[gmx-users] gmx trjconv -force option doesn't seem to work.
Hello! I have a question about gmx trjconv -force option because it seems to work at all. I'm using GROMACS-5.1.5 version and I want to extract forces using gmx trjconv command. So I tried. gmx trjconv -f alad.trr -s alad.tpr -n alad.ndx -novel -force yes -pbc mol -o test.gro However, the force was not obtained in test.gro. How do I get the force corresponding to specific coordinates. Thanks. Yeonju Go -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] cudaFuncGetAttributes failed: out of memory
Hello, I have encountered a weird problem. I've been using GROMACS with GPU on a server and always performance good. However when I just reran a job today and suddenly got this error: Command line: gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3 Back Off! I just backed up pull.log to ./#pull.log.1# --- Program: gmx mdrun, version 2019.4 Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) Fatal error: cudaFuncGetAttributes failed: out of memory For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It seems the GPU is 0 occupied and I can run other apps with GPU, but I cannot run GROMACS mdrun anymore, even if doing energy minimization. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to deal with unexpected reactions in umbrella sampling?
Dear Colleagues, I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However, as the reaction coordinate exceeds a certain value, an unexpected reaction, which is obviously unreasonable, often occurs during the umbrella sampling. So, how to deal with such problem? The only method I can think is to impose additional restraints to avoid this reaction, but the additional restraints will probably affect the umbrella sampling (although the additional restraints are not related to the reaction coordinate). Thanks, Qing -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to cap a single residue in gromacs
Hi, Without saying about the physical meaning of your model because I don't know what you are doing. About technical point, I used your PHE coordinate and using pymol to cap with ACE, NME as you said then execute pdb2gmx using amber99sb forcefield in gromacs, it works well. What is the error that you say? On Wed, Feb 19, 2020, 09:25 Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > Hi > > On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani wrote: > > > Dear Gromacs users > > I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand > > when I run pdb2gmx it gives me error:- > > Fatal error: > > In the chosen force field there is no residue type for 'PHE' as a > > standalone > > (starting & ending) residue > > > > I added ACE and NME terminals as below in the gro file:- > > > > 1ACE HC1 0.000 0.000 0.000 0. 0. 0. > > 1ACE CT2 0.000 0.000 0.000 0. 0. 0. > > 1ACE HC3 0.000 0.000 0.000 0. 0. 0. > > 1ACE HC4 0.000 0.000 0.000 0. 0. 0. > > 1ACE C5 0.000 0.000 0.000 0. 0. 0. > > 1ACE O6 0.000 0.000 0.000 0. 0. 0. > > 2PHE N7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 > > 2PHE H8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 > > 2PHE CA9 5.013 4.811 6.023 0.0535 0.3709 0.0960 > > 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 > > 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 > > 2PHEHB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 > > 2PHEHB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 > > 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 > > 2PHECD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 > > 2PHEHD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 > > 2PHECE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 > > 2PHEHE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 > > 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 > > 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 > > 2PHECE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 > > 2PHEHE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 > > 2PHECD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 > > 2PHEHD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 > > 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 > > 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 > > 3NME N 27 0.000 0.000 0.000 0. 0. 0. > > 3NME H 28 0.000 0.000 0.000 0. 0. 0. > > 3NME CT 29 0.000 0.000 0.000 0. 0. 0. > > 3NME H1 30 0.000 0.000 0.000 0. 0. 0. > > 3NME H1 31 0.000 0.000 0.000 0. 0. 0. > > 3NME H1 32 0.000 0.000 0.000 0. 0. 0. > > 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 > > 4G6PO1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 > > 4G6PO2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 > > 4G6PO3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 > > 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 > > 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 > > 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 > > 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 > > 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 > > 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 > > 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 > > 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 > > 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 > > 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 > > 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 > > 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 > > 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 > > 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 > > 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 > > 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 > > 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 > > 4G6PH61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 > > 4G6PH62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 > > 4G6PHO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 > > 4G6PHO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 > > 4G6PHO3 58 4.671 5.
Re: [gmx-users] GPU considerations for GROMACS
We recommend Intel Xeon if possible. You can see how we set up our GROMACS optimized workstations at https://www.exxactcorp.com/GROMACS-Certified-GPU-Systems If Xeon is not an option, at the very least use a high-end i7 or i9 9th/10th gen. With Memory the system should typically have 64GB to start, up to 128GB. For the GPU we typically start with RTX 2080 and go up from there. Can you explain a little more about your environment? What SSD? What dataset? What type of job are you running, etc? Thanks, Jason Hogrefe Exxact Corporation https://www.exxactcorp.com -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of hairul.ik...@gmail.com Sent: Tuesday, February 18, 2020 6:21 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] GPU considerations for GROMACS [EXTERNAL] Hello, Previously, I have helped building a workstation for my fellow researcher who heavily uses GROMACS for his MD simulations, with the following base specs: -CPU: 8 cores (Xeon E2278G) -RAM: 32GB -GPU: 1x RTX2080Ti With this setup, he managed to shrink down each simulation runtime to, say approximately 12 hours, compared to previous system (purely CPU only, no GPU support), which took days to complete. 1) Based on the current progress, we plan to build another system (which will also run GROMACS most of the time) using the existing workstation as reference. But currently we are unsure which setup (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, when running the same set of GROMACS simulation : Option 1: Retain same CPU, RAM and GPU specs (1x RTX2080Ti) Option 2: Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead of 1x RTX2080Ti 2) Besides building another system, we are considering to upgrade the existing system, too. For example, assuming the system has the expansion capability (enough PCI-e 16x slots, power supply), will adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) into existing setup will significantly cut down current runtime? If yes, by how much time reduction can we expect generally with this upgrade? Appreciate if someone can share their thoughts and experience. Thank you! -Hairul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU considerations for GROMACS
Hi, A CPU:GPU ratio of 4:1 is fairly well balanced these days (depending on the quality of the hardware), so you should expect to roughly double your throughput adding a second GPU to your current system. However, that doesn't mean your single simulation performance will double - it's a lot more efficient to run multiple simulations in parallel with these setups, because multiple GPUs don't scale perfectly. We can't make absolute statements about the performance you should expect, it depends a lot on workload among other things. Have you seen the "More bang for your buck" paper?. https://arxiv.org/abs/1903.05918 Kevin On Tue, Feb 18, 2020 at 6:21 AM hairul.ik...@gmail.com < hairul.ik...@gmail.com> wrote: > Hello, > > Previously, I have helped building a workstation for my fellow > researcher who heavily uses GROMACS for his MD simulations, with the > following base specs: > > -CPU: 8 cores (Xeon E2278G) > -RAM: 32GB > -GPU: 1x RTX2080Ti > > > With this setup, he managed to shrink down each simulation runtime to, > say approximately 12 hours, compared to previous system (purely CPU > only, no GPU support), which took days to complete. > > > 1) Based on the current progress, we plan to build another system > (which will also run GROMACS most of the time) using the existing > workstation as reference. But currently we are unsure which setup > (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, > when running the same set of GROMACS simulation : > > > Option 1: > Retain same CPU, RAM and GPU specs (1x RTX2080Ti) > > > Option 2: > Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead > of 1x RTX2080Ti > > > 2) Besides building another system, we are considering to upgrade the > existing system, too. For example, assuming the system has the > expansion capability (enough PCI-e 16x slots, power supply), will > adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) > into existing setup will significantly cut down current runtime? If > yes, by how much time reduction can we expect generally with this > upgrade? > > > Appreciate if someone can share their thoughts and experience. > Thank you! > > > -Hairul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Converting Charmm to gmx format using cgenff
Dear gmx users, I am trying to generate topology for small ligands using cgenff . I will like to confirm if the Charmm to gmx script available on the Mackerell website is compatible with all versions of charmm forcefield or can only be used with Charm36 forcefield. P.S. I have tried it with charm22* and did not get any error, I will just like to double check. Looking forward to your reply. Best regards, Maryam Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Selective RMSD calculation
Hi, You can calculate the rmsd by passing the index file of the ligand... gmx rms -h On Wed 19 Feb, 2020, 7:41 PM Peter Mawanga, wrote: > Hello everyone > > After fitting the protein-ligand system to the starting conformation, I > would like to extract the RMSD information for the ligand only but cannot > find such an option for a selective output. > > Please let me know if this can be achieved with the gmx tool, I couldn't > find such an option with both the "rms" and "rmsd" commands. > > -- > Thanks > Peter > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Selective RMSD calculation
Hello everyone After fitting the protein-ligand system to the starting conformation, I would like to extract the RMSD information for the ligand only but cannot find such an option for a selective output. Please let me know if this can be achieved with the gmx tool, I couldn't find such an option with both the "rms" and "rmsd" commands. -- Thanks Peter -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa)
Thank you, Alessandra, for your reply. I have tried TER in the PDB file but it doesn't work. It requires an N and C terminal for amino acid residue. I have prepared residue in avogadros and used these coordinates. ATOM 1 N PHE A 1 0.000 0.000 0.000 1.00 0.00 N1+ ATOM 2 CA PHE A 1 1.462 0.000 0.000 1.00 0.00 C ATOM 3 C PHE A 1 1.902 0.000 1.473 1.00 0.00 C ATOM 4 O PHE A 1 1.105 0.000 2.411 1.00 0.00 O ATOM 5 CB PHE A 1 2.020 1.225 -0.743 1.00 0.00 C ATOM 6 CG PHE A 1 3.442 1.037 -1.219 1.00 0.00 C ATOM 7 CD2 PHE A 1 4.512 1.642 -0.547 1.00 0.00 C ATOM 8 CE2 PHE A 1 5.823 1.440 -0.982 1.00 0.00 C ATOM 9 CZ PHE A 1 6.074 0.642 -2.097 1.00 0.00 C ATOM 10 CE1 PHE A 1 5.015 0.044 -2.777 1.00 0.00 C ATOM 11 CD1 PHE A 1 3.705 0.238 -2.340 1.00 0.00 C ATOM 12 H PHE A 1 -0.467 0.280 0.859 1.00 0.00 H ATOM 13 HA PHE A 1 1.790 -0.939 -0.463 1.00 0.00 H ATOM 14 HB1 PHE A 1 1.956 2.118 -0.106 1.00 0.00 H ATOM 15 HB2 PHE A 1 1.405 1.454 -1.623 1.00 0.00 H ATOM 16 HD2 PHE A 1 4.334 2.273 0.322 1.00 0.00 H ATOM 17 HE2 PHE A 1 6.649 1.912 -0.456 1.00 0.00 H ATOM 18 HZ PHE A 1 7.094 0.492 -2.441 1.00 0.00 H ATOM 19 HE1 PHE A 1 5.208 -0.570 -3.654 1.00 0.00 H ATOM 20 HD1 PHE A 1 2.885 -0.231 -2.885 1.00 0.00 H ATOM 21 HN PHE A 1 -0.339 0.853 -0.435 1.00 0.00 H ATOM 22 2HN PHE A 1 -0.339 -0.853 -0.435 1.00 0.00 H ATOM 23 OXT PHE A 1 3.231 -0.000 1.717 1.00 0.00 O1- However, it claims that in the chosen force field there is no residue type for 'PHE' as a standalone (starting & ending) residue I am using AMBER99SB-ILDN force field for protein. I have looked into the force field both CPHE and NPHE are different as below:- [ CPHE ] [ atoms ] NN -0.38210 1 HH0.26810 2 CACT -0.18250 3 HAH1 0.10980 4 CBCT -0.09590 5 HB1HC 0.04430 6 HB2HC 0.04430 7 CGCA 0.05520 8 CD1CA -0.13000 9 HD1HA 0.1408010 CE1CA -0.1847011 HE1HA 0.1461012 CZCA -0.0944013 HZHA 0.1280014 CE2CA -0.1847015 HE2HA 0.1461016 CD2CA -0.1300017 HD2HA 0.1408018 CC0.7660019 OC1O2 -0.8026020 OC2O2 -0.8026021 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZHZ CZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 C OC1 C OC2 -C N [ impropers ] -CCA N H CA OC1 C OC2 CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CE1 CE2CZHZ CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB [ NPHE ] [ atoms ] NN3 0.17370 1 H1H0.19210 2 H2H0.19210 3 H3H0.19210 4 CACT 0.07330 5 HAHP 0.10410 6 CBCT 0.03300 7 HB1HC 0.01040 8 HB2HC 0.01040 9 CGCA 0.0031010 CD1CA -0.1392011 HD1HA 0.1374012 CE1CA -0.1602013 HE1HA 0.1433014 CZCA -0.1208015 HZHA 0.1329016 CE2CA -0.1603017 HE2HA 0.1433018 CD2CA -0.1391019 HD2HA 0.1374020 CC0.6123021 OO -0.5713022 [ bonds ] NH1 NH2 NH3 NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZHZ CZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 C O C+N [ impropers ] CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CE1 CE2CZHZ CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB How should I build it. Thanks. Sadaf -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lis
Re: [gmx-users] Increase Graphene sheet size
Hi Alessandra, Many thanks again for your help :) That sounds great. I can simulate a box with the desired dimensions. I repeated the graphene sheet using genconf into dimensions greater the desired dimensions and then I created a box with the desired dimensions and I solvate it to visualize it. now I have an additional part of the graphene sheet which is out of the box, How can I remove it. I want my simulation and visualization to be with a specific dimensions which is the dimensions of the box. I would appreciate if you can further clarify how can I do that. Thanks, Mohamed On Wed, Feb 19, 2020 at 10:10 Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > HI, > > > > On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal > wrote: > > > Many thanks Alessandra for your reply :) > > > > gmx solvate will add water around my graphene sheet but will not increase > > the graphene sheet itself. Please correct me if I am wrong. > > > > > Yes/No, gmx solvate is normally used to add water or to build solvent box > but my suggestion was to use gmx solvate tools for your aim. > What I suggested was to use the tool to fill an empty box (of desidered > dimension) with copies of your graphene pre-equilibrated (small) sheet. > > Best regards > Alessandra > > > > I already simulated the graphene sheet but I need to increase its > dimension > > to a certain dimensions. > > > > any Ideas how to do that :) ? > > > > Thanks, > > Mohamed > > > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > > alessandra.villa.bio...@gmail.com> wrote: > > > > > Hi > > > > > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal < > > m.b.abdel...@gmail.com> > > > wrote: > > > > > > > Hello All, > > > > > > > > I want to create a graphene sheet with a specific dimensions > > > (10*15*0.284) > > > > nm. > > > > > > > > I created a .gro file as below ( as mentioned in this website > > > > > > > > > > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > > > ) > > > > > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > > > 4 > > > > 1GRM C1 1 0.061 0.071 0.000 > > > > 1GRM C2 2 0.184 0.142 0.000 > > > > 1GRM C3 3 0.184 0.284 0.000 > > > > 1GRM C4 4 0.061 0.355 0.000 > > > > 0.2459510.4260000.284000 > > > > > > > > Now I don't know how to use genconf to repeat it until it gives me > the > > > > required dimensions. As using genconf -nbox will repeat the above > into > > a > > > > specific number of boxes but I can't get a sheet with accurate > > dimensions > > > > of (10*15*0.284 nm). > > > > > > > > I tried to generate a sheet using gencong and then use editconf to > > change > > > > the dimensions to the required ones, but the problem is that using > > > editconf > > > > will put the graphene sheet in an empty box but will not change the > > > > dimension as I want. > > > > > > > > Another option is to divide the 10 (the required dimension) nm by > > > 0.245951 > > > > (the dimension in the above .gro file) and to use the genconf with > the > > > > result but it will be a lot of decimals and I am not sure if it will > > also > > > > give me the accurate dimension. > > > > > > > > Can anybody help me or guide me how to solve that problem. > > > > > > > > > > > you could try gmx solvate. It is not elegant solution but it may work, > > the > > > limitation is that you do not control on the orientation and other > > > geometrical parameter that may be relevant for graphene sheet. > > > > > > 1) generate an empty box with the desired dimension (empty.gro) > > > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro . -o > > > > > > or in alternative you can use -cs and -box > > > for all the options see > > > > > > > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > > > > > Best regards > > > Alessandra > > > > > > > > > > Thanks, > > > > Mohamed > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > htt
Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3
Hi, On Wed, Feb 19, 2020 at 11:06 AM Robert Cordina wrote: > Dear Alessandra, > > Many thanks for your reply. > Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that > "In the NERD force field, atoms/sites within a molecule that do not > interact by any other intramolecular potential are also allowed to interact > though the Lennard-Jones potential". In the paper all bond stretching, > bond bending and torsion angle parameters are given, so is nrexcl = 3 > correct? LJ potentials are 1-4 interactions, so this looks the right way > to do it to me, but I stand to be corrected. > Re compressibility, that was a typo from my part in the email, it's > correctly set at 0.1. > Re vdwtype, vdw-modifier, rvdw-switch, rvdw... I have read this section > multiple times but I'm still not sure how to translate the description in > the Sum paper to these settings. Any suggestions as to what "Interactions > were truncated and shifted at rc = 11 Å with energies shifted at this > distance" would mean for these settings? > > cutoff-scheme = Verlet > rcoulomb= 1.1 > coulombtype = Reaction-Field (I have to use this because I'm using the > epsilon-rf setting too right?) > epsilon-rf = a.bcd > > vdwtype = Cut-Off (?) > vdw-modifier= Potential-shift-Verlet or Potential-switch (?) > The sentence, you have reported, is not clear. It could be that the authors used vdwtype = cutoff vdw-modifier= Potential-shift (from mdp parameter of gromacs2020). rvdw = 1.1 But you should check with them, which treatment they use for the non-bonded interactions Best regards Alessandra rvdw-switch = 0 (?) > rvdw= 1.1 (will this just be the same as rcoulomb?) > > > Thanks again for your help. > > Best regards, > > Robert > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: 19 February 2020 08:47 > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Implementing the NERD Force Field in GROMACS > 2019.3 > > HI, > > Below some suggestions assuming that the energy terms are correctly > implemented (force field) > > On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina < > robert.cord...@strath.ac.uk> > wrote: > > > Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > > system, however I’m not entirely sure that I’m setting up the > > equilibration parameters in the mdp file correctly as I’m getting > > different simulation results from others who have published papers > > using this force field. All the bonding and non-bonding interactions > > have been typed up in the respective force-field files, and assuming > > those are correct (I’ve checked and re-checked them multiple times), > > the only thing I can think that is not correct are the mdp parameters. > > > > The Sum et al. paper, and another paper (Pizzirusso et al. > > J.Am.Chem.Soc.2018, 140, 12405−12414) state the following (text from > > Sum paper in italics, text from Pizzirusso paper in bold, what I’ve > > put in the mdp file in regular font) > > > > Both NVT and NPT calculations were performed using 40 molecules in a > > cubic box with periodic boundary conditions > > pbc = xyz > > > > > If you do not have a pre-built structure, your equilibration time may be > longer that in the original paper, the best is to ask the authors the > coordinate of pre-equilibrated system. > > > > > Interactions were truncated and shifted at rc = 11 Å with energies > > shifted at this distance > > rcoulomb = 1.1 (am I missing something here?) > > > > > here you miss the vdwtype; vdw-modifier; rvdw-switch¶; rvdw > > (see for definition: > > http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van > ) > > > > > The system evolved with a leapfrog algorithm using a 2 fs timestep > > integrator= md > > dt= 0.002 > > > > Constant temperature and constant pressure simulations were maintained > > with the Berendsen’s thermostat and barostat, respectively, by uniform > > scaling of the atomic velocities (temperature) and by uniform scaling > > of the atomic positions and box length (pressure) Atomistic MD was > > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > > temperature and pressure were kept constant using a Berendsen > > thermostat/barostat. Temperature and pressure couplings of 1 and > > 10 ps were used, respectively. Compressibility was fixed at 1 × 10-5 > > bar-1, and anisotropic pressure coupling was used in the MD simulations. > > tcoupl = Berendsen > > tau-t = 1.0 > > tc-grps = XXX > > > > system > > > ref-t = 350 > > > > pcoupl
Re: [gmx-users] Increase Graphene sheet size
HI, On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal wrote: > Many thanks Alessandra for your reply :) > > gmx solvate will add water around my graphene sheet but will not increase > the graphene sheet itself. Please correct me if I am wrong. > > Yes/No, gmx solvate is normally used to add water or to build solvent box but my suggestion was to use gmx solvate tools for your aim. What I suggested was to use the tool to fill an empty box (of desidered dimension) with copies of your graphene pre-equilibrated (small) sheet. Best regards Alessandra > I already simulated the graphene sheet but I need to increase its dimension > to a certain dimensions. > > any Ideas how to do that :) ? > > Thanks, > Mohamed > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > alessandra.villa.bio...@gmail.com> wrote: > > > Hi > > > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal < > m.b.abdel...@gmail.com> > > wrote: > > > > > Hello All, > > > > > > I want to create a graphene sheet with a specific dimensions > > (10*15*0.284) > > > nm. > > > > > > I created a .gro file as below ( as mentioned in this website > > > > > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > > ) > > > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > > 4 > > > 1GRM C1 1 0.061 0.071 0.000 > > > 1GRM C2 2 0.184 0.142 0.000 > > > 1GRM C3 3 0.184 0.284 0.000 > > > 1GRM C4 4 0.061 0.355 0.000 > > > 0.2459510.4260000.284000 > > > > > > Now I don't know how to use genconf to repeat it until it gives me the > > > required dimensions. As using genconf -nbox will repeat the above into > a > > > specific number of boxes but I can't get a sheet with accurate > dimensions > > > of (10*15*0.284 nm). > > > > > > I tried to generate a sheet using gencong and then use editconf to > change > > > the dimensions to the required ones, but the problem is that using > > editconf > > > will put the graphene sheet in an empty box but will not change the > > > dimension as I want. > > > > > > Another option is to divide the 10 (the required dimension) nm by > > 0.245951 > > > (the dimension in the above .gro file) and to use the genconf with the > > > result but it will be a lot of decimals and I am not sure if it will > also > > > give me the accurate dimension. > > > > > > Can anybody help me or guide me how to solve that problem. > > > > > > > > you could try gmx solvate. It is not elegant solution but it may work, > the > > limitation is that you do not control on the orientation and other > > geometrical parameter that may be relevant for graphene sheet. > > > > 1) generate an empty box with the desired dimension (empty.gro) > > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro . -o > > > > or in alternative you can use -cs and -box > > for all the options see > > > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > > > Best regards > > Alessandra > > > > > > > Thanks, > > > Mohamed > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3
Dear Alessandra, Many thanks for your reply. Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that "In the NERD force field, atoms/sites within a molecule that do not interact by any other intramolecular potential are also allowed to interact though the Lennard-Jones potential". In the paper all bond stretching, bond bending and torsion angle parameters are given, so is nrexcl = 3 correct? LJ potentials are 1-4 interactions, so this looks the right way to do it to me, but I stand to be corrected. Re compressibility, that was a typo from my part in the email, it's correctly set at 0.1. Re vdwtype, vdw-modifier, rvdw-switch, rvdw... I have read this section multiple times but I'm still not sure how to translate the description in the Sum paper to these settings. Any suggestions as to what "Interactions were truncated and shifted at rc = 11 Å with energies shifted at this distance" would mean for these settings? cutoff-scheme = Verlet rcoulomb= 1.1 coulombtype = Reaction-Field (I have to use this because I'm using the epsilon-rf setting too right?) epsilon-rf = a.bcd vdwtype = Cut-Off (?) vdw-modifier= Potential-shift-Verlet or Potential-switch (?) rvdw-switch = 0 (?) rvdw= 1.1 (will this just be the same as rcoulomb?) Thanks again for your help. Best regards, Robert -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Alessandra Villa Sent: 19 February 2020 08:47 To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I’m not entirely sure that I’m setting up the > equilibration parameters in the mdp file correctly as I’m getting > different simulation results from others who have published papers > using this force field. All the bonding and non-bonding interactions > have been typed up in the respective force-field files, and assuming > those are correct (I’ve checked and re-checked them multiple times), > the only thing I can think that is not correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405−12414) state the following (text from > Sum paper in italics, text from Pizzirusso paper in bold, what I’ve > put in the mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a > cubic box with periodic boundary conditions > pbc = xyz > > If you do not have a pre-built structure, your equilibration time may be longer that in the original paper, the best is to ask the authors the coordinate of pre-equilibrated system. > Interactions were truncated and shifted at rc = 11 Å with energies > shifted at this distance > rcoulomb = 1.1 (am I missing something here?) > > here you miss the vdwtype; vdw-modifier; rvdw-switch¶; rvdw (see for definition: http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van ) > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator= md > dt= 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen’s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling > of the atomic positions and box length (pressure) Atomistic MD was > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > temperature and pressure were kept constant using a Berendsen > thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 × 10-5 > bar-1, and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > system > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > compressibility is 10-5 bar-1 tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric εRF to correct for long-range interactions due to > electrostatics cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf= a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = ye
Re: [gmx-users] Increase Graphene sheet size
Many thanks Alessandra for your reply :) gmx solvate will add water around my graphene sheet but will not increase the graphene sheet itself. Please correct me if I am wrong. I already simulated the graphene sheet but I need to increase its dimension to a certain dimensions. any Ideas how to do that :) ? Thanks, Mohamed On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > Hi > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal > wrote: > > > Hello All, > > > > I want to create a graphene sheet with a specific dimensions > (10*15*0.284) > > nm. > > > > I created a .gro file as below ( as mentioned in this website > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > ) > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > 4 > > 1GRM C1 1 0.061 0.071 0.000 > > 1GRM C2 2 0.184 0.142 0.000 > > 1GRM C3 3 0.184 0.284 0.000 > > 1GRM C4 4 0.061 0.355 0.000 > > 0.2459510.4260000.284000 > > > > Now I don't know how to use genconf to repeat it until it gives me the > > required dimensions. As using genconf -nbox will repeat the above into a > > specific number of boxes but I can't get a sheet with accurate dimensions > > of (10*15*0.284 nm). > > > > I tried to generate a sheet using gencong and then use editconf to change > > the dimensions to the required ones, but the problem is that using > editconf > > will put the graphene sheet in an empty box but will not change the > > dimension as I want. > > > > Another option is to divide the 10 (the required dimension) nm by > 0.245951 > > (the dimension in the above .gro file) and to use the genconf with the > > result but it will be a lot of decimals and I am not sure if it will also > > give me the accurate dimension. > > > > Can anybody help me or guide me how to solve that problem. > > > > > you could try gmx solvate. It is not elegant solution but it may work, the > limitation is that you do not control on the orientation and other > geometrical parameter that may be relevant for graphene sheet. > > 1) generate an empty box with the desired dimension (empty.gro) > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro . -o > > or in alternative you can use -cs and -box > for all the options see > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > Best regards > Alessandra > > > > Thanks, > > Mohamed > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3
HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I’m not entirely sure that I’m setting up the equilibration > parameters in the mdp file correctly as I’m getting different simulation > results from others who have published papers using this force field. All > the bonding and non-bonding interactions have been typed up in the > respective force-field files, and assuming those are correct (I’ve checked > and re-checked them multiple times), the only thing I can think that is not > correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405−12414) state the following (text from Sum > paper in italics, text from Pizzirusso paper in bold, what I’ve put in the > mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a cubic > box with periodic boundary conditions > pbc = xyz > > If you do not have a pre-built structure, your equilibration time may be longer that in the original paper, the best is to ask the authors the coordinate of pre-equilibrated system. > Interactions were truncated and shifted at rc = 11 Å with energies shifted > at this distance > rcoulomb = 1.1 (am I missing something here?) > > here you miss the vdwtype; vdw-modifier; rvdw-switch¶; rvdw (see for definition: http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van ) > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator= md > dt= 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen’s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling of > the atomic positions and box length (pressure) > Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In > this ensemble, temperature and pressure were kept constant using a > Berendsen thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 × 10-5 bar-1, > and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > system > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > compressibility is 10-5 bar-1 tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric εRF to correct for long-range interactions due to > electrostatics > cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf= a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp= 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I’m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ= 1 > fudgeQQ = 1 > > check that nrexcl in topol.top is in line with the force field. > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > Best regards Alessandra > > Thanks in advance for your help. > > Robert > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I’m not entirely sure that I’m setting up the equilibration > parameters in the mdp file correctly as I’m getting different simulation > results from others who have published papers using this force field. All > the bonding and non-bonding interactions have been typed up in the > respective force-field files, and assuming those are correct (I’ve checked > and re-checked them multiple times), the only thing I can think that is not > correct a
Re: [gmx-users] How to cap a single residue in gromacs
Hi On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani wrote: > Dear Gromacs users > I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand > when I run pdb2gmx it gives me error:- > Fatal error: > In the chosen force field there is no residue type for 'PHE' as a > standalone > (starting & ending) residue > > I added ACE and NME terminals as below in the gro file:- > > 1ACE HC1 0.000 0.000 0.000 0. 0. 0. > 1ACE CT2 0.000 0.000 0.000 0. 0. 0. > 1ACE HC3 0.000 0.000 0.000 0. 0. 0. > 1ACE HC4 0.000 0.000 0.000 0. 0. 0. > 1ACE C5 0.000 0.000 0.000 0. 0. 0. > 1ACE O6 0.000 0.000 0.000 0. 0. 0. > 2PHE N7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 > 2PHE H8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 > 2PHE CA9 5.013 4.811 6.023 0.0535 0.3709 0.0960 > 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 > 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 > 2PHEHB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 > 2PHEHB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 > 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 > 2PHECD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 > 2PHEHD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 > 2PHECE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 > 2PHEHE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 > 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 > 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 > 2PHECE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 > 2PHEHE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 > 2PHECD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 > 2PHEHD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 > 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 > 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 > 3NME N 27 0.000 0.000 0.000 0. 0. 0. > 3NME H 28 0.000 0.000 0.000 0. 0. 0. > 3NME CT 29 0.000 0.000 0.000 0. 0. 0. > 3NME H1 30 0.000 0.000 0.000 0. 0. 0. > 3NME H1 31 0.000 0.000 0.000 0. 0. 0. > 3NME H1 32 0.000 0.000 0.000 0. 0. 0. > 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 > 4G6PO1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 > 4G6PO2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 > 4G6PO3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 > 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 > 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 > 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 > 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 > 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 > 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 > 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 > 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 > 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 > 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 > 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 > 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 > 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 > 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 > 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 > 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 > 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 > 4G6PH61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 > 4G6PH62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 > 4G6PHO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 > 4G6PHO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 > 4G6PHO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 > 4G6PHO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 > > NOTE that several atoms in the above gro file have the same (0. 0. 0.) coordinate/position. That may cause a crash when you start the simulation > However, it still claims the same error. > How should I add this in force field file? How can I use -ter command that > it can add N and C termini itself to the residue? > Yes the first thing I will do is to try is -ter. Different force fields have different termini definition (
Re: [gmx-users] Tabulated potentials
Hi, On Tue, Feb 18, 2020 at 12:12 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > So I am using Iterative Boltzmann Inversion to get the CG potentials for a > cellobiose-water solution. During the first step of the simulation by > gromacs, I get the error, which I think it might be due to some large > forces, causing the distance between the CG beads to increase to values > more than the length of the table. The bonded tables have values in > between 0 to 0.5 nm for r. > As far as I recall the error messages that you got was something like "A tabulated bond interaction table number 4 is out of the table range: r 0.575410, between table indices 575 and 576, table length 501" Your table is up to the 0.5 (501 lines), but the program is looking for a values of 0.575410 nm, that it is out of the range of the values for your table. Could it be that one of cellobiose-water distances is 0.575410 nm in the first frames? The errors seems to indicate that you need a longer table at least up 0.58 nm or more (even if it corresponds to high potential values). Note that if your table is for non-bonded interactions, then also the mdp parameters set requirement on the table lengths (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=table#tables ) Best regards Alessandra > My best, > Ali > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: maandag 17 februari 2020 9:34 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < > ali.khoday...@student.kuleuven.be> wrote: > > > Thank you Alessandra. However, fixing the topology did not remove the > > error. It still stands as before: > > > > A tabulated bond interaction table number 4 is out of the table range: > > r 0.575410, between table indices 575 and 576, table length 501 > > > > > Where exactly did you get this error? > > It looks like that your table is not covering all the request values (that > means that it is too short) or the file is missing same values. > > Best regards > Alessandra > > > > > Anyone has any idea why it could be happening? > > > > My best, > > Ali > > > > > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > > Alessandra Villa > > Sent: donderdag 13 februari 2020 16:28 > > To: gmx-us...@gromacs.org; gromacs.org_gmx-users < > > gromacs.org_gmx-users@maillist.sys.kth.se> > > Subject: Re: [gmx-users] Tabulated potentials > > > > Hi, > > > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > > ali.khoday...@student.kuleuven.be> wrote: > > > > > Dear Gromacs users, > > > > > > I’ve got a question regarding the tabulated potentials for bonded > > > interactions. > > > > > > Gromacs recognises and reads the non-bonded potential tables through > > > the energy groups specified. But how can I refer each bond type to > > > its > > table? > > > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > > each water molecule is coarse-grained as one bead. Overall, there > > > are > > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > > types, and 2 dihedral potential tables for two types of dihedrals. > > > The tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > > > Now my question is, how does gromacs recognise which table is > > regarding > > > which bonded term? The simulation crashes at the very beginning > > > giving me the following error: > > > > > > > > In topol.top one specifies which table is used for which interaction > > (bond, angle, dihedral). See the table below for the synthases > > > > > > http://manual.gromacs.org/documentation/current/reference-manual/topol > > ogies/topology-file-formats.html#topology-file > > > > Best regards > > Alessandra > > > > > > > > > A tabulated bond interaction table number 1 is out of the table range: > > > r 0.511823, between table indices 511 and 512, table length 501 > > > > > > I believe this is caused due to high forces on atoms indeed, but it > > > might be also because tables are not specified to the correct bond > type. > > > > > > > > > Kind regards, > > > Ali > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > or send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Maili
