Re: [gmx-users] lincs warning
Hi Afsane, You need to provide more details of the simulation, such as how you generated the configuration and topology, what force field you used and so on, or we can not give you any advice. Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Afsane Farhadi Sent: Sunday, April 26, 2020 01:16 To: Discussion List for GROMACS Users Subject: [gmx-users] lincs warning Hi gromacs users I generated a mixed box of methane and carbondioxide with insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and carbondioxide are optimized and the energy minimization of mixed gas is ok (potential energy is about -2e+03))but when I want to run a npt run ,the lincs warning are showing( bond rotate more than 30 degree).I repeated energy minimization but it didn't work right Can any body help me please? Sent from Yahoo Mail on Android -- 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.org_gmx-users@maillist.sys.kth.se
Hi Netaly, Although I do not know the exact reason of the failure, after skimming through your command, I think that you probably need to assign absolute path to CMAKE_INSTALL_PREFIX and have access to the internet for downloading REGRESSIONTEST and FFTW package. If you are new to GROMACS, I recommend installation from simple case, such as only CPU no GPU. Only after successfully installing CPU only version GROMACS, run to the next level CPU+GPU. This step-by-step installation practice can give you a feeling of choosing CMake options. Cheers, Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Netaly Khazanov Sent: Sunday, April 26, 2020 15:38 To: Discussion list for GROMACS users Subject: [gmx-users] gromacs installation (2020&2019) Dear All, I am trying to install gromacs 2020 and 2019 versions on CentOS release 6.10 (Final) linux system. I passed throuht cmake compilation. Using command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=gromacs2020 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ I've used gcc 5 version (tried also 6 version) However, I am struggling through make execution : in gromacs 2019 - [ 37%] Built target libgromacs_generated [ 37%] Built target libgromacs_external Scanning dependencies of target gpu_utilstest_cuda [ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so [ 37%] Built target gpu_utilstest_cuda in gromacs 2020- [ 27%] Built target linearalgebra [ 27%] Built target scanner [ 27%] Built target tng_io_obj [ 27%] Built target modularsimulator It just stuck on the line and doesn't continue to run. Any suggestions will be appreciated. Thanks in advance. -- Netaly -- 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] How to report bugs or issues?
-Original Messages- From: "Paul bauer" Sent Time: 2020-03-25 00:40:13 (Wednesday) To: gromacs.org_gmx-users@maillist.sys.kth.se, "gmx-annou...@gromacs.org" Cc: Subject: [gmx-users] GROMACS has switched to use Gitlab Hello gmx users! I just finished the transition of our project database to use the Gitlab servers. This means that from now on issues should be reported using the issue tracker at https://gitlab.com/gromacs/gromacs/-/issues instead of redmine.gromacs.org. The redmine and gerrit servers have been set be read only from now on, so that you can still access information there, but it wont be able to report new things there any more. Cheers Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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 solve the "LINCS WARNING" problem
Hi Jinyoung, I'm glad to hear that you have found the problem. You can always use grompp to check your topology of the whole system. If you want to understand the GROMACS topology, check Chapter 5. Topologies in GROMACS Manual. Words in the end: If you have mastered the basic process of protein-ligand simulation with GROMOS ff, you probably wander why we droped GROMOS ff and use others (https://redmine.gromacs.org/issues/2884). Bye, Yu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 변진영 Sent: Monday, April 20, 2020 15:27 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem Hi Yu I simulated the both case (1), (2) for only all-atom ligand system and only protein system respectively you mentioned. I run the each case; the NVT and NPT equilibration with 200ps and 1ns respectively. And there are no problems during NVT and NPT equilibration. And while I wrote the ligand only topology file, I realized that there is specific order in writing topology file (before I don’t exactly know about the order.) Below is the last section of my topology file: ; Include Position restraint file #ifdef POSRES #include "../PROTEIN/posre.itp" #endif #include "../LIGAND/lig.itp" #ifdef POSRES_LIG #include "../LIGAND/lig_posre.itp" #endif ; Include water topology #include "gromos54a7_atb_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "gromos54a7_atb_lipid.ff/ions.itp" [ system ] ; Name --- in water [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 SOL 30059 NA 4 — Is there any problem with my topology file and Is it the right order? Thank you very much b, You > 2020. 4. 17. 오후 3:34, Yu Du 작성: > > Hi Jinyoung, > > You made it clear. > > If you do not have special needs in all-atom version of the ligand, you can > also try the united-atom topology of the very same ligand. > > To check the origin of LINCS WARNING, I suggest running MD simulation with > only protein and only ligand in the same process you followed in a divide and > conquer strategy. > > Could you run the following simulation to pinpoint the error? > > (1) Simulation only all-atom ligand in the system. > (2) Simulation only protein in the system. > (3) Simulation only united-atom ligand in the system if it's possible. > > In the end, I noticed that you used ATB topology, so you need to strictly > follow the instruction in the ATB ff file folders for protein-ligand > simulation. > > PS: gmx-users mail list do not receive attachment. > > Cheers, > Yu > > -- > 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] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals
Hi Micholas, Also a word of warning for the original suggestion of using VMD. Two words of caution: 1) Be sure you unwrap your trajectories carefully before using vmd for the analysis (otherwise you may get odd 'spikes' in your distances due to the PBC), 2) Since vmd doesn't have any topology information, all of the bonds/angles/dihedral information is inferred, so make sure you are using your selections very carefully. Yes, I really omitted the versatile tools that GROMACS have provided and heavily relied on VMD. VMD indeed needs a careful preprocess of trajectories and selection of atom set for correct and reliable analysis. Thanks for your caveats. Yu -- 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] Measuring bond distances, angles and dihedrals
Hi Robert, Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD. But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice. It is fairly flexible and can almost satisfy all your requirements. Cheers, Yu -- 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 solve the "LINCS WARNING" problem
Hi Jinyoung, You made it clear. If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand. To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process you followed in a divide and conquer strategy. Could you run the following simulation to pinpoint the error? (1) Simulation only all-atom ligand in the system. (2) Simulation only protein in the system. (3) Simulation only united-atom ligand in the system if it's possible. In the end, I noticed that you used ATB topology, so you need to strictly follow the instruction in the ATB ff file folders for protein-ligand simulation. PS: gmx-users mail list do not receive attachment. Cheers, Yu -- 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] Measuring bond distances, angles and dihedrals
Hi Robert, I have only used MDTraj for distance calculation between trajectories, no experience in parameters extraction. If MDTraj cannot satisfy your custom requirement, that I recommend VMD Tcl scripts to extract related information. It probably takes you a week to master the VMD system, but it deserves the efforts and time. Cheers, Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Robert Cordina Sent: Friday, April 17, 2020 01:37 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Measuring bond distances, angles and dihedrals Hi, I've carried out a number of equilibrations and I now want to extract bond distances, bond angles and dihedrals from the resulting trajectories. I'm using MDTraj to do this, which is working perfectly fine, however I'm not too happy with the results as they are not exactly how I want them. I am using modelling quite small molecules, so I'm only measuring distances, angles and dihedrals a few atoms apart. I'm doing this to start parameterising a new coarse-grained force field, and for example I get a bond angle of 160 degrees, when really it should be 180 degrees. This is happening because I'm calculating the angle between specific atoms spaced only 3-4 atoms apart which might be on opposite sides of a straight chain of carbon atoms. What I'd like to get out is the angle between the centroid of the groups of atoms that would form the coarse-grained beads. Does anyone have any suggestions if this can be done in GROMACS, or in any Python library which works with GROMACS? Thanks, 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. -- 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 solve the "LINCS WARNING" problem
If you haven't solved your LINCS WARNING, you need to show more details of how you got that problem, including the generation of your ligand topology file. There are maybe some errors in your ligand topology that you didn't figure out. Cheers, Yu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 변진영 Sent: Thursday, April 16, 2020 21:43 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem Thank you for reply Du, You You said that "If you want more suggestion, you need to provide some details of the generation of ligand's topology” Du you mean that I modify my topology file manually?? > 2020. 4. 14. 오후 5:08, Yu Du 작성: > > Hi Jinyoung, > > I guess that the LINCS WARNING you encountered maybe came from hiden errors > in the configuration of either protein or ligand OR more directly from the > ligand's topology. You need to carefully check the configuration of protein > and ligand, e.g. side chain goes through benzene ring. > > After a careful check, If you want more suggestion, you need to provide some > details of the generation of ligand's topology. > > Du, Yu > PhD Student, > Shanghai Institute of Organic Chemistry > 345 Ling Ling Rd., Shanghai, China. > Zip: 200032, Tel: (86) 021 5492 5275 > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of 변진영 > > Sent: Tuesday, April 14, 2020 14:32 > To: gmx-us...@gromacs.org > Subject: [gmx-users] How to solve the "LINCS WARNING" problem > > Dear GROMACS users, > > Since I have run the nvt and npt processes for the protein-ligand > interaction, I met the the warning messages below > > Step 231785, time 463.57 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000176, max 0.003912 (between atoms 3035 and 3037) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3035 3036 34.00.1090 0.1087 0.1090 > > …. > > Step 231825, time 463.65 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3024 3025 90.00.1090 0.1236 0.1090 > 3026 3027 100.80.1090 6.6242 0.1090 > 3028 3029 162.51.7683 5245.4102 0.1090 > 3033 3034 106.70.1090 426.5654 0.1090 > 3035 3037 90.00.3851 0.7991 0.1090 > 3038 3039 90.00.6045 0.4497 0.1090 > 3038 3040 90.00.1123 0.2833 0.1090 > 3041 3042 59.00.1020 0.1020 0.1020 > Wrote pdb files with previous and current coordinates > > Step 231826, time 463.652 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 191384000.00, max 4098777344.00 (between atoms 3033 and 3034) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 1423 1424 140.40.1000 503.9983 0.1000 > 3024 3025 61.10.1236 223337872. 0.1090 > 3026 3027 168.86.6242 149263.5000 0.1090 > 3028 3029 165.8 5245.4102 263929.4375 0.1090 > 3031 3032 116.20.1090 223428336. 0.1090 > 3033 3034 179.9 426.5654 446766720. 0.1090 > 3035 3036 35.3 29.6105 831.0708 0.1090 > 3035 3037 102.90.7991 775.3371 0.1090 > 3038 3039 90.00.4497 0.6355 0.1090 > 3038 3040 47.70.2833 0. 0.1090 > step 231826: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > So I checked the my input configuration. the 3035, 3028, 3035 atoms are > ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. > Why does the LINCS warning occurs? and How I solve this problem? > > Many Thanks > > Jinyoung > -- > 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 visi
Re: [gmx-users] GROMACS PBS GPU JOB submission
Hi Tuanan, I think your problem can be separated into several parts: First, use one PBS script contains 4 GMX commands, shown as follows, may solve your problems: #PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod1.tpr -deffnm TEST1 -ntomp 1 -gpu_id 0 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod2.tpr -deffnm TEST2 -ntomp 1 -gpu_id 1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod3.tpr -deffnm TEST3 -ntomp 1 -gpu_id 2 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod4.tpr -deffnm TEST4 -ntomp 1 -gpu_id 3 Then, you should optimize the number of CPU used by one GPU to get the best performance. Last, check mdrun in the GMX manual, use pin and related options to set the CPU range which each subjob uses to avoid the interference between them. Cheers, Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Tuanan Lourenço Sent: Thursday, April 16, 2020 21:34 To: gmx-us...@gromacs.org Subject: [gmx-users] GROMACS PBS GPU JOB submission Hi everyone I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue system is PBS. I am having some issues with the GPU selection, what I want is to use 1 GPU per job but GROMACS is always using all the four GPUs. My submission script is the following: #PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod.tpr -deffnm TEST -ntomp 1 However, looking to the gromacs log file I see "On host gn01 4 GPUs auto-selected for this run". I know if I use the flag -gpu_id I can tell for GROMACS what GPU I want to use and in this case, everything is ok, GROMACS does what I say. But this can be a problem if I submit more than one job to the node, because the jobs will use the same GPU card. My question is; there is any way to say for GROMACS or PBS to use the GPU that is available at that moment? I have 4 GPU in the server, thus, I want to submit 4 jobs each one using one GPU. Thank you very much. -- __ Dr. Tuanan C. Lourenço -- 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] How to solve the "LINCS WARNING" problem
Hi Jinyoung, I guess that the LINCS WARNING you encountered maybe came from hiden errors in the configuration of either protein or ligand OR more directly from the ligand's topology. You need to carefully check the configuration of protein and ligand, e.g. side chain goes through benzene ring. After a careful check, If you want more suggestion, you need to provide some details of the generation of ligand's topology. Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 변진영 Sent: Tuesday, April 14, 2020 14:32 To: gmx-us...@gromacs.org Subject: [gmx-users] How to solve the "LINCS WARNING" problem Dear GROMACS users, Since I have run the nvt and npt processes for the protein-ligand interaction, I met the the warning messages below Step 231785, time 463.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000176, max 0.003912 (between atoms 3035 and 3037) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3035 3036 34.00.1090 0.1087 0.1090 …. Step 231825, time 463.65 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3024 3025 90.00.1090 0.1236 0.1090 3026 3027 100.80.1090 6.6242 0.1090 3028 3029 162.51.7683 5245.4102 0.1090 3033 3034 106.70.1090 426.5654 0.1090 3035 3037 90.00.3851 0.7991 0.1090 3038 3039 90.00.6045 0.4497 0.1090 3038 3040 90.00.1123 0.2833 0.1090 3041 3042 59.00.1020 0.1020 0.1020 Wrote pdb files with previous and current coordinates Step 231826, time 463.652 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 191384000.00, max 4098777344.00 (between atoms 3033 and 3034) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1423 1424 140.40.1000 503.9983 0.1000 3024 3025 61.10.1236 223337872. 0.1090 3026 3027 168.86.6242 149263.5000 0.1090 3028 3029 165.8 5245.4102 263929.4375 0.1090 3031 3032 116.20.1090 223428336. 0.1090 3033 3034 179.9 426.5654 446766720. 0.1090 3035 3036 35.3 29.6105 831.0708 0.1090 3035 3037 102.90.7991 775.3371 0.1090 3038 3039 90.00.4497 0.6355 0.1090 3038 3040 47.70.2833 0. 0.1090 step 231826: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. Why does the LINCS warning occurs? and How I solve this problem? Many Thanks Jinyoung -- 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.
