[gmx-users] Re: grompp for minimization: note warning
Dear Mark The UNIX tool diff is your friend for comparing files. Thanks for your suggestion. I used diff and sdiff toll for comparing 2 files (before and after correction). diff old.gro new.gro These tolls did not give me any output file or text containing difference between 2 files. In this condition, how should I find difference between 2 gro files? Best wishes for you -- 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: grompp for minimization: note warning
If diff says there are no changes, then you're not comparing with the file you changed... On Sep 25, 2013 1:59 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear Mark The UNIX tool diff is your friend for comparing files. Thanks for your suggestion. I used diff and sdiff toll for comparing 2 files (before and after correction). diff old.gro new.gro These tolls did not give me any output file or text containing difference between 2 files. In this condition, how should I find difference between 2 gro files? Best wishes for you -- 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: grompp for minimization: note warning
Dear Tsjerk Thanks for your reply Before correcting the gro file, I knew that gro file is fixed format. I did this correction very carefully. Part of the gro file before and after correction is as follows: - before: - 14DOPCN4 755 0.260 1.726 6.354 14DOPCC5 756 0.263 1.741 6.204 14DOPCC1 757 0.136 1.777 6.423 14DOPCC2 758 0.279 1.580 6.384 14DOPCC3 759 0.383 1.799 6.403 14DOPCC6 760 0.386 1.685 6.132 14DOPCP8 761 0.628 1.683 6.064 14DOPC OM9 762 0.640 1.548 6.123 14DOPC OM10 763 0.747 1.771 6.072 14DOPC OS7 764 0.511 1.755 6.145 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C34 772 0.490 2.037 5.777 14DOPC OS35 773 0.541 2.029 5.644 14DOPC C36 774 0.591 2.142 5.593 14DOPC O37 775 0.595 2.252 5.646 14DOPC C38 776 0.674 2.092 5.476 14DOPC C18 777 -0.004 1.897 5.786 14DOPC C19 778 -0.138 1.837 5.744 14DOPC C20 779 -0.147 1.817 5.593 14DOPC C21 780 -0.196 1.678 5.552 14DOPC C22 781 -0.181 1.637 5.406 14DOPC C23 782 -0.252 1.722 5.301 14DOPC C24 783 -0.241 1.664 5.163 14DOPC C25 784 -0.267 1.738 5.054 14DOPC C26 785 -0.312 1.881 5.044 14DOPC C27 786 -0.368 1.918 4.907 14DOPC C28 787 -0.266 1.941 4.795 14DOPC C29 788 -0.324 2.015 4.674 14DOPC C30 789 -0.377 1.920 4.567 14DOPC C31 790 -0.377 1.984 4.428 14DOPC C32 791 -0.439 1.894 4.321 14DOPC C33 792 -0.358 1.890 4.191 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038 14DOPC C49 803 1.266 1.407 4.902 14DOPC C50 804 1.338 1.469 4.782 14DOPC C51 805 1.307 1.406 4.646 14DOPC C52 806 1.160 1.394 4.607 14DOPC C53 807 1.119 1.442 4.468 14DOPC C54 808 0.980 1.407 4.414 - after: - 14DOPCC1 755 0.136 1.777 6.423 14DOPCC2 756 0.279 1.580 6.384 14DOPCC3 757 0.383 1.799 6.403 14DOPCN4 758 0.260 1.726 6.354 14DOPCC5 759 0.263 1.741 6.204 14DOPCC6 760 0.386 1.685 6.132 14DOPC OS7 761 0.511 1.755 6.145 14DOPCP8 762 0.628 1.683 6.064 14DOPC OM9 763 0.640 1.548 6.123 14DOPC OM10 764 0.747 1.771 6.072 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C18 772 -0.004 1.897 5.786 14DOPC C19 773 -0.138 1.837 5.744 14DOPC C20 774 -0.147 1.817 5.593 14DOPC C21 775 -0.196 1.678 5.552 14DOPC C22 776 -0.181 1.637 5.406 14DOPC C23 777 -0.252 1.722 5.301 14DOPC C24 778 -0.241 1.664 5.163 14DOPC C25 779 -0.267 1.738 5.054 14DOPC C26 780 -0.312 1.881 5.044 14DOPC C27 781 -0.368 1.918 4.907 14DOPC C28 782 -0.266 1.941 4.795 14DOPC C29 783 -0.324 2.015 4.674 14DOPC C30 784 -0.377 1.920 4.567 14DOPC C31 785 -0.377 1.984 4.428 14DOPC C32 786 -0.439 1.894 4.321 14DOPC C33 787 -0.358 1.890 4.191 14DOPC C34 788 0.490 2.037 5.777 14DOPC OS35 789 0.541 2.029 5.644 14DOPC C36 790 0.591 2.142 5.593 14DOPC O37 791 0.595 2.252 5.646 14DOPC C38 792 0.674 2.092 5.476 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038
Re: [gmx-users] Re: grompp for minimization: note warning
The UNIX tool diff is your friend for comparing files. On Fri, Sep 20, 2013 at 1:53 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear Tsjerk Thanks for your reply Before correcting the gro file, I knew that gro file is fixed format. I did this correction very carefully. Part of the gro file before and after correction is as follows: - before: - 14DOPCN4 755 0.260 1.726 6.354 14DOPCC5 756 0.263 1.741 6.204 14DOPCC1 757 0.136 1.777 6.423 14DOPCC2 758 0.279 1.580 6.384 14DOPCC3 759 0.383 1.799 6.403 14DOPCC6 760 0.386 1.685 6.132 14DOPCP8 761 0.628 1.683 6.064 14DOPC OM9 762 0.640 1.548 6.123 14DOPC OM10 763 0.747 1.771 6.072 14DOPC OS7 764 0.511 1.755 6.145 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C34 772 0.490 2.037 5.777 14DOPC OS35 773 0.541 2.029 5.644 14DOPC C36 774 0.591 2.142 5.593 14DOPC O37 775 0.595 2.252 5.646 14DOPC C38 776 0.674 2.092 5.476 14DOPC C18 777 -0.004 1.897 5.786 14DOPC C19 778 -0.138 1.837 5.744 14DOPC C20 779 -0.147 1.817 5.593 14DOPC C21 780 -0.196 1.678 5.552 14DOPC C22 781 -0.181 1.637 5.406 14DOPC C23 782 -0.252 1.722 5.301 14DOPC C24 783 -0.241 1.664 5.163 14DOPC C25 784 -0.267 1.738 5.054 14DOPC C26 785 -0.312 1.881 5.044 14DOPC C27 786 -0.368 1.918 4.907 14DOPC C28 787 -0.266 1.941 4.795 14DOPC C29 788 -0.324 2.015 4.674 14DOPC C30 789 -0.377 1.920 4.567 14DOPC C31 790 -0.377 1.984 4.428 14DOPC C32 791 -0.439 1.894 4.321 14DOPC C33 792 -0.358 1.890 4.191 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038 14DOPC C49 803 1.266 1.407 4.902 14DOPC C50 804 1.338 1.469 4.782 14DOPC C51 805 1.307 1.406 4.646 14DOPC C52 806 1.160 1.394 4.607 14DOPC C53 807 1.119 1.442 4.468 14DOPC C54 808 0.980 1.407 4.414 - after: - 14DOPCC1 755 0.136 1.777 6.423 14DOPCC2 756 0.279 1.580 6.384 14DOPCC3 757 0.383 1.799 6.403 14DOPCN4 758 0.260 1.726 6.354 14DOPCC5 759 0.263 1.741 6.204 14DOPCC6 760 0.386 1.685 6.132 14DOPC OS7 761 0.511 1.755 6.145 14DOPCP8 762 0.628 1.683 6.064 14DOPC OM9 763 0.640 1.548 6.123 14DOPC OM10 764 0.747 1.771 6.072 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C18 772 -0.004 1.897 5.786 14DOPC C19 773 -0.138 1.837 5.744 14DOPC C20 774 -0.147 1.817 5.593 14DOPC C21 775 -0.196 1.678 5.552 14DOPC C22 776 -0.181 1.637 5.406 14DOPC C23 777 -0.252 1.722 5.301 14DOPC C24 778 -0.241 1.664 5.163 14DOPC C25 779 -0.267 1.738 5.054 14DOPC C26 780 -0.312 1.881 5.044 14DOPC C27 781 -0.368 1.918 4.907 14DOPC C28 782 -0.266 1.941 4.795 14DOPC C29 783 -0.324 2.015 4.674 14DOPC C30 784 -0.377 1.920 4.567 14DOPC C31 785 -0.377 1.984 4.428 14DOPC C32 786 -0.439 1.894 4.321 14DOPC C33 787 -0.358 1.890 4.191 14DOPC C34 788 0.490 2.037 5.777 14DOPC OS35 789 0.541 2.029 5.644 14DOPC C36 790 0.591 2.142 5.593 14DOPC O37 791 0.595 2.252 5.646 14DOPC C38 792 0.674 2.092 5.476 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797
Re: [gmx-users] Re: grompp for minimization: note warning
Hi Shahab, You edited the .gro file, but you made an error. So you have to read the manual to understand the file format and then see where and how your edited file doesn't match. Cheers, Tsjerk On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Tsjerk Thanks for your consideration. I ignored Warning 1. WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Based on your suggestion, I checked non-matching atom names between topol.top and system.gro files. I corrected system.gro file accordance with topol.top file. I did this work very carefully. I was watchful to not disturb the format of the system.gro file, so that when I saw system gro file (before and after the correction) by an editor program, both of them were same. But, when I use grompp, I encountered with: Fatal error: Something is wrong in the coordinate formatting of file sys.gro. Note that gro is fixed format (see the manual). How to solve this problem? Any help will highly appreciated. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Tsjerk Thanks for your consideration. I ignored Warning 1. WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Based on your suggestion, I checked non-matching atom names between topol.top and system.gro files. I corrected system.gro file accordance with topol.top file. I did this work very carefully. I was watchful to not disturb the format of the system.gro file, so that when I saw system gro file (before and after the correction) by an editor program, both of them were same. But, when I use grompp, I encountered with: Fatal error: Something is wrong in the coordinate formatting of file sys.gro. Note that gro is fixed format (see the manual). How to solve this problem? Any help will highly appreciated. Best wishes for you. -- 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: grompp for minimization: note warning
Hi Shahab, What did you do exactly? Can you state your complete protocol (1. fetched this structure file there, 2. got the topology from there, 3. did something, 4. ran grompp like this, etc)? Use brief, clear explanations and the command lines as you issued them. Cheers, Tsjerk On Tue, Sep 17, 2013 at 2:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 8:47 AM, shahab shariati wrote: Dear Justin Very very thanks for your quick reply. I am very confused and amazed. After visualization of atom 618 ( where the maximum force is), what should I do to resolve me problem. Any help will highly appreciated. I honestly have no idea. There's something nasty going on there, but only you have the ability to see it. You can always try a smaller value of emstep, a different EM algorithm, etc. Try setting nstxout = 1 and visualize the entire EM trajectory to see where things start to go out of control. And finally, if it really isn't working, ask the people who provided the coordinates - they're supposed to be pre-equilibrated, so if you can't get it to minimize, maybe there's something wrong that's happened before you even got your hands on the file. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Tsjerk Thanks for your consideration. My system contains 2 components: (DOPC cholesterol) lipids + water molecules. I get force field parameters from lipid book (for dopc and cholesterol). I used input coordinate file (system.gro) from following web site: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html em.mdp file is as follows: - ; em.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions - For doing minimization, I used following command: grompp -f em.mdp -c system.gro -p topol.top -o em.tpr and then I get following result: - WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Analysing residue names: Warning: file does not end with a newline, last line: IB+ Ion There are: 128 Other residues There are: 1706 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 29019.00 Largest charge group radii for Van der Waals: 1.541, 1.514 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (3.054313) is larger than rlist (1.20) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116 Estimate for the relative computational load of the PME mesh part: 0.62 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 133 Mb of data There was 1 note There were 2 warnings - I used -maxwarn option and I obtained em.tpr file. Then, for doing minimization, I used following command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log and then I get following result: - Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 881 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 - When I see created gro file (em.gro) by VMD, some dopc or cholesterol molecules are broken to 2 or 3 parts. I tested different ways: 1) change of parameters in em.mdp file ( emstep, nstep, EM algorithm ) 2) change of box size 3) I used the newest version of gromacs (4.6.3) But, unfortunatele, my problem was not solved. Certainly, I can not use this structure for next step (equilibration). How to solve this problem. Any help will highly appreciated. Best wishes for you -- 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.
Re: [gmx-users] Re: grompp for minimization: note warning
Hi Shahab, That site has a lot of structures. It would be better to explicitly state which one you took. However, in this case, the better question is, how did you write the topology, and did you check the correspondence of the order of molecules/atoms in the topology file and the structure file? I guess the answer to the latter is no... - WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Never ignore this warning, unless you understand why this is okay. Cheers, Tsjerk -- 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: grompp for minimization: note warning
Dear Justin I used newer version of gromacs (4.6.1), but my problem was not solved. Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: grompp for minimization: note warning
On 9/17/13 5:03 AM, shahab shariati wrote: Dear Justin I used newer version of gromacs (4.6.1), but my problem was not solved. You're still working with outdated software. Please follow my suggestion of trying 4.6.3. The larger issue, in the end, is the unphysical configuration of the drug in the membrane. Independent of Gromacs version, that setup will always fail. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Thanks for your reply You're still working with outdated software. Please follow my suggestion of trying 4.6.3. I try to install 4.6.3. The larger issue, in the end, is the unphysical configuration of the drug in the membrane. Independent of Gromacs version, that setup will always fail. I did minimization in 2 other states: 1) without drug (only membrane: DOPC nad cholesterol). 2) with drug but, this time, I put drug into water molecules not into membrane. Then I did mdrun for both of states. In both of state, there are not following issues: Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates -- There are following outputs: for state 1) - Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 881 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 for state 2) Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Back Off! I just backed up em.trr to ./#em.trr.1# Back Off! I just backed up em.edr to ./#em.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Steepest Descents converged to machine precision in 845 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.9664772e+05 Maximum force = 1.0986521e+04 on atom 241 Norm of force = 4.4174323e+02 --- When I see created gro file from minimization (em.gro), I see some dopc and cholesterol molecules were broken and they devided 2 or 3 parts. Input gro file (system.gro) has 1835 residues. Created gro file from minimization (em.gro) has 1835 residues. But when I load em.gro file in VMD, there are 1950 residues in graphical representation -- selections -- residues part. Can I deduce my problem has not dependent to presence of drug? Are there problem about my force field parameters or topology file ? I get force field parameters from lipid book (for dopc and cholesterol) and from prodrg server (for drug). Please help me to resolve this issue. Best wishes for you -- 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: grompp for minimization: note warning
On 9/17/13 7:02 AM, shahab shariati wrote: Dear Justin Thanks for your reply You're still working with outdated software. Please follow my suggestion of trying 4.6.3. I try to install 4.6.3. The larger issue, in the end, is the unphysical configuration of the drug in the membrane. Independent of Gromacs version, that setup will always fail. I did minimization in 2 other states: 1) without drug (only membrane: DOPC nad cholesterol). 2) with drug but, this time, I put drug into water molecules not into membrane. Then I did mdrun for both of states. In both of state, there are not following issues: Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates -- There are following outputs: for state 1) - Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 881 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 As I suggested before, visualize the output file and figure out what is around atom 618 to cause such forces. for state 2) Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Back Off! I just backed up em.trr to ./#em.trr.1# Back Off! I just backed up em.edr to ./#em.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Steepest Descents converged to machine precision in 845 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.9664772e+05 Maximum force = 1.0986521e+04 on atom 241 Norm of force = 4.4174323e+02 --- Same advice as above. When I see created gro file from minimization (em.gro), I see some dopc and cholesterol molecules were broken and they devided 2 or 3 parts. Input gro file (system.gro) has 1835 residues. Created gro file from minimization (em.gro) has 1835 residues. But when I load em.gro file in VMD, there are 1950 residues in graphical representation -- selections -- residues part. What VMD thinks is a fragment, molecule, or residue is basically irrelevant. It's guessing based on guessing connectivity. Your topology is definitive; VMD is not. Can I deduce my problem has not dependent to presence of drug? There seem to be problems in both cases. Solve the issue with the membrane first. Are there problem about my force field parameters or topology file ? I get force field parameters from lipid book (for dopc and cholesterol) and from prodrg server (for drug). PRODRG generates notoriously bad parameters, particularly the charges. See http://pubs.acs.org/doi/abs/10.1021/ci100335w. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post?
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Thanks for your time and consideration. As I suggested before, visualize the output file and figure out what is around atom 618 to cause such forces. I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc molecule (this dopc molecule is intact and is not broken). There are other dopc and cholesterol molecules around atom 618. How I understand what around this atom cause such forces. Excuse me. Please give me more explanation about your suggestion. May be, I did not understand your mean truly. Should I remove this dopc molecule and then run minimization again? PRODRG generates notoriously bad parameters, particularly the charges. I know this issue, charges and charges groups obtained from prodrg (in itp file) were compared with charges and charges groups in similar structures being in rtp file of gromos (because my drug is very similar to cytosine). Then I corrected them. -- 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: grompp for minimization: note warning
On 9/17/13 8:17 AM, shahab shariati wrote: Dear Justin Thanks for your time and consideration. As I suggested before, visualize the output file and figure out what is around atom 618 to cause such forces. I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc molecule (this dopc molecule is intact and is not broken). There are other dopc and cholesterol molecules around atom 618. How I understand what around this atom cause such forces. Excuse me. Please give me more explanation about your suggestion. Usually when large forces arise, the cause is fairly obvious. There will be some atom very close to the one on which the maximum force acts. It may not always be obvious. May be, I did not understand your mean truly. Should I remove this dopc molecule and then run minimization again? No. PRODRG generates notoriously bad parameters, particularly the charges. I know this issue, charges and charges groups obtained from prodrg (in itp file) were compared with charges and charges groups in similar structures being in rtp file of gromos (because my drug is very similar to cytosine). Then I corrected them. OK, that's a reasonable starting point. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. I am very confused and amazed. After visualization of atom 618 ( where the maximum force is), what should I do to resolve me problem. Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
On 9/16/13 9:47 AM, shahab shariati wrote: Dear Justin My input coordinate file is a gro file (sys.gro). When I visualize that by VMD, all things is ok and true. After minimization, I obtained a gro file (em.gro). When I visualize that by VMD, About 5 DOPC molecules leave bilayer structure and 1 DOPC molecule not only leaves bilayer structure, but also some bonds were broken (there is a broken molecule). Before, I mentioned that my input coordinate file (em.gro) is obtained from reliable website. How to resolve this issue? I attached 2 gro file (sys.gro and em.gro). Resolvation of this issue is very critical and important for me. Please guide me about that. Excuse me for sending this e-mail to personal address. I have to send 2 gro files to you. The proper protocol is to upload the files somewhere publicly accessible and post a download link. I generally do not like large, unrequested attachments. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. As for the charge group error from grompp, I still can see no reason for it. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. Please guide me to resolve these issues. Best wishes -- 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: grompp for minimization: note warning
On 9/16/13 10:52 AM, shahab shariati wrote: Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? I have no idea. I don't know how the box was set or why it was set in that way. It's certainly wrong, but it may not solve the underlying issue. Visualize the area around the drug - there is severe atomic overlap between the lipids and the drug molecule. Clearly it was not built in a manner that will be stable. As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. As I said, I don't know. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. Please guide me to resolve these issues. Best wishes -- 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
