[gmx-users] force field parameters for Fe3O4?
Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- 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 increase the volatile gpu-util
Dear gromacs users, I am running CG MD simulation on a Rocks cluster using the following command: gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job & I tried the different value for the -ntomp option. With -ntomp 16 run will finish sooner than the other values for -ntomp. In this state, volatile gpu-util is 47%. How to increase this parameter? nvidia-smi command: |*---+--+--+ *|* GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. *ECC | |* Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute *M. | |*===+==+==| *|* 2 TITAN X (Pascal)On | :C1:00.0 Off | * N/A | |* 43% 71CP2 130W / 250W |183MiB / 12189MiB | 47% E. *Process | +---+--+--+ Any help will be highly appreciated. -- 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] volatile gpu-util
Dear gromacs users, I am running CG MD simulation on a Rocks cluster using the following command: gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job & I tried the different value for the -ntomp option. With -ntomp 16 run will finish sooner than the other values for -ntomp. In this state, volatile gpu-util is 47%. How to increase this parameter? nvidia-smi command: |---+--+--+ | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 2 TITAN X (Pascal)On | :C1:00.0 Off | N/A | | 43% 71CP2 130W / 250W |183MiB / 12189MiB | 47% E. Process | +---+--+--+ Any help will be highly appreciated. -- 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] problem: gromacs run on gpu
Dear Gromacs users, I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using command: gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on All things are ok. When I use this command in a script to do md simulation by queuing system: - #!/bin/bash #$ -S /bin/bash #$ -q gpu.q #$ -cwd #$ -N cell_1 #$ -e error_1.dat #$ -o output_1.dat echo "Job started at date" gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on echo "Job Ended at date" - I encountered with following error: Program: gmx mdrun, VERSION 5.1.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: Invalid command-line options In command-line option -pin Invalid value: on For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Halting program gmx mdrun -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. --- How to resolve this error? Any help will be highly appreciated -- 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] problem: gromacs run on gpu
*Dear Szilárd ,* *Thanx for your answer. * *For the following command, should I use -pin on?* gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 32 -gpu_id 0 Best wishes -- 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] problem: gromacs run on gpu
*Dear Nikhil and Szilárd,* Thanks for your answers. I want to use only one of GPUs (for example ID =1). Should I use option -gpu_id 1? Information of my system hardware is as follows: Running on 1 node with total 96 cores, 192 logical cores, 3 compatible GPUs Hardware detected on host cschpc.ut.ac.ir (the node of MPI rank 0). Since there is 1 node in my system, should I use both of -ntmpi and -ntomp or just -ntomp? Should I obtain optimum values for -ntmpi and -ntomp using trial and error? Is not there another way? Best wishes. -- 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] problem: gromacs run on gpu
Dear Gromacs users, I installed Gromacs 5.1.3. on GPU in Rocks cluster system. After using command: gmx_mpi mdrun -nb gpu -v -deffnm old_gpu, I encountered with: = GROMACS: gmx mdrun, VERSION 5.1.3 Executable: /home/karami_leila1/513/gromacs/bin/gmx_mpi Data prefix: /home/karami_leila1/513/gromacs Command line: gmx_mpi mdrun -nb gpu -v -deffnm new_gpu Running on 1 node with total 96 cores, 192 logical cores, 3 compatible GPUs Hardware detected on host cschpc.ut.ac.ir (the node of MPI rank 0): CPU info: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E7-8890 v4 @ 2.20GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 GPU info: Number of GPUs detected: 3 #0: NVIDIA TITAN X (Pascal), compute cap.: 6.1, ECC: no, stat: compatible #1: NVIDIA Tesla K40c, compute cap.: 3.5, ECC: no, stat: compatible #2: NVIDIA Tesla K40c, compute cap.: 3.5, ECC: no, stat: compatible Reading file new_gpu.tpr, VERSION 5.1.3 (single precision) Using 1 MPI process Using 192 OpenMP threads 3 compatible GPUs are present, with IDs 0,1,2 1 GPU auto-selected for this run. Mapping of GPU ID to the 1 PP rank in this node: 0 NOTE: potentially sub-optimal launch configuration, gmx_mpi started with less PP MPI process per node than GPUs available. Each PP MPI process can use only one GPU, 1 GPU per node will be used. --- Program gmx mdrun, VERSION 5.1.3 Source code file: /root/gromacs_source/gromacs-5.1.3/src/programs/mdrun/resource-division.cpp, line: 571 Fatal error: Your choice of 1 MPI rank and the use of 192 total threads leads to the use of 192 OpenMP threads, whereas we expect the optimum to be with more MPI ranks with 2 to 6 OpenMP threads. If you want to run with this many OpenMP threads, specify the -ntomp option. But we suggest to increase the number of MPI ranks. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Halting program gmx mdrun -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. = How to resolve this problem? Any help will be highly appreciated. -- 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] MD simulation of peptide amphiphile using CG method
Dear James, Thanks for your answer. As I understand, PyCGTOOL generates the coarse-grained molecular dynamics models from atomistic simulation trajectories. But, I don't want to do the atomistic simulation. Also, ATB only generates a complete topology for molecules containing < 40 atoms, while I have 5 PA molecules with > 40 atoms, apiece. Since my molecules contain amino acids bonded to the hydrocarbon chain (which are default beads in Martini force field), I think there is a straightforward way for treatment of that. Unfortunately, I don't have experience about that. My problem is how to relate amino acids to hydrocarbon chain? When I use martinize.py, in structure and topology output files, there are only amino acids and not hydrocarbon chain. Should I modify martini_v2.2_aminoacids.itp by adding hydrocarbon tail parameter to it? Best, LK -- 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] MD simulation of peptide amphiphile using CG method
Dear Peter, Thanks for your answer. > you'd best redirect this question to the Martini forum (cgmartini.nl), > since this is more of a forcefield question than a Gromacs question. You are right. At first, I asked my question in Martini forum, but no one didn't answer me. > look at the tutorials on the Martini webpage. There are tutorials for protein and lipid molecules separately, while my molecule contains some amino acids bonded covalently to hydrocarbon chain. > There's also one on parametrizing a new molecule. In this tutorial, DPGS lipid was selected for the template. In this case, only beads were displaced, while in my molecule, there is a new covalent bond. My main question is how to treat with that? -- 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] MD simulation of peptide amphiphile using CG method
Dear gromacs users, I want to do MD simulation of peptide amphiphile using CG method. My molecule is shown in the following link: https://ln.sync.com/dl/db2c92bf0#i8jm6yin-5uz4tn32-nq37ewxa-3vrkmt4b Can I use the default beads definition for my molecule (containing hydrocarbon chain and amino acids)? What itp files should I include in topology files? martini_v2.2.itp martini_v2.2_aminoacids.itp martini_v2.0_lipids.itp martini_v2.0_ions.itp I am a beginner in CG method. Any help will highly be appreciated. Best, -- 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 concatenate tpr files?
Dear Justin and Erik, Thanks for your answers. How to resolve my problem? How to obtain a reasonable RMSD curve from 10 consecutive MD runs? How to make an appropriate tpr for calculating RMSD? Best, -- 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 concatenate tpr files?
Dear Justin, Thanks for your answer. > If you use gmx convert-tpr to simply change the number of steps > (much easier and cleaner!) Based on your suggestion, I used following command to extend first tpr to all steps. gmx convert-tpr -f final.xtc -s md1.tpr -n index.ndx -o new.tpr -extend 10 After that, RMSDs with md1.tpr and new.tpr are the same. Please, check this link: https://ln.sync.com/dl/d123d6b00#6nqcqdrf-cgebd3c7-htj4vydi-vfiihiy6 Note that there are no problem in the other analysis such as gmx mindist, gmx angle anf gmx gyrate. Best, -- 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 concatenate tpr files?
Dear gromacs users, About the concatenation trajectory files, I have a question. I did 10 MD simulations (each section 10 ns). Now, I want to concatenate all of the trajectories and determine RMSD on whole trajectory. To do this, I used the following command: gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr md8.trr md9.trr md10.trr -o all_md.xtc –settime The whole trajectory file made correctly. To determined RMSD, I used the following command. gmx rms -f all_md.xtc -s *.tpr -n index.ndx -o rmsd.xvg -tu ns I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …? I tried this command with md1.tpr and md10.tpr and in each time, RMSD had the different values. So, should I concatenate the tpr files and use the complete tpr file. How can I concatenate the tpr files? Best -- 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] g_mmpbsa
Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- 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] g_mmpbsa
Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- 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] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)
Dear gromacs users I installed topolbuild version 1.3. I used following command line: ./topolbuild -n khob -dir ../dat/gromacs/ -ff gmx53a6.dat -meas I encountered with following error: Fatal error. Source code file: readmol2.c, line: 162 Atomic symbol O2 in atom type not found. How to resolve this problem? Any help will highly appreciated. -- 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] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)
my mol2file is as follows: @TRIPOSMOLECULE C:\Users\scc\Desktop\22.pdb 30 31 0 0 0 SMALL GASTEIGER @TRIPOSATOM 1 O2 0.99910.0511 -0.0859 O2 1 C1 -0.2444 2 C2 2.22660.0511 -0.0859 Car 1 C1 0.3522 3 N3 2.87602.9655 -4.9849 Nar 1 C1 -0.1783 4 C4 2.22662.3904 -4.0182 Car 1 C1 0.1230 5 N4 0.83012.3904 -4.0182 Npl 1 C1 -0.3430 6 C5 2.89811.7958 -3.0187 Car 1 C1 -0.0056 7 C6 2.22661.2012 -2.0192 Car 1 C1 0.0152 8 N1 2.87600.6262 -1.0526 Nar 1 C1 -0.2700 9 C1*4.31050.6262 -1.0526 C3 1 C1 0.1680 10 H1*4.66721.1419 -1.9196 H 1 C1 0.0867 11 O4*6.2372 -0.7744 -3.5532 O3 1 C1 -0.3456 12 C4*4.8172 -0.7744 -3.5532 C3 1 C1 0.1126 13 H4*4.4605 -1.2673 -4.4334 H 1 C1 0.0647 14 C3*4.3105 -1.5070 -2.3216 C3 1 C1 0.1135 15 H3*3.2405 -1.5070 -2.3216 H 1 C1 0.0647 16 O3*4.7839 -2.8457 -2.3391 O3 1 C1 -0.3864 17 C2*4.8172 -0.8068 -1.0713 C3 1 C1 0.1286 18 H2*5.8872 -0.8068 -1.0713 H 1 C1 0.0665 19 O2*4.3439 -1.49130.0793 O3 1 C1 -0.3847 20 C5*4.31050.6586 -3.5345 C3 1 C1 0.0730 21 O5*2.89050.6586 -3.5345 O3 1 C1 -0.3924 22 H410.33011.9477 -3.2739 H 1 C1 0.1437 23 H420.33012.8332 -4.7625 H 1 C1 0.1437 24 H5 3.93011.7958 -3.0187 H 1 C1 0.0666 25 H6 1.19461.2012 -2.0192 H 1 C1 0.0812 26 H3*5.7839 -2.8457 -2.3391 HO 1 C1 0.2100 27 H2*4.6772 -2.43400.0670 HO 1 C1 0.2101 28 H5*14.66721.1515 -2.6543 H 1 C1 0.0584 29 H5*24.66721.1743 -4.4015 H 1 C1 0.0584 30 H5*2.55720.1979 -4.3571 HO 1 C1 0.2095 @TRIPOSBOND 1 1 22 2 2 3 ar 3 2 8 ar 4 3 4 ar 5 4 51 6 4 6 ar 7 5221 8 5231 9 6 7 ar 10 6241 11 7 8 ar 12 7251 13 8 91 14 9111 15 9171 16 9101 1711121 1812131 1912141 2012201 2114171 2214161 2314151 2416261 2517181 2617191 2719271 2820211 2920281 3020291 3121301 leilakar...@dena.kntu.ac.ir -- 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] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)
my mol2file is as follows: @TRIPOSMOLECULE C:\Users\scc\Desktop\22.pdb 30 31 0 0 0 SMALL GASTEIGER @TRIPOSATOM 1 O2 0.99910.0511 -0.0859 O2 1 C1 -0.2444 2 C2 2.22660.0511 -0.0859 Car 1 C1 0.3522 3 N3 2.87602.9655 -4.9849 Nar 1 C1 -0.1783 4 C4 2.22662.3904 -4.0182 Car 1 C1 0.1230 5 N4 0.83012.3904 -4.0182 Npl 1 C1 -0.3430 6 C5 2.89811.7958 -3.0187 Car 1 C1 -0.0056 7 C6 2.22661.2012 -2.0192 Car 1 C1 0.0152 8 N1 2.87600.6262 -1.0526 Nar 1 C1 -0.2700 9 C1*4.31050.6262 -1.0526 C3 1 C1 0.1680 10 H1*4.66721.1419 -1.9196 H 1 C1 0.0867 11 O4*6.2372 -0.7744 -3.5532 O3 1 C1 -0.3456 12 C4*4.8172 -0.7744 -3.5532 C3 1 C1 0.1126 13 H4*4.4605 -1.2673 -4.4334 H 1 C1 0.0647 14 C3*4.3105 -1.5070 -2.3216 C3 1 C1 0.1135 15 H3*3.2405 -1.5070 -2.3216 H 1 C1 0.0647 16 O3*4.7839 -2.8457 -2.3391 O3 1 C1 -0.3864 17 C2*4.8172 -0.8068 -1.0713 C3 1 C1 0.1286 18 H2*5.8872 -0.8068 -1.0713 H 1 C1 0.0665 19 O2*4.3439 -1.49130.0793 O3 1 C1 -0.3847 20 C5*4.31050.6586 -3.5345 C3 1 C1 0.0730 21 O5*2.89050.6586 -3.5345 O3 1 C1 -0.3924 22 H410.33011.9477 -3.2739 H 1 C1 0.1437 23 H420.33012.8332 -4.7625 H 1 C1 0.1437 24 H5 3.93011.7958 -3.0187 H 1 C1 0.0666 25 H6 1.19461.2012 -2.0192 H 1 C1 0.0812 26 H3*5.7839 -2.8457 -2.3391 HO 1 C1 0.2100 27 H2*4.6772 -2.43400.0670 HO 1 C1 0.2101 28 H5*14.66721.1515 -2.6543 H 1 C1 0.0584 29 H5*24.66721.1743 -4.4015 H 1 C1 0.0584 30 H5*2.55720.1979 -4.3571 HO 1 C1 0.2095 @TRIPOSBOND 1 1 22 2 2 3 ar 3 2 8 ar 4 3 4 ar 5 4 51 6 4 6 ar 7 5221 8 5231 9 6 7 ar 10 6241 11 7 8 ar 12 7251 13 8 91 14 9111 15 9171 16 9101 1711121 1812131 1912141 2012201 2114171 2214161 2314151 2416261 2517181 2617191 2719271 2820211 2920281 3020291 3121301 -- 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] constraint pulling
Dear Justin My system contains lipid + drug + water molecules. At first, I put drug molecule in middle of bilayer. Based on your tutorial, after minimization and equilibration, I generated configurations. After using distance.pl script, summary_distances.dat file is irregular such that no increasing trend is not seen in the distances. Some times distance increased and some time decreased. Is there problem in generating configuration step? pull code part of mdp file is as follows: pull = constraint pull_geometry = distance pull_constr_tol = 1e-6 pull_dim = N N Y pull_ngroups= 1 pull_group0 = CHOL_DOPC pull_group1 = drug pull_vec1 = 0 0 1 pull_rate1= 0 pull-start = yes How to resolve this issue? Best wishes -- 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] constraint pulling
Dear gromacs users I will use pull = constraint (constraint pulling) for PMF calculations. There is a tutorial about PMF from Justin in which he used pull = umbrella (umbrella sampling). In justin tutorial, step are as follows: 1) preparation of system 2) minimization equilibration 3) generate configuration 4) umbrella sampling 5) WHAM which gives PMF curve I conceive in my case (pull = constraint), steps 1, 2 and 3 are similar to justin case (pull = umbrella). Since, WHAM analyzes output files generated by umbrella sampling, I have not idea about steps 4 and 5. I did not know how to obtain PMF curve in my case. If my notion is wrong, please give me more explanation such that I do this PMF calculation using constraint pulling method. Please tell me steps needed for constraint pulling. Is there a tutorial about PMF calculation using constraint pulling method? Any help will highly appreciated -- 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.
