convert it. No, it is not. A periodic system has no center, and the centering algorithm is merely a convenience for visualization. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation
Thank you Justin. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 1:26 PM Subject: Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation On 10/6/12 3:15 AM, Shima Arasteh wrote: In my own, I want to simulate POPC-water and then insert a protein in it. Then run a new simulation for my new system. I got the starting structure from Prof.Klauda website. Then dear Peter provides this link to get some useful files: http://uab.hyperfine.info/~pcl/files/popc36/ Regarding to the pblished paper, written by Peter, NPT equilibration had been done. I also followed them and did the NPT. But now, I'm wondering when NPT is needed to be done and when NPT NVT are both needed? As long as the system is stable and you obtain converged observables, then there's nothing wrong with doing NPT as your only equilibration. Not all systems are very well behaved and do require NVT first before switching on pressure coupling, so it is often advisable. There are no hard and fast rules for equilibration, however. Every system is different, so a universal recipe is not really possible. If your method worked, then you're fine. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction energy..
On 10/6/12 2:28 AM, rama david wrote: Hi justin, the out put of g_energy are like - 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:energy-energy 51 LJ-SR:energy-energy 52 LJ-LR:energy-energy 53 Coul-14:energy-energy 54 LJ-14:energy-energy 55 Coul-SR:energy-extra34 56 LJ-SR:energy-extra34 57 LJ-LR:energy-extra3458 Coul-14:energy-extra34 59 LJ-14:energy-extra3460 Coul-SR:energy-rest 61 LJ-SR:energy-rest 62 LJ-LR:energy-rest 63 Coul-14:energy-rest 64 LJ-14:energy-rest 65 Coul-SR:extra34-extra34 66 LJ-SR:extra34-extra34 67 LJ-LR:extra34-extra34 68 Coul-14:extra34-extra34 69 LJ-14:extra34-extra34 70 Coul-SR:extra34-rest 71 LJ-SR:extra34-rest 72 LJ-LR:extra34-rest 73 Coul-14:extra34-rest74 LJ-14:extra34-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein When I used g_enemat with the groups.dat file like these 2 extra34 energy I got the output roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) Now When I changed the groups.dat like 2 energy extra34 ( change in the order of the index groups ) I got the following output, Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames Segmentation fault (core dumped) Based on the energy names, this is the appropriate setup, but unfortunately I have no idea why it does not work. I have noticed that there is a problem with g_enemat - the -lj flag specifies both LJ-SR and LJ-LR terms to be written - which may be complicating matters. Please try your command with -nolj to test. So What is wrong ?? Is I am doing any wrong ?? 2. I am using the temp 310 so the reference temp by default is 300 Should I have to change it to 310 (-tempreal 300 reference temperature for free energy calculation ) As stated in the description, the -temp option is for free energy calculations. Are you requesting a free energy calculation? You haven't provided your command line. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction energy..
Hi justin, I tried as per your suggestion. command line g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free the out put is like , Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) why program not work ?? Is it bug??? or Am I doing any stupid mistake??? Thank you in advance .. With best wishes and regards, Rama david On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/6/12 2:28 AM, rama david wrote: Hi justin, the out put of g_energy are like --**--**- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:energy-energy 51 LJ-SR:energy-energy 52 LJ-LR:energy-energy 53 Coul-14:energy-energy 54 LJ-14:energy-energy 55 Coul-SR:energy-extra34 56 LJ-SR:energy-extra34 57 LJ-LR:energy-extra3458 Coul-14:energy-extra34 59 LJ-14:energy-extra3460 Coul-SR:energy-rest 61 LJ-SR:energy-rest 62 LJ-LR:energy-rest 63 Coul-14:energy-rest 64 LJ-14:energy-rest 65 Coul-SR:extra34-extra34 66 LJ-SR:extra34-extra34 67 LJ-LR:extra34-extra34 68 Coul-14:extra34-extra34 69 LJ-14:extra34-extra34 70 Coul-SR:extra34-rest 71 LJ-SR:extra34-rest 72 LJ-LR:extra34-rest 73 Coul-14:extra34-rest74 LJ-14:extra34-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein When I used g_enemat with the groups.dat file like these 2 extra34 energy I got the output roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) Now When I changed the groups.dat like 2 energy extra34 ( change in the order of the index groups ) I got the following output, Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames Segmentation fault (core dumped) Based on the energy names, this is the appropriate setup, but unfortunately I have no idea why it does not work. I have noticed that there is a problem with g_enemat - the -lj flag specifies both LJ-SR and LJ-LR terms to be written - which may be complicating matters. Please try your command with -nolj to test. So What is wrong ?? Is I am doing any wrong ?? 2. I am using the temp 310 so the reference temp by default is 300 Should I have to change it to 310 (-tempreal 300
Re: [gmx-users] Model of water
I used TIPS3P in everything, because after all, it's CHARMM's water and no reviewer can complain about using it with CHARMM. If you want a faster simulation you can try using the regular TIP3P and see if the bilayer metrics remain satisfactory for you. If you still have doubts, run simulations with both TIPS3P and TIP3P and decide if the differences are significant. IIRC Thomas Piggot's latest CHARMM36 Gromacs paper Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study has some results on POPC in TIP3P vs. TIPS3P. When using genbox, you always use spc216.gro as the starting solvent coordinates. The waters will adopt the correct physical properties specified by the model and forcefield during equilibration. On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote: As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Model of water
Thanks for your explanation. Do you mean genbox will adapt the model and the force field automatically? Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 3:27 PM Subject: Re: [gmx-users] Model of water I used TIPS3P in everything, because after all, it's CHARMM's water and no reviewer can complain about using it with CHARMM. If you want a faster simulation you can try using the regular TIP3P and see if the bilayer metrics remain satisfactory for you. If you still have doubts, run simulations with both TIPS3P and TIP3P and decide if the differences are significant. IIRC Thomas Piggot's latest CHARMM36 Gromacs paper Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study has some results on POPC in TIP3P vs. TIPS3P. When using genbox, you always use spc216.gro as the starting solvent coordinates. The waters will adopt the correct physical properties specified by the model and forcefield during equilibration. On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote: As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Model of water
To use tip3p water model, I copied popc.top and popc.itp in my working directory. I removed the line of #include tips3p from top file. Also removed SOL in moleculetypes. Then I ran genbox : #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top genbox added SOL but there is not any water model including in my top file, so I added #include charmm36.ff/tip3p.itp to top file manually: Next, I ran energy minimization. Is my procedure correct? How would I be sure that tip3p is used as water model? Thanks for your suggestions. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 3:27 PM Subject: Re: [gmx-users] Model of water I used TIPS3P in everything, because after all, it's CHARMM's water and no reviewer can complain about using it with CHARMM. If you want a faster simulation you can try using the regular TIP3P and see if the bilayer metrics remain satisfactory for you. If you still have doubts, run simulations with both TIPS3P and TIP3P and decide if the differences are significant. IIRC Thomas Piggot's latest CHARMM36 Gromacs paper Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study has some results on POPC in TIP3P vs. TIPS3P. When using genbox, you always use spc216.gro as the starting solvent coordinates. The waters will adopt the correct physical properties specified by the model and forcefield during equilibration. On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote: As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Model of water
On 10/6/12 8:59 AM, Shima Arasteh wrote: To use tip3p water model, I copied popc.top and popc.itp in my working directory. I removed the line of #include tips3p from top file. Also removed SOL in moleculetypes. Then I ran genbox : #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top genbox added SOL but there is not any water model including in my top file, so I added #include charmm36.ff/tip3p.itp to top file manually: Next, I ran energy minimization. Is my procedure correct? How would I be sure that tip3p is used as water model? Your approach is correct. genbox will not write topology information (i.e. #include statements) to your topology for you. It adds coordinates to your configuration and updates the [molecules] section, nothing more. It is up to you to tell grompp what parameters to apply to the water molecules. If your topology #includes a TIP3P topology, that's what grompp will use. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction energy..
On 10/6/12 6:26 AM, rama david wrote: Hi justin, I tried as per your suggestion. command line g_enemat -f ener.edr -groups groups.dat -temp 310 -nolj -free the out put is like , Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 3 elements Last energy frame read 5 time 1.000 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) why program not work ?? Is it bug??? or Am I doing any stupid mistake??? It might be a bug, but I'm not sure yet. Please run the command without the -free option (and thus without -temp) to further reduce complexity. Then manually add the -coul flag. It should be set by default, but at this point the screen output seems to indicate that no energy terms are being detected. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible
Could you explain to me how this would effect your domain decomposition? Original-Nachricht Datum: Fri, 05 Oct 2012 23:05:33 -0400 Von: Justin Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible On 10/5/12 5:19 PM, Sonia Aguilera wrote: Thank you a lot, I only changed the couple-intramol setting (couple-intramol=yes) and now it´s running just fine. However I have a doubt about something. In the manual says the following when using couple-intramol=no In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects I don´t understand the real effects and implications of this on my simulation. Does it mean that it is better to run with couple-intramol=no? I also read that using couple-intramol=yes has it's advantages: This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. Again, I don't understand what is the real meaning of that. Can you please make this clear for me? Consider what (de)coupling means. You are manipulating the interactions of a chosen molecule with its surroundings as a function of lambda. If you tell mdrun that your calculation should not couple intramolecular interactions (couple-intramol = no) then what that is saying is that all nonbonded interactions within that given molecule are always calculated at full strength. That is what the manual is telling you - the calculation implies that intramolecular terms are always on, as if the molecule were in a vacuum. If you do couple intramolecular interactions (couple-intramol = yes), then any nonbonded interactions within your molecule of choice are also scaled as a function of lambda. This may be beneficial for large molecules, since if you are not coupling intramolecular interactions, you may get unnaturally strong interactions within the solute molecule since the interactions with the surrounding solvent are weakened as a function of lambda. Thus you can get odd geometries that get trapped and are detrimental to your sampling. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Model of water
OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 4:44 PM Subject: Re: [gmx-users] Model of water On 10/6/12 8:59 AM, Shima Arasteh wrote: To use tip3p water model, I copied popc.top and popc.itp in my working directory. I removed the line of #include tips3p from top file. Also removed SOL in moleculetypes. Then I ran genbox : #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top genbox added SOL but there is not any water model including in my top file, so I added #include charmm36.ff/tip3p.itp to top file manually: Next, I ran energy minimization. Is my procedure correct? How would I be sure that tip3p is used as water model? Your approach is correct. genbox will not write topology information (i.e. #include statements) to your topology for you. It adds coordinates to your configuration and updates the [molecules] section, nothing more. It is up to you to tell grompp what parameters to apply to the water molecules. If your topology #includes a TIP3P topology, that's what grompp will use. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible
On 10/6/12 10:23 AM, lloyd riggs wrote: Could you explain to me how this would effect your domain decomposition? Pairs are two-body interactions. If they are applied to protein atoms that are very far apart (which is not normally the case) then the DD cell sizes get very large. -Justin Original-Nachricht Datum: Fri, 05 Oct 2012 23:05:33 -0400 Von: Justin Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible On 10/5/12 5:19 PM, Sonia Aguilera wrote: Thank you a lot, I only changed the couple-intramol setting (couple-intramol=yes) and now it´s running just fine. However I have a doubt about something. In the manual says the following when using couple-intramol=no In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects I don´t understand the real effects and implications of this on my simulation. Does it mean that it is better to run with couple-intramol=no? I also read that using couple-intramol=yes has it's advantages: This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. Again, I don't understand what is the real meaning of that. Can you please make this clear for me? Consider what (de)coupling means. You are manipulating the interactions of a chosen molecule with its surroundings as a function of lambda. If you tell mdrun that your calculation should not couple intramolecular interactions (couple-intramol = no) then what that is saying is that all nonbonded interactions within that given molecule are always calculated at full strength. That is what the manual is telling you - the calculation implies that intramolecular terms are always on, as if the molecule were in a vacuum. If you do couple intramolecular interactions (couple-intramol = yes), then any nonbonded interactions within your molecule of choice are also scaled as a function of lambda. This may be beneficial for large molecules, since if you are not coupling intramolecular interactions, you may get unnaturally strong interactions within the solute molecule since the interactions with the surrounding solvent are weakened as a function of lambda. Thus you can get odd geometries that get trapped and are detrimental to your sampling. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
Yes, the system is only POPC and water. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Fwd: Re: [gmx-users] Model of water
Original Message Subject: Re: [gmx-users] Model of water Date: Sat, 06 Oct 2012 10:47:18 -0400 From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound#mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
# grep -c P popc-solv.gro 1628 What should I do with this number? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:17 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
On 10/6/12 10:52 AM, Shima Arasteh wrote: # grep -c P popc-solv.gro 1628 What should I do with this number? The letter P can theoretically match a lot of lines in a POPC system. Be sure you're grepping for a specific atom name, rather than something that can match both atom and residue names. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
The total atom of popc-solv.gro is 74672 grep HW gives me 48698 grep P gives me 1628 Section of moleculetypes in top file is as [ molecules ] Compound #mols POPC 238 SOL 24348 I am confused! Am I need to change the number of gro or top file? Actually I can't make connection between gro and top, so the coordinate doesn't match topology yet!! Please help me :( Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 6:22 PM Subject: Re: [gmx-users] Model of water # grep -c P popc-solv.gro 1628 What should I do with this number? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:17 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
On 10/6/12 11:52 AM, Shima Arasteh wrote: The total atom of popc-solv.gro is 74672 grep HW gives me 48698 Assuming you meant to type 48696 like you reported before, this means there are 24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If you grep for OW (since it is unique to each water molecule), you can confirm the count. grep P gives me 1628 I already said this grep was insufficiently precise and thus it is not possible to connect this information with the topology. Section of moleculetypes in top file is as [ molecules ] Compound#mols POPC 238 SOL 24348 I am confused! Am I need to change the number of gro or top file? Actually I can't make connection between gro and top, so the coordinate doesn't match topology yet!! You need to make the topology agree with the coordinate file. Do not make manual adjustments to the .gro file. Sometimes it's better to start over and be more careful. A mismatch between coordinates and topology always boils down to errors in bookkeeping. -Justin Please help me :( Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 6:22 PM Subject: Re: [gmx-users] Model of water # grep -c P popc-solv.gro 1628 What should I do with this number? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:17 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound#mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? Elie Date: Fri, 5 Oct 2012 13:06:34 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/5/12 1:00 PM, Elie M wrote: I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] directive, I plug the info there with the corresponding values of bo and kb and according to the format there, and I save. 3- i run grompp again but in vain as I still get the same number of errors (as I expect they should decrease in number if things were fixed). Am I still missing something that i should have done apart from filling in the numbers in ffoplsaabon.itp? Whatever changes you made were apparently ineffectual. You need to make sure that you are adding parameters in the correct directives (i.e. bonds in [bondtypes], angles in [angletypes], etc). Without seeing exactly what you've done, all I can say is that whatever you did wasn't correct. The approach is theoretically sound, though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] protein-membrane simulation- number of lipids
I want to simulate a system of protein and POPC. I downloaded popc.pdb file from Dr.Klauda website. This pdb file contains 72 lipids. I want to know if this number of lipids would be enough for protein-membrane simukation? Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
Dear Justin, I downloaded popc.pdb file from http://terpconnect.umd.edu/~jbklauda/research/download.html. This pdb file has water molecules. So I tried to run these commands and don't run genbox: 1.editconf -f popc.pdb -o popc.gro -c -d 1.0 -bt cubic 2.grompp -f em.mdp -c popc.gro -p topol.top -o em.tpr I also added the SOL molecules manually as it is written at the end of the popc.pdb file downloaded. But this fatal errors comes out: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' Warning: atom name 2 in topol.top and popc.gro does not match (C12 - C11) Warning: atom name 3 in topol.top and popc.gro does not match (C13 - C12) Warning: atom name 4 in topol.top and popc.gro does not match (C14 - C13) Warning: atom name 5 in topol.top and popc.gro does not match (C15 - C14) Warning: atom name 6 in topol.top and popc.gro does not match (H12A - H11) Warning: atom name 7 in topol.top and popc.gro does not match (H12B - H12) Warning: atom name 8 in topol.top and popc.gro does not match (H13A - H21) Warning: atom name 9 in topol.top and popc.gro does not match (H13B - H22) Warning: atom name 10 in topol.top and popc.gro does not match (H13C - H23) Warning: atom name 11 in topol.top and popc.gro does not match (H14A - H31) Warning: atom name 12 in topol.top and popc.gro does not match (H14B - H32) Warning: atom name 13 in topol.top and popc.gro does not match (H14C - H33) Warning: atom name 14 in topol.top and popc.gro does not match (H15A - H41) Warning: atom name 15 in topol.top and popc.gro does not match (H15B - H42) Warning: atom name 16 in topol.top and popc.gro does not match (H15C - H43) Warning: atom name 17 in topol.top and popc.gro does not match (C11 - C15) Warning: atom name 18 in topol.top and popc.gro does not match (H11A - H51) Warning: atom name 19 in topol.top and popc.gro does not match (H11B - H52) Warning: atom name 20 in topol.top and popc.gro does not match (P - P1) Warning: atom name 21 in topol.top and popc.gro does not match (O13 - O3) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 36]: 8382 non-matching atom names atom names from topol.top will be used atom names from popc.gro will be ignored Analysing residue names: There are: 72 Other residues There are: 2242 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42393.00 Largest charge group radii for Van der Waals: 0.040, 0.040 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 96x96x96, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.59 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 191 Mb of data There was 1 note There was 1 warning --- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1584 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Would you please give me advice? Thanks for all your explanation. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 7:25 PM Subject: Re: [gmx-users] Model of water On 10/6/12 11:52 AM, Shima Arasteh wrote: The total atom of popc-solv.gro is 74672 grep HW gives me 48698 Assuming you meant to type 48696 like you reported before, this means there are 24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If you grep for OW (since it is unique to each water molecule), you can confirm the count. grep P gives me 1628 I already said this grep was insufficiently precise and thus it is not possible to connect this information with the topology. Section of moleculetypes in top file is as [ molecules ] Compound #mols POPC 238 SOL 24348 I am confused! Am I need to change the number of gro or top file? Actually I can't make connection between gro and top, so the coordinate doesn't match topology yet!! You need to make the topology agree with the coordinate file. Do not make manual adjustments to the .gro file. Sometimes it's better to start over and be more careful. A mismatch between coordinates and topology always boils down to errors in
Re: [gmx-users] Error with grompp
On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] protein-membrane simulation- number of lipids
On 10/6/12 1:23 PM, Shima Arasteh wrote: I want to simulate a system of protein and POPC. I downloaded popc.pdb file from Dr.Klauda website. This pdb file contains 72 lipids. I want to know if this number of lipids would be enough for protein-membrane simukation? Only if it's a very small protein. Small lipid patches often have problems with violations of the minimum image convention if the protein is anything larger than a very small peptide, and even then it's questionable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
On 10/6/12 1:27 PM, Shima Arasteh wrote: Dear Justin, I downloaded popc.pdb file from http://terpconnect.umd.edu/~jbklauda/research/download.html. This pdb file has water molecules. So I tried to run these commands and don't run genbox: 1.editconf -f popc.pdb -o popc.gro -c -d 1.0 -bt cubic If you have a pre-equilibrated membrane, complete with water, this doesn't make sense. You're introducing empty space around the whole system. 2.grompp -f em.mdp -c popc.gro -p topol.top -o em.tpr I also added the SOL molecules manually as it is written at the end of the popc.pdb file downloaded. I don't understand why you need to do this. But this fatal errors comes out: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' Warning: atom name 2 in topol.top and popc.gro does not match (C12 - C11) Warning: atom name 3 in topol.top and popc.gro does not match (C13 - C12) Warning: atom name 4 in topol.top and popc.gro does not match (C14 - C13) Warning: atom name 5 in topol.top and popc.gro does not match (C15 - C14) Warning: atom name 6 in topol.top and popc.gro does not match (H12A - H11) Warning: atom name 7 in topol.top and popc.gro does not match (H12B - H12) Warning: atom name 8 in topol.top and popc.gro does not match (H13A - H21) Warning: atom name 9 in topol.top and popc.gro does not match (H13B - H22) Warning: atom name 10 in topol.top and popc.gro does not match (H13C - H23) Warning: atom name 11 in topol.top and popc.gro does not match (H14A - H31) Warning: atom name 12 in topol.top and popc.gro does not match (H14B - H32) Warning: atom name 13 in topol.top and popc.gro does not match (H14C - H33) Warning: atom name 14 in topol.top and popc.gro does not match (H15A - H41) Warning: atom name 15 in topol.top and popc.gro does not match (H15B - H42) Warning: atom name 16 in topol.top and popc.gro does not match (H15C - H43) Warning: atom name 17 in topol.top and popc.gro does not match (C11 - C15) Warning: atom name 18 in topol.top and popc.gro does not match (H11A - H51) Warning: atom name 19 in topol.top and popc.gro does not match (H11B - H52) Warning: atom name 20 in topol.top and popc.gro does not match (P - P1) Warning: atom name 21 in topol.top and popc.gro does not match (O13 - O3) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 36]: 8382 non-matching atom names atom names from topol.top will be used atom names from popc.gro will be ignored These warnings suggest that the coordinate file is out of sync with respect to the atoms in the topology. Bad things will happen, because the wrong parameters are mapped to the wrong atoms. -Justin Analysing residue names: There are:72 Other residues There are: 2242 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42393.00 Largest charge group radii for Van der Waals: 0.040, 0.040 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 96x96x96, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.59 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 191 Mb of data There was 1 note There was 1 warning --- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1584 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Would you please give me advice? Thanks for all your explanation. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 7:25 PM Subject: Re: [gmx-users] Model of water On 10/6/12 11:52 AM, Shima Arasteh wrote: The total atom of popc-solv.gro is 74672 grep HW gives me 48698 Assuming you meant to type 48696 like you reported before, this means there are 24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If you grep for OW (since it is unique to each water molecule), you can confirm the count. grep P gives me 1628 I already said this grep was insufficiently precise and thus it is not possible to connect this information with the topology. Section of moleculetypes in top file is as [ molecules ] Compound#mols POPC 238
RE: [gmx-users] Error with grompp
Yes I just saw that. thanks for turning my attention. The top file assigned this order of the atomsdo you think switching the order of the atoms in the top file would solve the problem? Elie Date: Sat, 6 Oct 2012 13:26:38 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 with grompp
On 10/6/12 1:57 PM, Elie M wrote: Yes I just saw that. thanks for turning my attention. The top file assigned this order of the atomsdo you think switching the order of the atoms in the top file would solve the problem? In principle, I don't think it should matter, but it's something you can check yourself in less time than it takes to send an email :) -Justin Elie Date: Sat, 6 Oct 2012 13:26:38 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Yeah sorry about that. i thought about it at the moment I was sending the e-mail..The problem I am so desperate about getting all files correct to minimize my polymer. It has really taken a long time. Anyhow you were right. Switching the order did not do anything; the error is still there. Now it is a bit weird because the bond is there in the file then why it cannot find it? Any suggestions? Elie Date: Sat, 6 Oct 2012 13:59:10 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:57 PM, Elie M wrote: Yes I just saw that. thanks for turning my attention. The top file assigned this order of the atomsdo you think switching the order of the atoms in the top file would solve the problem? In principle, I don't think it should matter, but it's something you can check yourself in less time than it takes to send an email :) -Justin Elie Date: Sat, 6 Oct 2012 13:26:38 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 with grompp
On 10/6/12 2:30 PM, Elie M wrote: Yeah sorry about that. i thought about it at the moment I was sending the e-mail..The problem I am so desperate about getting all files correct to minimize my polymer. It has really taken a long time. Anyhow you were right. Switching the order did not do anything; the error is still there. Now it is a bit weird because the bond is there in the file then why it cannot find it? Any suggestions? I will attempt to debug this. Please send me (off-list): 1. Your coordinate file 2. Your topology 3. The .mdp file you are using 4. The force field files -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] difference between the tabulated and Cut-off Electicstatics potentials
Dear gmxers, I am trying to perform two separate const-NPT MD simulations using tablulated and Cut-off Electrostatics potentials. I find that for the two cases the density of system is stablized at different values (1200 vs. 1400 g/cm3). Since the partial charges are all zeros in the top files, I assume the two potentials generate same results. But why not as expected? Could you please give me some hints? Yours sincerely, Chaofu Wu -- 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 Usage of Constraints
Dear justin Thank you for your previous reply I am running NPT Equlibration at 20 ps with dt 0.0002 in 10 steps Without usage of Lincs Algorithm and its related parameters it runs Successfully . But When I Increase dt from 0.0002 to 0.002 then I have got error as follows in grompp WARNING 1 [file 2KDQTR.top, line 71]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Then I have used the Lincs Algorithm and its related parameter Then I have got Error during Mdrun as follows I saw there Are Plenty Of discussion in Mailing list But I am Not Able to come to conclusion relative constraint deviation after LINCS: rms 0.015272, max 0.577865 (between atoms 120 and 122) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Wrote pdb files with previous and current coordinates 129 131 39.1 0.1475 0.1664 0.1330 129 130 37.8 0.1191 0.1243 0.1230 125 126 38.5 0.1738 0.1508 0.1530 124 129 103.2 0.0962 0.9157 0.1530 124 125 124.3 0.1725 0.8648 0.1530 122 124 169.9 0.4717 2.5621 0.1470 122 123 168.0 0.2655 3.1890 0.1000 120 122 176.3 0.5957 7.3414 0.1330 120 121 172.8 0.5550 6.4843 0.1230 What does the Above Fact Indicates I mean the Problem is in Topology or in MD Parameter file ? With Regards S.Vidhyasankar -- 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
