[gmx-users] Periodic Boundary Conditions g_mindist -pi
Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type= cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps= Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- 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] Periodic Boundary Conditions g_mindist -pi
Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub shubi...@gmail.com wrote: Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type = cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps = Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf reference structure?
Hi, The reference is used for fitting. The RMSF is calculated with respect to the average (fitted) structure, unless you explicitly specify that deviations from the reference should be used. Cheers, Tsjerk On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote: Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? It does take the reference structure from -s. Whether you actually want the RMSF from the non-physical time-averaged structure is up to you. IIRC you might be able to get such an average from g_cluster. Mark -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gromacs QM/MM compilation with gaussian
Hi there! We are trying to compile gromacs with Gaussian 03 rev D.02 (we also have g09). We followed the instructions in http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf despite that they do no fit exactly with the g03 rev d03 version,for instance, FrcNCN is no in l710 but in utilam.F Despite of that, we compiled gromacs and apparently everything was fine, but we get a segmentation fault when we run gromacs. We have the following questions 1.- Is it possible to get a more detailed/or specific instructions? 2.- I think that three variables GAUSS_EXE, GAUSS_DIR and DEVEL_DIR should be defined. Where should GAUSS_EXE and GAUSS_DIR point exactly? Thanks for your attention, any help will be appreciated. Regards, Txema Mercero IZO/SGI UPV/EHU -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Periodic Boundary Conditions g_mindist -pi
Hi Tsjerk, Thank you for your reply. I am aware of the trajconv option but I wanted to know if there is a way to avoid these kind of jumps over the periodic boundaries during the mdrun and not post process? Thanks, Ifat message: 4 Date: Wed, 16 Feb 2011 11:19:14 +0200 From: ifat shub shubi...@gmail.com Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: gmx-users@gromacs.org Message-ID: AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type= cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps= Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub shubi...@gmail.com wrote: Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp
Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi
On 16/02/2011 10:30 PM, ifat shub wrote: Hi Tsjerk, Thank you for your reply. I am aware of the trajconv option but I wanted to know if there is a way to avoid these kind of jumps over the periodic boundaries during the mdrun and not post process? No. mdrun does not know in advance what your visualization requirements are, and frankly there are better things to do with expensive compute cluster time. Post-processing a small number of frames elsewhere is much better use of resources. Mark message: 4 Date: Wed, 16 Feb 2011 11:19:14 +0200 From: ifat shub shubi...@gmail.com mailto:shubi...@gmail.com Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com mailto:sgjftmrf-0nvmzzogfs%2bxhyxv5u6ggfnhr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type= cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps= Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com mailto:abxfur%2badkenmxem...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk
[gmx-users] initial structures for md simulations
Dear All, I want to generate some initial crystalline structures of my target molecules for md simulations. Are there any free softwares to do this? And are there any complete sources that give the theoretical structures of organic molecules ( like hydrocarbons ) determined by the experiments and give the x-ray, neutron scattering, NMR, IR or Raman results of organic molecules apart from the articles ? Could you please share your thoughts about this issue ? Thank you very much for your attention. Kind regards. -- 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: Periodic Boundary Conditions g_mindist -pi
On Wed, Feb 16, 2011 at 1:00 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2011 10:30 PM, ifat shub wrote: Hi Tsjerk, Thank you for your reply. I am aware of the trajconv option but I wanted to know if there is a way to avoid these kind of jumps over the periodic boundaries during the mdrun and not post process? No. mdrun does not know in advance what your visualization requirements are, and frankly there are better things to do with expensive compute cluster time. Post-processing a small number of frames elsewhere is much better use of resources. Or: No. mdrun takes the internal representation that is most efficient, and there are better things to do with expensive compute cluster time than writing out a trajectory without jumps, which might not even be what you want in the end. :) Tsjerk Mark message: 4 Date: Wed, 16 Feb 2011 11:19:14 +0200 From: ifat shub shubi...@gmail.com Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: gmx-users@gromacs.org Message-ID: AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type = cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps = Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub shubi...@gmail.com wrote: Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing
Re: [gmx-users] initial structures for md simulations
On 16/02/2011 11:24 PM, oguz gurbulak wrote: /Dear All/, I want to generate some initial crystalline structures of my targetmolecules for md simulations. /Are there any free softwares/ to do this? Some sources for obtaining initial coordinates can be found here http://www.gromacs.org/Documentation/File_Formats/Coordinate_File. I doubt there is going to be software to generate crystalline structures (whatever you mean by that). You could get a structure and replicate it with (e.g. genconf). And are there any complete sources that give the theoretical structures of organic molecules ( like hydrocarbons ) determined by the experiments and give the x-ray, neutron scattering, NMR, IR or Raman results of organic molecules apart from the articles ? Could you please share your thoughts about this issue ? Theoretical structures you compute according to some model. Experimental data tends to live in original literature and lots of specialist databases. Which do you actually want? Google is your friend either way. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub shubi...@gmail.com wrote: Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type= cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps= Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo
Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
to compile gromacs with Gaussian 03 rev D.02 (we also have g09). We followed the instructions in http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf despite that they do no fit exactly with the g03 rev d03 version,for instance, FrcNCN is no in l710 but in utilam.F Despite of that, we compiled gromacs and apparently everything was fine, but we get a segmentation fault when we run gromacs. We have the following questions 1.- Is it possible to get a more detailed/or specific instructions? 2.- I think that three variables GAUSS_EXE, GAUSS_DIR and DEVEL_DIR should be defined. Where should GAUSS_EXE and GAUSS_DIR point exactly? Thanks for your attention, any help will be appreciated. Regards, Txema Mercero IZO/SGI UPV/EHU -- Message: 2 Date: Wed, 16 Feb 2011 13:30:29 +0200 From: ifat shub shubi...@gmail.com Subject: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi To: gmx-users@gromacs.org Message-ID: AANLkTi=71Moj0kH4=tr3_gdh54b1wsnei0hundx++...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi Tsjerk, Thank you for your reply. I am aware of the trajconv option but I wanted to know if there is a way to avoid these kind of jumps over the periodic boundaries during the mdrun and not post process? Thanks, Ifat message: 4 Date: Wed, 16 Feb 2011 11:19:14 +0200 From: ifat shub shubi...@gmail.com Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: gmx-users@gromacs.org Message-ID: AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type = cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps = Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID
Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub shubi...@gmail.com wrote: Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type= cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps= Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- -- 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! End of gmx-users Digest, Vol 82, Issue 125 ** -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/daa11467/attachment-0001.html -- Message: 3 Date: Wed, 16 Feb 2011 23:00:32 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users
[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub shubi...@gmail.com wrote: Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns. Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps? Here is the mdp file I used: --run.mdp-- integrator = md nsteps = 100 dt = 0.001 coulombtype = pme vdw-type= cut-off tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 nstxout = 100 nstvout = 0 nstxtcout = 100 nstenergy = 100 comm_mode = Linear ; Angular comm_grps= Protein xtc_grps = Protein energygrps = Protein -- Thanks, Ifat The output: 343.7 10.813 5.924 16.445 16.445 16.445 343.8 10.809 5.949 16.445 16.445 16.445 343.9 10.804 5.959 16.445 16.445 16.445 344 10.808 5.974 16.445 16.445 16.445 344.1 0.18 21.982 16.445 16.445 16.445 344.2 10.778 5.977 16.445 16.445 16.445 344.3 10.768 5.996 16.445 16.445 16.445 344.4 10.764 6.016 16.445 16.445 16.445 344.5 10.722 6.029 16.445 16.445 16.445 344.6 10.774 6.01 16.445 16.445 16.445 344.7 0.174 21.984 16.445 16.445 16.445 344.8 0.176 21.98 16.445 16.445 16.445 344.9 0.17 22.002 16.445 16.445 16.445 345 0.173 21.981 16.445 16.445 16.445 345.1 0.191 21.954 16.445 16.445 16.445 345.2 0.183 21.958 16.445 16.445 16.445 345.3 0.181 22.012 16.445 16.445 16.445 345.4 0.17 22.054 16.445 16.445 16.445 345.5 0.168 22.054 16.445 16.445 16.445 345.6 0.189 22.039 16.445 16.445 16.445 345.7 0.171 22.007 16.445 16.445 16.445 345.8 0.186 22.031 16.445 16.445 16.445 345.9 0.171 22.077 16.445 16.445 16.445 346 0.187 21.99 16.445 16.445 16.445 346.1 0.173 21.984 16.445 16.445 16.445 346.2 0.181 22.02 16.445 16.445 16.445 346.3 10.82 5.984 16.445 16.445 16.445 346.4 10.81 6.002 16.445 16.445 16.445 346.5 10.819 6.008 16.445 16.445 16.445 346.6 10.813 5.996 16.445 16.445 16.445 346.7 10.781 6.006 16.445 16.445 16.445 346.8 10.793 6.026 16.445 16.445 16.445 346.9 10.745 5.985 16.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- 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
[gmx-users] Re: Re: g_rmsf reference structure? (Tsjerk Wassenaar)
Thank you very much for the clarification! Message: 1 Date: Wed, 16 Feb 2011 10:46:18 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] g_rmsf reference structure? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTi=6-rmt6k+kz1+qpfsa-ottgfpiry5+eppv+...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, The reference is used for fitting. The RMSF is calculated with respect to the average (fitted) structure, unless you explicitly specify that deviations from the reference should be used. Cheers, Tsjerk On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote: Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? It does take the reference structure from -s. Whether you actually want the RMSF from the non-physical time-averaged structure is up to you. IIRC you might be able to get such an average from g_cluster. Mark -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- -- 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! End of gmx-users Digest, Vol 82, Issue 126 ** -- 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 system
Aldo Segura wrote: Dear gmx-users, I completed a MD (10 ns) of my protein-membrane system. When I perform a visual inspection (VMD) of md_0_1.gro file I observed a few water molecules within the bilayer. In previous steps (e.g. equilibration) this was not observed. Could be expected such behavior? Membrane protein systems take a long time (tens of ns or maybe more) to equilibrate, so some water may drift in and out during the initial few ns as voids in the lipids open and close. Nothing to worry about, unless for some reason they persist out past the expected equilibration time. -Justin Best regards, *//* */== = Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx mailto:asegu...@ipn.mx; aldoseg...@gmail.com mailto:aldoseg...@gmail.com == ===/* -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond and 4.5.2 version
Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2.GreetingsZuzanaOn 02/15/11, Zuzana Benkova zuzana.benk...@savba.sk wrote:Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund er...@xray.bmc.uu.se wrote:Justin A. Lemkul skrev 2011-02-09 23.03:Zuzana Benkova wrote:Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.I would appreciate any help. Thank you in advance.Try pulling the latest stable development version. This issue was reported in 4.5.1:http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.htmlbut not fixed until after 4.5.3 was released:http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html-JustinGreetingsZuzanaAre people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se http://folding.bmc.uu.se/-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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] Re: angle constrain, constrained PF6 anion
Hello, I got your files. However, the error is completely another than you mention and it occurs directly at the first time-step of the simulation. Inner product between old and new vector = 0.0! constraint #1 atoms 1377 and 1381 Wrote pdb files with previous and current coordinates step 0Inner product between old and new vector = 0.0! constraint #1 atoms 2177 and 2181 Wrote pdb files with previous and current coordinates Inner product between old and new vector = 0.0! constraint #1 atoms 2 and 6 Wrote pdb files with previous and current coordinates Segmentation fault There are a number of strange things in your configuration with the unhealthy defined constraints in topology as probably the most severe one. If you have constraints, why do you define bonds force constants at the same time? Good luck with your study, Vitaly On Wed, Feb 16, 2011 at 1:58 PM, gyorgy.han...@fc.up.pt wrote: Hi Vitaly, Thanks for your answer. I was busy with other stuff these last two weeks, that's why I have time to reply only now. So the system is the BMIM PF6 ionic liquid. We chose two potentials to describe the system, and both treat the anion as rigid. We cannot use LINCS because it shouldn't be used if one constrains not only bonds but angles too, so we have to use SHAKE. But with SHAKE I encountered some strange things as I wrote in my first thread. In the attachement I am sending you all the files needed for the simulation, maybe you'll find the problem. I havent mentioned but we try to constrain the angles by adding fictious bonds. Maybe there is something wrong with this... Thank you in advance for your help. All the best, Gyorgy Quoting Vitaly Chaban vvcha...@gmail.com: Hey Gyorgy, Your current topology file(s) is(are) also important to analyze the situation and fix the problem. Pass my kind regards to Julia... Dr. Vitaly V. Chaban, Ph.D. Department of Chemistry University of Rochester Rochester, New York 14627-0216 The United States of America = The mdp file is attached. Best, Gyorgy Quoting Justin A. Lemkul jalem...@vt.edu: gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we decided to use SHAKE. However, SHAKE seems to work a bit strangely: I know SHAKE mustn't be used with domain decomposition, but even if I set the corresponding variable to NO in the mdp file, the simulation crashes on 8 procs and gives the following error message: Fatal error: 1 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group. If I try to run mdrun with -pd (to 'really' switch off domain decomposition), the simulation doesn't chrash but gives nonsense (the energy seems to increase constantly). I am not an expert user so maybe I do something wrong but, anyway, does anyone have an idea how to constrain this anion with Gromacs? I checked mailing list archive but couldn't find any answer corresponding to my question. Without seeing a complete .mdp file, it's not possible to fully diagnose this problem. The combination of SHAKE + particle decomposition should be stable, but there are a whole host of different things that can go wrong. -Justin Thanks in advance. Gyorgy -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- next part -- title = BMIM PF6 bulk simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS ;l_bfgs integrator = md;steep ; Start time and timestep in ps tinit = 0 dt = 0.0001 ! just to see if it starts nsteps = 25000 ; mode for center of mass motion removal comm-mode = linear ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal ; ENERGY MINIMIZATION OPTIONS ; Force
Re: [gmx-users] g_hbond and 4.5.2 version
Hi, That suggets it's related to the new merge-on-the-fly-code and not the pbc handling. And it's me, not Justin, who's fixing and probably creating the bugs. :-) Cheers, Erik Zuzana Benkova skrev 2011-02-16 19.58: Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2. Greetings Zuzana On 02/15/11, *Zuzana Benkova * zuzana.benk...@savba.sk wrote: Hello Justin, I was using cubic boxes. Greetings Zuzana On 02/15/11, *Erik Marklund * er...@xray.bmc.uu.se wrote: Justin A. Lemkul skrev 2011-02-09 23.03: Zuzana Benkova wrote: Dear GROMACS users, I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance. Try pulling the latest stable development version. This issue was reported in 4.5.1: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html but not fixed until after 4.5.3 was released: http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html -Justin Greetings Zuzana Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mpirun error?
Dear Gromacs, My colleague has attempted to issue this command: mpirun -np 8 (or 7) mdrun_mpi .. (etc) According to him, he gets the following error message: MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec.c, line: 5888 Fatal error: There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 0.955625 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings However, when he uses say, -np 6, he seems to get no error. Any insight on why this might be happening? Also, when he saves the output to a file, sometimes he sees the following: NOTE: Turning on dynamic load balancing Is this another flag that might be causing the crash? What does that line mean? Thanks! 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] mpirun error?
Justin Kat wrote: Dear Gromacs, My colleague has attempted to issue this command: mpirun -np 8 (or 7) mdrun_mpi .. (etc) According to him, he gets the following error message: MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec.c, line: 5888 Fatal error: There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 0.955625 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings However, when he uses say, -np 6, he seems to get no error. Any insight on why this might be happening? When any error comes up, the first port of call should be the Gromacs site, followed by a mailing list search. In this case, the website works quite nicely: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm Also, when he saves the output to a file, sometimes he sees the following: NOTE: Turning on dynamic load balancing Is this another flag that might be causing the crash? What does that line mean? See the manual and/or Gromacs 4 paper for an explanation of dynamic load balancing. This is a normal message. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Protein-membrane system
Dear Aldo, It is totally OK to see water molecules within the bilayer, both in simulations and real life. If I am not totally wrong, 3000 water molecule per lipids per second are being transferred across the bilayer without any protein involvement. If your system is stable, the lipids density profile seems OK as well as its the thickness, you are fine. Cheers, Itamar. On 17/02/11 5:48 AM, Justin A. Lemkul wrote: Aldo Segura wrote: Dear gmx-users, I completed a MD (10 ns) of my protein-membrane system. When I perform a visual inspection (VMD) of md_0_1.gro file I observed a few water molecules within the bilayer. In previous steps (e.g. equilibration) this was not observed. Could be expected such behavior? Membrane protein systems take a long time (tens of ns or maybe more) to equilibrate, so some water may drift in and out during the initial few ns as voids in the lipids open and close. Nothing to worry about, unless for some reason they persist out past the expected equilibration time. -Justin Best regards, *//* */== = Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx mailto:asegu...@ipn.mx; aldoseg...@gmail.com mailto:aldoseg...@gmail.com == ===/* -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] zero atoms for FE P
Hello, I tried to follow the FE tutorials and get my own system working but it seems I am missing something coz I get a blank dgdl file. log file is saying: There are 0 atoms and 0 charges for free energy perturbation Removing pbc first time What I do is running EM (lambda 0) on a solvated system which is already equilibrated (and density is obtained by NPT) followed by a MD NVT since density has to be fixed. My guess is I am making mistake in combining itp file of hexane into polymer (solute). EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md PE60-0c-itp.top is: == ; Include forcefield parameters #include ffoplsaa.itp #include Hexane-0c.itp [ moleculetype ] ; Namenrexcl Polymer 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_135 1 EthB C1 1 0 12.011 ; qtot 0 2 opls_140 1 EthBH11 1 0 1.008 ; qtot 0 3 opls_140 1 EthBH12 1 0 1.008 ; qtot 0 4 opls_140 1 EthBH13 1 0 1.008 ; qtot 0 5 opls_136 1 EthB C2 2 0 12.011 ; qtot 0 . . ; Include generic topology for ions #include ions.itp [ system ] ; Name Polymer [ molecules ] ; Compound#mols Polymer 4 Hexane 480 === Please help me what wrong is... Thanks moeed -- 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] zero atoms for FE P
Moeed wrote: Hello, I tried to follow the FE tutorials and get my own system working but it seems I am missing something coz I get a blank dgdl file. log file is saying: There are 0 atoms and 0 charges for free energy perturbation Removing pbc first time What I do is running EM (lambda 0) on a solvated system which is already equilibrated (and density is obtained by NPT) followed by a MD NVT since density has to be fixed. My guess is I am making mistake in combining itp file of hexane into polymer (solute). EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md PE60-0c-itp.top is: == ; Include forcefield parameters #include ffoplsaa.itp #include Hexane-0c.itp [ moleculetype ] ; Namenrexcl Polymer 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_135 1 EthB C1 1 0 12.011 ; qtot 0 2 opls_140 1 EthBH11 1 0 1.008 ; qtot 0 3 opls_140 1 EthBH12 1 0 1.008 ; qtot 0 4 opls_140 1 EthBH13 1 0 1.008 ; qtot 0 5 opls_136 1 EthB C2 2 0 12.011 ; qtot 0 . . ; Include generic topology for ions #include ions.itp [ system ] ; Name Polymer [ molecules ] ; Compound#mols Polymer 4 Hexane 480 === Please help me what wrong is... Probably the most important piece of information is your .mdp file, but you didn't post it, so please do. -Justin Thanks moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Protein-membrane system
Hi, 3000 water molecule per lipids per second corresponds to 0.000384 water molecules transferred across the membrane per nano second (assume the system contains 128 lipids). It seems water translocation should not be observed in a simulation of 10 ns, but I am not sure. And I only find one reference paper(Biophysical Journal, Volume 96, 2009, pg4493–4501) about the water translocation across the membrane, in which a asymmetric membrane is used. I also have similar observations for my protein-membrane system. I observed 10~15 times water translocation arosss the membrane during 100 ns simulation when my protein adsorbed on the membrane. I am wondering these water translocation is normal in all-atom simulations or they are due to the protein-induced membrane deformation? Any comment is highly appreciated, thank you! best regards, Jianguo From: Itamar Kass itamar.k...@monash.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 17 February 2011 07:20:19 Subject: Re: [gmx-users] Protein-membrane system Dear Aldo, It is totally OK to see water molecules within the bilayer, both in simulations and real life. If I am not totally wrong, 3000 water molecule per lipids per second are being transferred across the bilayer without any protein involvement. If your system is stable, the lipids density profile seems OK as well as its the thickness, you are fine. Cheers, Itamar. On 17/02/11 5:48 AM, Justin A. Lemkul wrote: Aldo Segura wrote: Dear gmx-users, I completed a MD (10 ns) of my protein-membrane system. When I perform a visual inspection (VMD) of md_0_1.gro file I observed a few water molecules within the bilayer. In previous steps (e.g. equilibration) this was not observed. Could be expected such behavior? Membrane protein systems take a long time (tens of ns or maybe more) to equilibrate, so some water may drift in and out during the initial few ns as voids in the lipids open and close. Nothing to worry about, unless for some reason they persist out past the expected equilibration time. -Justin Best regards, *//* */== = Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx mailto:asegu...@ipn.mx; aldoseg...@gmail.com mailto:aldoseg...@gmail.com == ===/* -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] RE: simulation of a metal binding sites
Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
