Re: [gmx-users] Analysis with .sh file
> > > Dear all, > > I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 > and I found out that now that while I'm trying to use a .sh, as I was > doing in the version 5.0.4, now I'm receiving back an error since the > syntax is wrong. I'm wondering if someone could please help me. > > What is the script in your .sh file? There is not enough information to find out what goes wrong. > Regards, > > Riccardo > > > > -- > > -- 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] Build polymers with pdb2gmx
Dear GMX users, I am new to polymer simulation and want to build a polymer system for Gromacs. I have followed Justin's instruction to make polyethylene by editing the rtp and hdb file. But I have a couple of questions regarding a larger polymer configuration: 1. The example system (polyethylene) only has one repeat unit, is there a way to define the number of repeat unit and then generate the PDB file? I am also wondering if there is a way to make the configuration with random torsion? I currently use Gaussview to copy and paste, and the initial PDB is just a linear chain. Like this...^^O^^O^^O^^ 2. Since the PDB file is straightly from Gaussview, the atom names in the file are all in basic form (C, H, O...), in order for the pdb2gmx to work, I have to manually match and replace them according to the .rtp file. For larger repeat unit, is there a better way to do this? Thanks for your help and suggestions. -- Shi Li Research Assistant, Ph.D. Candidate Department of Chemistry & Center for Applied Energy Research (CAER) University of Kentucky Email: sli...@g.uky.edu -- 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] Define intermolecular interactions in L-J simulation
> > > Den 2019-10-23 kl. 18:22, skrev Li, Shi: > > Dear GMX users, > > > > I am wondering if there is a way to define the intermolecular interaction > > to simulation a binary LJ system. For example, I have two atoms A and B, > > they share the same LJ parameter, and I want to change the interaction > > parameter between A and B, so that I would expect different behaviors > from > > the simulation (mix or phase separation). > > > > I checked the manual and found this can be defined in the topology file > as > > [intermolecular_interactions] and use the [pairs] interaction then list > the > > atom pairs. But it is still confusing if I have a system containing 500 A > > and 500 B, how can I apply this to the entire binary system. I was > > assumed that I can use atomtype instead of atom number? But how and where > > to specify that? > > > > Any suggestions? > > > > Thanks, > > Shi > > > Use > [ nonbonded_types ] > A A 1 c6 c12 > B B 1 c6 c12 > A B 1 c6 c12 > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > > > Thank you so much! This works very well. Shi > > -- 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] Define intermolecular interactions in L-J simulation
Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A and B, so that I would expect different behaviors from the simulation (mix or phase separation). I checked the manual and found this can be defined in the topology file as [intermolecular_interactions] and use the [pairs] interaction then list the atom pairs. But it is still confusing if I have a system containing 500 A and 500 B, how can I apply this to the entire binary system. I was assumed that I can use atomtype instead of atom number? But how and where to specify that? Any suggestions? Thanks, Shi -- 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 make all parts of a protein in the periodic box in when running "gmx editconf" command
> > Message: 3 > Date: Thu, 22 Aug 2019 21:53:25 +0800 > From: "sunyeping" > To: "gromacs.org_gmx-users" > > Subject: [gmx-users] How to make all parts of a protein in the > periodic box in when running "gmx editconf" command > Message-ID: > <0c07c92c-a134-4057-a8a2-13a1143ae486.sunyep...@aliyun.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > I run the"gmx editconf" command to make a periodic cubic box around my > protein for adding water: > > gmx editconf -f protein.gro -o newbox.gro -c -d 1.0 > > Then I visualize the priodic box in VMD. I find that one end of my protein > is out of the box (Please see the part in red circle in image at > https://drive.google.com/file/d/1M6msh1UA0fOZ4GOuGJVlJHTOtHrzwh7u/view?usp=sharing). > Even if I increase the value of "-d" option to 1.5, this end of the > protein is still out of the box. This will result in visualization problem > of the MD trajectory. This part at one end of the molecule which is out of > the box will jump to the other end of the molecule in VMD and pymol. Please > see the part in the red circle in the image at ( > https://drive.google.com/file/d/1GAP4oS78nAB6p-ZhPmT9A-6ZZnohhkeq/view?usp=sharing). > The is the image for em.gro the structure after energy minimization. The > trjconv command with -pbc cluster -center -ur cpmpact command cannot solve > the problem. > > Have you tired the -pbc nojump flag see if that can give you a different representation of the structure? Shi > So could you tell me how to keep all part of the protein in the periodic > box when running "gmx editconf" command? Thank you in advance. > > Yeping > > -- > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 184, Issue 58 > ** > -- 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] Simulated Annealing on Gromacs 2019
Hi GMX users, I am running an annealing simulation with version 2019, I found that once I have the annealing section in my .mdp file. The temperature coupling information is not recognized and written into the mdout.mdp. And my simulated annealing process was kept at 0 K through the whole time. Once I remove the annealing section, everything runs fine. Can anyone help me look into this issue? Here is the annealing section I used. *; Simulated Annealing* *annealing= single ; Single, linear sequence of annealing points.* *annealing-npoints = 2 ; two reference points (beginning & end)* *annealing-time = 0 14000 ; Time (NOT step number) to change temperature.* *annealing-temp = 100 800 * Best, Shi -- 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] Simulation with vacuum interface
Dear GMX user, I have a system box with half liquid molecules and half vacuum(vacuum on the z-direction), I want to apply an NPT simulation to study the behavior on the liquid-vacuum interface. Normally the box will just shrink to fit the liquid. Is there a way to apply NPT on the system while maintaining the vacuum space? Many thanks. Shi -- 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] Gmx gangle (Shi Li)
> > > > Hi, > > > > I would check the documentation of gmx gangle for how it works, > > particularly for how to define a plane. > > Thank you so much Mark. As a GROMACS lover, I like to make a suggestion; I > think sth it would be REALLY helpful if you provide some proper examples > for gromacs tools, with results. You have straightforward tutorials and > useful manual, but some instructions in using tools, are a little ambiguous > and misleading. This also reduces the number of questions. > You only need 3 atoms to define the plane, you may use more than that in the index, but I think the rest will be ignored, or you may run into some errors. Simply make an index file (like plane.ndx) with the content: [ Plane1 ] atom#1 atom#2 atom3# [ Vector1 ] atom#4 atom#5 then include "*-n plane.ndx -g1 plane -g2 vector -group1 Plane1 -group2 Vector1*" in your *gmx gangle* should do the work. If your vector is sure along the Y axes, you may just use* -g2 y *and delete the -group2 part. Although I don't think it is good idea to calculate angle between a plane and a vector, you may lose information of the rotation along the vector. Also, I agree with Mark that 4.5.4 is way too old. I will at least use version 2016 and later. which should fix many bugs. Have fun! Shi > > > Also, 4.5.4 is prehistoric, please > > do yourself a favor > > I would like, but I remember that I wanted to use cutoff-scheme=group and i > couldnt come up with errors in gmx. These calculations are for more than > one year ago (and now I want some more analysis), i was a freshman, > > > and use a version with the seven years of improvements > > > I was a freshman, dear smiling man -:) > > > since then :-) > > > I am waiting for you. > > Best > > > > > Mark > > > > On Tue., 11 Dec. 2018, 10:14 rose rahmani, > wrote: > > > > > Hi, > > > > > > I don't really understand how gmx gangke works!!! > > > > > > I want to calculate angle between amino acid ring and surface during > > > simulation. > > > I mad3 an index for 6 atoms of ring(a_CD1_CD2_CE1_CE2_CZ_CG) and two > > atoms > > > of surface. Surface is in xy plane and amino acid is in different Z > > > distances. > > > > > > > > > I assumed 6 ring atoms are defining a pkane and two atoms of surface > are > > > defining a vector( along Y). And i expected that the Average angle > > between > > > this plane and vector during simulation is calculated by gmx gangle > > > analysis. > > > > > > gmx gangle -f umbrella36_3.xtc -s umbrella36_3.tpr -n index.ndx -oav > > > angz.xvg -g1 plane -g2 vector -group1 -group2 > > > > > > Available static index groups: > > > Group 0 "System" (4331 atoms) > > > Group 1 "Other" (760 atoms) > > > Group 2 "ZnS" (560 atoms) > > > Group 3 "WAL" (200 atoms) > > > Group 4 "NA" (5 atoms) > > > Group 5 "CL" (5 atoms) > > > Group 6 "Protein" (33 atoms) > > > Group 7 "Protein-H" (17 atoms) > > > Group 8 "C-alpha" (1 atoms) > > > Group 9 "Backbone" (5 atoms) > > > Group 10 "MainChain" (7 atoms) > > > Group 11 "MainChain+Cb" (8 atoms) > > > Group 12 "MainChain+H" (9 atoms) > > > Group 13 "SideChain" (24 atoms) > > > Group 14 "SideChain-H" (10 atoms) > > > Group 15 "Prot-Masses" (33 atoms) > > > Group 16 "non-Protein" (4298 atoms) > > > Group 17 "Water" (3528 atoms) > > > Group 18 "SOL" (3528 atoms) > > > Group 19 "non-Water" (803 atoms) > > > Group 20 "Ion" (10 atoms) > > > Group 21 "ZnS" (560 atoms) > > > Group 22 "WAL" (200 atoms) > > > Group 23 "NA" (5 atoms) > > > Group 24 "CL" (5 atoms) > > > Group 25 "Water_and_ions" (3538 atoms) > > > Group 26 "OW" (1176 atoms) > > > Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms) > > > Group 28 "a_320_302_319_301_318_311" (6 atoms) > > > Group 29 "a_301_302" (2 atoms) > > > Specify any number of selections for option 'group1' > > > (First analysis/vector selection): > > > (one per line, for status/groups, 'help' for help, Ctrl-D to > end) > > > > 27 > > > Selection '27' parsed > > > > 27 > > > Selection '27' parsed > > > > Available static index groups: > > > Group 0 "System" (4331 atoms) > > > Group 1 "Other" (760 atoms) > > > Group 2 "ZnS" (560 atoms) > > > Group 3 "WAL" (200 atoms) > > > Group 4 "NA" (5 atoms) > > > Group 5 "CL" (5 atoms) > > > Group 6 "Protein" (33 atoms) > > > Group 7 "Protein-H" (17 atoms) > > > Group 8 "C-alpha" (1 atoms) > > > Group 9 "Backbone" (5 atoms) > > > Group 10 "MainChain" (7 atoms) > > > Group 11 "MainChain+Cb" (8 atoms) > > > Group 12 "MainChain+H" (9 atoms) > > > Group 13 "SideChain" (24 atoms) > > > Group 14 "SideChain-H" (10 atoms) > > > Group 15 "Prot-Masses" (33 atoms) > > > Group 16 "non-Protein" (4298 atoms) > > > Group 17 "Water" (3528 atoms) > > > Group 18 "SOL" (3528 atoms) > > > Group 19 "non-Water" (803 atoms) > > > Group 20 "Ion" (10 atoms) > > > Group 21 "ZnS" (560 atoms) > > > Group 22 "WAL" (200 atoms) > > > Group 23 "NA" (5 atoms) > > > Group 24 "CL" (5 atoms) > > > Group 25 "Water_and_ions" (3538 atoms) > > >
[gmx-users] Calculate solubility parameters with Gromacs
Dear GMX users, I am trying to calculated the Hansen solubility parameter with GROMACS. I have these sections from my edr file. --- 1 Bond 2 Angle3 Ryckaert-Bell. 4 Improper-Dih. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 LJ-recip. 12 Potential ... --- So, if I want to pull out the energy from dispersion force, do I combine LJ-14, LJ-(SR) and LJ-recip. and the energy from dipolar intermolecular force is the sum of Coulomb-14, Coulomb-(SR) and Coul.-recip.?? I don't know if this is correct or not, because my Hvap (Ugas-Uliq+RT) from gas and liquid simulation seems reasonable, but the dispersion and bipolar energy have large variation with experiment measurements. Thanks, Shi -- 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] GROMACS XRD analysis
Dear GMX users, I am trying to do x-ray diffraction analysis on my simulation results. I found in the old 4.6 version, there was an option to do this under the g_rdf module with -energy flag, but then it was removed after 5.0. The only similar module I can find now is gmx saxs module. I compared the old *g_rdf *with the new *gmx saxs* module, they seemed to give exactly the same result for my simulation. However, the result looked much like a rdf plot, as for a liquid system, I can still get signal(a peak), which doesn't seem right for an XRD plot (should be no signal for a melted system). So I am wondering if there is a tool in GMX to do an XRD analysis? Is there difference for the old g_rdf and saxs module after version 5.0? Thanks, Shi -- 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] Output center of mass of each molecules in a system.
Dear GMX users, I want to output the center of mass of each molecule in my simulation box. I think I should use gmx traj, with -com option. But this only gave me the center of mass for the whole system. If my system only contains 100 same solvent molecules, is there a method to output the center of mass for each individual molecule in the system? Thank you for any help! Shi -- 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] gmx insert-molecules
Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule to insert 10 molecule B into the system box. The problem is molecule B is slightly larger than molecule A. So in some cases, I couldn't insert the exact 10 molecules of B into the system. Is there a way to automatically adjust the size of the box according to the radius of molecule B, so that they can fit in? Or, is there a better solution to do this? Or, is there a way to ignore the overlapping of molecules? In that case, even the inserted molecule is overlapping with surrounding molecules, it can still be inserted in? Many thanks, Shi -- 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] Randomly replace molecules with another molecule
Dear Gromacs users, I am wondering if there is a better way to randomly replace some molecules in a system box with another type of molecule. For example, I have a system with 1000 molecule A as the solvent and I have another molecule B as the solute. I want to generate a series of systems with different concentration of B. Is there some gmx command to do that? I tried to use gmx insert-molecuels, but then I will need to first create a series of system A in order to insert different number of B. I don't know if gmx genion could do that or not, as I tried to use this but I am not sure how to make the replacement with B as both of them are charge neutral. If you have a better solution. Please let me know! Thank you! Shi -- 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] No CUDA-capable device is detected
Dear GMX users, I have a problem with the Gromacs jobs run on GPU node. I have the output in the log file attached below. Anyone know if the CUDA and GROMACS are compiled correctly according to this output? Is so, why does the job cannot run on GPU? Thank you very much! gmx_mpi mdrun -deffnm em GROMACS version:2016.1 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support:CUDA SIMD instructions: AVX_256 FFT library:fftw-3.3.5-sse2-avx-avx_128_fma RDTSCP usage: enabled TNG support:enabled Hwloc support: disabled Tracing support:disabled Built on: Tue Jan 17 15:14:56 EST 2017 Built by: sli259@compute-gpu-0-2.local [CMAKE] Build OS/arch: Linux 2.6.32-642.11.1.el6.x86_64 x86_64 Build CPU vendor: Intel Build CPU brand:Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz Build CPU family: 6 Model: 63 Stepping: 2 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /home/sli259/program/gromacs/openmpi/bin/mpicc GNU 4.9.3 C compiler flags:-mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /home/sli259/program/gromacs/openmpi/bin/mpic++ GNU 4.9.3 C++ compiler flags: -mavx-std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /home/sli259/program/gromacs/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch= compute_30,code=sm_30;-gencode;arch=compute_35,code= sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch= compute_50,code=sm_50;-gencode;arch=compute_52,code= sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch= compute_61,code=sm_61;-gencode;arch=compute_60,code= compute_60;-gencode;arch=compute_61,code=compute_61;- use_fast_math;;;-Xcompiler;,-mavx,,;-Xcompiler;-O3,- DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,; CUDA driver:8.0 CUDA runtime: 0.0 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Running on 1 node with total 12 cores, 24 logical cores, 0 compatible GPUs Hardware detected on host compute-gpu-0-2.local (the node of MPI rank 0): -- 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] No CUDA-capable device is detected
Dear GMX users, I have a problem with the Gromacs jobs run on GPU node. I have the output in the log file attached below. Anyone know if the CUDA and GROMACS are compiled correctly according to this output? Is so, why does the job cannot run on GPU? Thank you very much! gmx_mpi mdrun -deffnm em GROMACS version:2016.1 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support:CUDA SIMD instructions: AVX_256 FFT library:fftw-3.3.5-sse2-avx-avx_128_fma RDTSCP usage: enabled TNG support:enabled Hwloc support: disabled Tracing support:disabled Built on: Tue Jan 17 15:14:56 EST 2017 Built by: sli259@compute-gpu-0-2.local [CMAKE] Build OS/arch: Linux 2.6.32-642.11.1.el6.x86_64 x86_64 Build CPU vendor: Intel Build CPU brand:Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz Build CPU family: 6 Model: 63 Stepping: 2 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /home/sli259/program/gromacs/openmpi/bin/mpicc GNU 4.9.3 C compiler flags:-mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /home/sli259/program/gromacs/openmpi/bin/mpic++ GNU 4.9.3 C++ compiler flags: -mavx-std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /home/sli259/program/gromacs/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;;;-Xcompiler;,-mavx,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,; CUDA driver:8.0 CUDA runtime: 0.0 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Running on 1 node with total 12 cores, 24 logical cores, 0 compatible GPUs Hardware detected on host compute-gpu-0-2.local (the node of MPI rank 0): -- 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] PMF simulation in Gromacs 2016.1
Dear Gromacs users, I am comparing the PMF simulations using the Gromacs 2016 version with old version 5.0.5. I found the *gmx wham* in Gromacs 5.0.5 couldn't process the tpr files generated by Gromacs 2016.1 . (tpx version 100 vs. tpx version 110). The new Gromacs 2016.1 can process the tpr files that generated from Gromacs 5.0.5, but the results are different, most of the energy in the new output .xvg file is zero, but using the old version to process the same input files, the resulting .xvg is fine. While using the Gromacs 2016.1 to process the tpx version 110 files(generated by the new version). The resulting .xvg also shows a lot of zero energies. I am not sure where I did wrong or how to fix this problem, any suggestion will be appreciated. Thanks. Shi -- 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] Strange in PMF calculation
Dear Gromacs users, I am doing some PMF simulations of 2 molecules in vacuum and my resulting profile has a strange look. I attached an eps files here, anyone can give me some suggestion on why there is fluctuation at longer distance? Thank you very much! Shi -- 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] Plus / Minus sign in rtp file
Dear Gmx users, I have a problem with the plus and minus signs while editing the .rtp file. In the manual, it mentioned that it refers to the previous and next residue. But what is the rule to include this? Say i have a benzene and on C1 and C3 both bonded with a same residue. How should I include the plus/minus? I had many trails and each time the residues will both bonded with the same carbon (C1), leading to a long bond in the topology. This is an example I used in the. rtp file. Can anyone tell my why this is wrong and what is the rule? ;Benzene [ bonds ] C1 +CT -CT C3 ... [ residue ] ... CT +C3 CT -C1 Many thanks, Shi -- 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.
