[gmx-users] Install errors
Hi, I'm trying to install the gromacs version 4.6.5. with the "Quick and dirty installation". When I give the command make the platform gives me back this message of error: "clang: error: unsupported option '-dumpspecs' clang: error: no input files CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206 (message): Error generating /Users/Valentina/Software/gromacs-4.6.6/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_memtestG80_core.cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2" How may I avoid this problem? Thanks, Valentina -- Valentina Loconte, PhD student Department of Biomedical Sciences University of Padova Viale G. Colombo 3 35131 Padova, Italy -- 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] too many lincs warnings
hello users I had done energy minimisation of protein-ligand complex and i got negative potential. Also the ligand was at right place after EM run but when I tried the positional restrained run, too many lincs warnings came and md run stopped suddenly. I am using charmm force field and mdp file settings for position restrined run are:- define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 5; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 500; save coordinates every 0.2 ps nstvout= 500; save velocities every 0.2 ps nstenergy= 500; save energies every 0.2 ps nstlog= 500; update log file every 0.2 ps ; Bond parameters continuation= yes; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) rvdw-switch = 1.0 ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 300; temperature for Maxwell distribution gen_seed= -1; generate a random seed Please tell me if there is something wrong with mdp settings or is it some other problem? -- 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 pull along Z direction?
Hello: I am going to calculate the PMF of a small molecule accross the lipids bilyaers. I am just wondering how can we define the parameters along Z direction? thank you very much ALbert -- 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] delete molecule with command line?
Hello: I am just wondering is it possible to delet water molecules within 4A of a ligand through Gromacs command line? Everytime I have to do this in VMD which is a little bit complecated. thank you very much. Albert -- 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] Extending simulation problem.
Dear Gromacs experts, I googled for answer and I found these: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_1_ps but still I am confused about what happens in my simulation. I did 5 ns simulation and I would like to add extra 5 ns on top of that so that new results (energies, temperature, trajectory, etc.) will be appended to already existing files after first 5 ns simulation. Now I used this command to run MD simulation for the first time: \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1 After this in the same directory I run: tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr \$MDRUN -s npt-md-ext.tpr -cpi state.cpt I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of previous simulation. What can cause that? Is it because of used files names or I did something else wrong? Best wishes, Dawid Grabarek -- 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] Extending simulation problem.
Oh I forgot that I used -append option in the latter \$MDRUN command: \$MDRUN -s npt-md-ext.tpr -cpi state.cpt -append 2014-08-20 11:33 GMT+01:00 Dawid das : > Dear Gromacs experts, > > I googled for answer and I found these: > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_1_ps > > but still I am confused about what happens in my simulation. I did 5 ns > simulation and I would like to add extra 5 ns on top of that so that new > results (energies, temperature, trajectory, etc.) will be appended to > already existing files after first 5 ns simulation. Now I used this command > to run MD simulation for the first time: > > \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e > mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1 > > After this in the same directory I run: > > tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr > > \$MDRUN -s npt-md-ext.tpr -cpi state.cpt > > I tried both state.cpt and prev_state.cpt and the beginning of new simulation > looks exactly the same > > that means temperature, energies, etc. are the same as if I started from 0ns > step, not from 5ns step of > > previous simulation. What can cause that? Is it because of used files names > or I did something else wrong? > > Best wishes, > > Dawid Grabarek > > -- 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] Forcefield parameters for Zinc and phosphorylated residues
Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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] Forcefield parameters for Zinc and phosphorylated residues
This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter wrote: > Hi, > > I have two questions regarding the parameterisation of Zinc ions and a > phosphorylated TYR residue within two different protein systems. > > > 1. Zinc parameters: > > I have three zinc ions within one protein system. I want to use a bonded > model so that they do not fly out of my protein upon simulation. Is there > any documentation on the parameters for such a model in the GROMOS > forcefield? > > 2. Phosphorylated TYR > > In another system I have a phosphorylated TYR residue. PDB2GMX does not > like this and after looking inot the manual I have found that you can add > parameters for this to the existing forcefields. Much like the previous > question, is there any documentation on the addition of parameters for > phosphorylated residues in the GROMOS forcefield? > > Any pointers for these questions would be greatly appreciated. > > Cheers, > Mike Carter > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. > 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the addressee only. If > the message is received by anyone other than the addressee, please return > the message to the sender by replying to it and then delete the message > from your computer and network. > -- > 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] Forcefield parameters for Zinc and phosphorylated residues
Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, "bipin singh" wrote: >This might help. > >http://vienna-ptm.univie.ac.at/ > > > >*Thanks and Regards,Bipin Singh* > > > >On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter >wrote: > >> Hi, >> >> I have two questions regarding the parameterisation of Zinc ions and a >> phosphorylated TYR residue within two different protein systems. >> >> >> 1. Zinc parameters: >> >> I have three zinc ions within one protein system. I want to use a bonded >> model so that they do not fly out of my protein upon simulation. Is >>there >> any documentation on the parameters for such a model in the GROMOS >> forcefield? >> >> 2. Phosphorylated TYR >> >> In another system I have a phosphorylated TYR residue. PDB2GMX does not >> like this and after looking inot the manual I have found that you can >>add >> parameters for this to the existing forcefields. Much like the previous >> question, is there any documentation on the addition of parameters for >> phosphorylated residues in the GROMOS forcefield? >> >> Any pointers for these questions would be greatly appreciated. >> >> Cheers, >> Mike Carter >> >> The Institute of Cancer Research: Royal Cancer Hospital, a charitable >> Company Limited by Guarantee, Registered in England under Company No. >> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 >>3RP. >> >> This e-mail message is confidential and for use by the addressee only. >>If >> the message is received by anyone other than the addressee, please >>return >> the message to the sender by replying to it and then delete the message >> from your computer and network. >> -- >> 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. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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] CUDA5.5 and ICC 14
Hi, Per Nvidia's docs and that error, CUDA 5.5 is only supported with that icc version. In practice, I understand that other icc versions work fine with GROMACS, but you would need to go and comment out that #error message. Alternatively, CUDA 6.5 supports icc 14.0 (only). Mark On Wed, Aug 20, 2014 at 8:26 AM, Theodore Si wrote: > Hi, > > I am using CUDA 5.5 and Intel ICC 14.0.1 to compile GROMACS and this > happened: > > [ 0%] Building NVCC (Device) object src/gromacs/gmxlib/gpu_utils/ > CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o > In file included from /usr/local/cuda-5.5/include/cuda_runtime.h(59), > from /home/theo/gromacs-5.0/src/gromacs/gmxlib/gpu_utils/ > gpu_utils.cu(0): > /usr/local/cuda-5.5/include/host_config.h(72): catastrophic error: #error > directive: -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 > is supported! > #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 > is supported! >^ > > CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): > Error generating > /home/theo/gromacs-5.0/build/src/gromacs/gmxlib/gpu_utils/ > CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o > > > make[2]: *** [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./ > gpu_utils_generated_gpu_utils.cu.o] Error 1 > make[1]: *** [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] > Error 2 > make: *** [all] Error 2 > > Does this mean that I cannot make them work together? > > BR, > Theo > -- > 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] Install errors
Hi, You should be using a supported host compiler for your version of CUDA (check its docs, probably gcc 4.7 or 4.8, for example), rather than clang. Mark On Wed, Aug 20, 2014 at 9:59 AM, Valentina Loconte < valentina.loco...@studenti.unipd.it> wrote: > Hi, > I'm trying to install the gromacs version 4.6.5. with the "Quick and dirty > installation". When I give the command make the platform gives me back this > message of error: > > "clang: error: unsupported option '-dumpspecs' > > clang: error: no input files > > CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206 > (message): > > Error generating > > > > /Users/Valentina/Software/gromacs-4.6.6/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o > > > > make[2]: *** > > [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_memtestG80_core.cu.o] > Error 1 > > make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 > > make: *** [all] Error 2" > > How may I avoid this problem? > > Thanks, > > Valentina > > -- > Valentina Loconte, PhD student > Department of Biomedical Sciences > University of Padova > Viale G. Colombo 3 > 35131 Padova, Italy > -- > 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] Energy drift
Thanks for your response, Mark. Can you help me to check the parameters for my mdp file to see if it is correct? Can you send me a mdp file for NVE? I will test it today. By the way, my GROMACS version is single precision? Does it matter? >Given that their bond constant for N-N is ~4.5 times higher than their bond >constant for C-H, and both have comparable equilibrium lengths, and >unconstrained C-H bonds are normally treated with either 1fs or 0.5fs, and >that time step should be rather shorter than the period of bond >oscillation, I'd have serious reservations about the quality of that model, >and your results suggest reason for that. If you've got the parameters >right, then you should be able to suppress (post-equilibration) NVE drift >from integration inaccuracy by taking a time step that is small enough. How >small is small enough? >Mark >Thank you ; ; File 'mdout.mdp' was generated ; By user: root (0) ; On host: geol-bao9.lsu.edu ; At date: Tue Aug 19 09:20:49 2014 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/roe include = ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) define = ; RUN CONTROL PARAMETERS integrator = md-vv ; Start time and timestep in ps tinit= 0.0 dt = 0.001 nsteps = 500 ; For exact run continuation or redoing part of a run init-step= 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation-part = 1 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 500 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax-shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 50 nstvout = 50 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 50 nstcalcenergy= 100 nstenergy= 50 ; Output frequency and precision for .xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the .xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) cutoff-scheme= Verlet ; nblist update frequency nstlist = 1 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic-molecules = no ; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, ; a value of -1 means: use rlist verlet-buffer-drift = 0.005 ; nblist cut-off rlist= 1.8 ; long-range cut-off for switched potentials rlistlong= -1 nstcalclr= -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off coulomb-modifier = Potential-shift-Verlet rcoulomb-switch = 0 rcoulomb = 1.8 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 1 epsilon-rf = 0 ; Method for doing Van der Waals vdw_type = cut-off vdw-modifier = Potential-shift-Verlet ; cut-off lengths rvdw-switch = 0 rvdw = 1.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = Enerpres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Separate tables between energy group pairs energygrp-table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 ; EWALD/PME/PPPM parameters pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 3d epsilon-surface = 0 optimi
Re: [gmx-users] Increase the box size or decrease rlist
I could solve the fatal error by giving box vectors 4.84331 4.84331 6.69130 while generating .gro file from .pdb using editconf. Then, the following warning: WARNING 1 [file minim.mdp]: You are using full electrostatics treatment PME for a system without charges. This costs a lot of performance for just processing zeros, consider using Cut-off instead. So, should i give -maxwarn 1 or change the electrostatics from 'PME' to 'Cut-off'. Can anyone please suggest? Thanking You, On Wed, Aug 20, 2014 at 8:55 AM, pragna lakshmi wrote: > Thank u Justin for your reply. > I have realized that stockholm lipids are derived from Amber ff. But i am > unable to get parameters for POPC derived from charmm ff. Is there any > source for that? > The box vectors that are listed in POPC.gro are0.0 0.0 > 0.0 > > > > On Tue, Aug 19, 2014 at 11:50 PM, Justin Lemkul wrote: > >> >> >> On 8/19/14, 2:14 PM, pragna lakshmi wrote: >> >>> Dear all, >>> I am trying to do MD simulation of POPC membrane simulation with >>> peripheral >>> attachment of protein ligand complex. Steps that i have performed so far >>> are: >>> >>> 1. orienting the protein with editcong -princ command >>> 2. rotating it along the y-axis with editconf -rotate 0 40 0 command >>> 3. separation of protein ligand files into individual files and >>> generation >>> of topology file of protein from pdb2gmx and ligand from swissparam. >>> (charmm 36ff was used for protein topology generation. source: >>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs ) >>> 4. The protein and ligand files were merged followed by necessary changes >>> in topology file. >>> 5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's website >>> whereas its itp file was taken from Stockholm_Lipids website. >>> >> >> The Stockholm lipids are derived from Amber force fields. You can't >> combine them with CHARMM protein parameters and expect anything physically >> meaningful. If you're using the CHARMM protein force field, use the CHARMM >> lipid parameters. >> >> >> 6. After this, when i am running the command >>> grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr >>> i am facing the fatal error: >>> ERROR: The cut-off length is longer than half the shortest box vector or >>>longer than the smallest box diagonal element. Increase the box size >>> or >>>decrease rlist. >>> >> >> What are the box vectors listed in POPC.gro? >> >> >> As it is suggesting, I have decreased rlist, rcoulomb and rvdw from 1.2 >>> to >>> 1.0. But still the same error is raising. >>> >> >> Don't mess with these settings just to make an error message go away. >> The nonbonded setup is a fixed feature of the force field, and lipids are >> especially sensitive to changes here. I just posted the proper settings >> for the CHARMM force field a few days ago; use those settings and don't >> deviate unless you have proof that what you're doing is superior. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> 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. >> > > > > -- > Pragna Lakshmi.T, > Ph.D. Scholar, > IPLS Project, > Pondicherry University, > Pondicherry, > India - 605014. > -- Pragna Lakshmi.T, Ph.D. Scholar, IPLS Project, Pondicherry University, Pondicherry, India - 605014. -- 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] Energy drift
On Wed, Aug 20, 2014 at 3:55 PM, Xiaobin Cao wrote: > Thanks for your response, Mark. Can you help me to check the parameters > for my mdp file to see if it is correct? Can you send me a mdp file for > NVE? I will test it today. > Just turn off T and P coupling! > By the way, my GROMACS version is single precision? Does it matter? Generally not, if everything else is correct. But you can try double precision to see for yourself. Mark > >Given that their bond constant for N-N is ~4.5 times higher than their > bond > >constant for C-H, and both have comparable equilibrium lengths, and > >unconstrained C-H bonds are normally treated with either 1fs or 0.5fs, and > >that time step should be rather shorter than the period of bond > >oscillation, I'd have serious reservations about the quality of that > model, > >and your results suggest reason for that. If you've got the parameters > >right, then you should be able to suppress (post-equilibration) NVE drift > >from integration inaccuracy by taking a time step that is small enough. > How > >small is small enough? > > >Mark > > >Thank you > > -- > 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] CHARMM36 sucrose?
Just wanted to post a quick update: The psf I had didn't have the linkage in it explicitly (it was relying on the patches we mentioned before). I ended up just swapping over to gromos53a6 instead and using the automated topology builder to run the simulation. I am still going to try to write something to take the psf and make a top with the linkage so I can use the charmm force-field, but that's now a side project. Thanks again -Micholas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, August 19, 2014 9:52 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] CHARMM36 sucrose? On 8/19/14, 9:48 PM, Smith, Micholas D. wrote: > Thanks for getting back to me. > > Any suggestions on tools to build the sucrose residue? At the moment I also > have a psf for the composite (as if I was using CHARMM), so I can (in > principle) convert the psf to a .top, but curious to see if you or anyone > else has a tool for automating the addition of the linkages. > No, I don't have anything, though it's something I'm thinking about. If you already have the .psf, converting it to a .top should be straightforward. -Justin > -Micholas > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Justin > Lemkul > Sent: Tuesday, August 19, 2014 9:10 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] CHARMM36 sucrose? > > On 8/19/14, 9:03 PM, Smith, Micholas D. wrote: >> So the topology file that is written for the sucrose molecule is: [ >> moleculetype ] >> ; Namenrexcl >> Other 3 >> >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass typeB >> chargeB massB >> ; residue 0 AGLC rtp AGLC q 0.0 >>1 CC3162 01 AGLC C1 1 0.34 12.011 ; >> qtot 0.34 >>2 HCA1 01 AGLC H1 2 0.09 1.008 ; >> qtot 0.43 >> . >> . (this is filled out correctly) >> . >> residue 0 BFRU rtp BFRU q 0.0 >> 25 OC3C51 02 BFRU O5 25 -0.415.9994 ; >> qtot -0.4 >> . >> . (again, correct here) >> . >> 48 HCP1 02 BFRUHO4 48 0.42 1.008 ; >> qtot 0 >> >> [ bonds ] >> ; aiaj functc0c1c2c3 >> 1 2 1 >> 1 3 1 >> 1 7 1 >> 1 8 1 >> 3 4 1 >> 5 6 1 >> 5 7 1 >> 516 1 >> 520 1 >> 8 9 1 >> 810 1 >> 812 1 >> 1011 1 >> 1213 1 >> 1214 1 >> 1216 1 >> 1415 1 >> 1617 1 >> 1618 1 >> 1819 1 >> 2021 1 >> 2022 1 >> 2023 1 >> 2324 1 (!bond joining AGLC and BFRU, seems to be missing...) >> 2526 1 >> 2529 1 >> 2627 1 >> 2636 1 >> 2641 1 >> 2728 1 >> 2728 1 >> 2930 1 >> 2931 1 >> 2945 1 >> 3132 1 >> ... more bonds (these look correct) >> >> Pairs also seem fine. It looks like it is something to do with the bonding >> of the two residues. Is their a way to get gromacs to recognize the chain >> (the shared linkage/ether bond) >> > > If you're using the default residues included in the force field, no. All of > the monosaccharides are just that - individual sugars. If you want linkages, > you have to design your own residues. Gromacs does not have the same patching > capability that CHARMM has, to modify bonded interactions within the chain. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Bal
Re: [gmx-users] Increase the box size or decrease rlist
You can't have a sensible bilayer with atomistic water and have no charged atoms! Please reconsider however you are generating that input. Mark On Wed, Aug 20, 2014 at 4:33 PM, pragna lakshmi wrote: > I could solve the fatal error by giving box vectors 4.84331 4.84331 6.69130 > while generating .gro file from .pdb using editconf. > Then, the following warning: > WARNING 1 [file minim.mdp]: > You are using full electrostatics treatment PME for a system without > charges. > This costs a lot of performance for just processing zeros, consider using > Cut-off instead. > > > So, should i give -maxwarn 1 or change the electrostatics from 'PME' to > 'Cut-off'. Can anyone please suggest? > > Thanking You, > > > > On Wed, Aug 20, 2014 at 8:55 AM, pragna lakshmi > wrote: > > > Thank u Justin for your reply. > > I have realized that stockholm lipids are derived from Amber ff. But i am > > unable to get parameters for POPC derived from charmm ff. Is there any > > source for that? > > The box vectors that are listed in POPC.gro are0.0 0.0 > > 0.0 > > > > > > > > On Tue, Aug 19, 2014 at 11:50 PM, Justin Lemkul wrote: > > > >> > >> > >> On 8/19/14, 2:14 PM, pragna lakshmi wrote: > >> > >>> Dear all, > >>> I am trying to do MD simulation of POPC membrane simulation with > >>> peripheral > >>> attachment of protein ligand complex. Steps that i have performed so > far > >>> are: > >>> > >>> 1. orienting the protein with editcong -princ command > >>> 2. rotating it along the y-axis with editconf -rotate 0 40 0 command > >>> 3. separation of protein ligand files into individual files and > >>> generation > >>> of topology file of protein from pdb2gmx and ligand from swissparam. > >>> (charmm 36ff was used for protein topology generation. source: > >>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs ) > >>> 4. The protein and ligand files were merged followed by necessary > changes > >>> in topology file. > >>> 5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's > website > >>> whereas its itp file was taken from Stockholm_Lipids website. > >>> > >> > >> The Stockholm lipids are derived from Amber force fields. You can't > >> combine them with CHARMM protein parameters and expect anything > physically > >> meaningful. If you're using the CHARMM protein force field, use the > CHARMM > >> lipid parameters. > >> > >> > >> 6. After this, when i am running the command > >>> grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr > >>> i am facing the fatal error: > >>> ERROR: The cut-off length is longer than half the shortest box vector > or > >>>longer than the smallest box diagonal element. Increase the box size > >>> or > >>>decrease rlist. > >>> > >> > >> What are the box vectors listed in POPC.gro? > >> > >> > >> As it is suggesting, I have decreased rlist, rcoulomb and rvdw from 1.2 > >>> to > >>> 1.0. But still the same error is raising. > >>> > >> > >> Don't mess with these settings just to make an error message go away. > >> The nonbonded setup is a fixed feature of the force field, and lipids > are > >> especially sensitive to changes here. I just posted the proper settings > >> for the CHARMM force field a few days ago; use those settings and don't > >> deviate unless you have proof that what you're doing is superior. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >> Department of Pharmaceutical Sciences > >> School of Pharmacy > >> Health Sciences Facility II, Room 601 > >> University of Maryland, Baltimore > >> 20 Penn St. > >> Baltimore, MD 21201 > >> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >> http://mackerell.umaryland.edu/~jalemkul > >> > >> == > >> -- > >> 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. > >> > > > > > > > > -- > > Pragna Lakshmi.T, > > Ph.D. Scholar, > > IPLS Project, > > Pondicherry University, > > Pondicherry, > > India - 605014. > > > > > > -- > Pragna Lakshmi.T, > Ph.D. Scholar, > IPLS Project, > Pondicherry University, > Pondicherry, > India - 605014. > -- > 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://w
[gmx-users] Regarding error in NPT SIMULATION in VACUM
Dear Justin Thank you for your previous reply When I run NPT equlibiriation for My CNT CNCASSED CYCLICPETIDE in VACUM I have Got the Following error after 3 lacs steps out of 10 lacs The X-size of the box (7.750338) times the triclinic skew factor (1.00) is smaller than the number of DD cells (8) times the smallest allowed cell size (0.969134) My Box size is 10.83680 10.88700 10.19300 MY NPT parameters are title = NPT Equilibration for KALP15-DPPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100 ; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein CNT CL ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CNT_protein CL ; Scale COM of reference coordinates refcoord_scaling = com How to Solve this error? Please Help me Which Parameter Shoul I Cahnge in . mdp file? Thanks in Advance -- 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 subject)
Dear Justin Thank you for your previous reply When I run NPT equlibiriation for My CNT CNCASSED CYCLICPETIDE in VACUM I have Got the Following error after 3 lacs steps out of 10 lacs The X-size of the box (7.750338) times the triclinic skew factor (1.00) is smaller than the number of DD cells (8) times the smallest allowed cell size (0.969134) My Box size is 10.83680 10.88700 10.19300 MY NPT parameters are title = NPT Equilibration for KALP15-DPPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100 ; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein CNT CL ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CNT_protein CL ; Scale COM of reference coordinates refcoord_scaling = com How to Solve this error? Please Help me Which Parameter Shoul I Cahnge in . mdp file? Thanks in Advance -- 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 pull along Z direction
Hi Albert, For pulling along the Z axis it is enough to align your system to this axis (you can use editconf for that). You can then either use the pull-geometry = distanceand pull-dim = N N Yor you can use pull-geometry = direction and pull-vec = 0 0 z=the distance between your pulling groups Lalita Hello: I am going to calculate the PMF of a small molecule accross the lipids bilyaers. I am just wondering how can we define the parameters along Z direction? thank you very much ALbert On Wed, Aug 20, 2014 at 12:00 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. too many lincs warnings (Meenakshi Rajput) >2. how to pull along Z direction? (Albert) >3. delete molecule with command line? (Albert) > > > -- > > Message: 1 > Date: Wed, 20 Aug 2014 13:29:30 +0530 > From: Meenakshi Rajput > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] too many lincs warnings > Message-ID: > < > cah5gtb+c8iub7em9sflhx4nfa6puudfv-jun9q9nmxabzgg...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > hello users > I had done energy minimisation of protein-ligand complex and i got negative > potential. Also the ligand was at right place after EM run but when I tried > the positional restrained run, too many lincs warnings came and md run > stopped suddenly. I am using charmm force field and mdp file settings for > position restrined run are:- > define= -DPOSRES; position restrain the protein > ; Run parameters > integrator= md; leap-frog integrator > nsteps= 5; 2 * 5 = 100 ps > dt= 0.002; 2 fs > ; Output control > nstxout= 500; save coordinates every 0.2 ps > nstvout= 500; save velocities every 0.2 ps > nstenergy= 500; save energies every 0.2 ps > nstlog= 500; update log file every 0.2 ps > ; Bond parameters > continuation= yes; first dynamics run > constraint_algorithm = lincs; holonomic constraints > constraints= all-bonds; all bonds (even heavy atom-H bonds) > constrained > lincs_iter= 1; accuracy of LINCS > lincs_order= 4; also related to accuracy > ; Neighborsearching > cutoff-scheme = Verlet > ns_type= grid; search neighboring grid cells > nstlist= 10; 10 fs > rlist= 1.2; short-range neighborlist cutoff (in nm) > rcoulomb= 1.2; short-range electrostatic cutoff (in nm) > rvdw= 1.2; short-range van der Waals cutoff (in nm) > rvdw-switch = 1.0 > ; Electrostatics > coulombtype= PME; Particle Mesh Ewald for long-range > electrostatics > pme_order= 4; cubic interpolation > fourierspacing= 0.16; grid spacing for FFT > ; Temperature coupling is on > tcoupl= V-rescale; modified Berendsen thermostat > tc-grps= Protein Non-Protein; two coupling groups - more > accurate > tau_t= 0.10.1; time constant, in ps > ref_t= 300 300; reference temperature, one for each group, > in K > ; Pressure coupling is off > pcoupl= no ; no pressure coupling in NVT > ; Periodic boundary conditions > pbc= xyz; 3-D PBC > ; Dispersion correction > DispCorr= EnerPres; account for cut-off vdW scheme > ; Velocity generation > gen_vel= yes; assign velocities from Maxwell distribution > gen_temp= 300; temperature for Maxwell distribution > gen_seed= -1; generate a random seed > > Please tell me if there is something wrong with mdp settings or is it some > other problem? > > > -- > > Message: 2 > Date: Wed, 20 Aug 2014 10:17:39 +0200 > From: Albert > To: gmx-us...@gromacs.org > Subject: [gmx-users] how to pull along Z direction? > Message-ID: <53f459a3.1070...@gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello: > > I am going to calculate the PMF of a small molecule accross the lipids > bilyaers. I am just wondering how can we define the parameters along Z > direction? > > thank you very much > ALbert > > > -- > > Message: 3 > Date: Wed, 20 Aug 2014 11:27:31 +0200 > From: Albert > To: gmx-us...@gr
Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues
Hi Mike, As well as the link that Bipin sent, you can also get parameters for GROMOS phosphorylated residues (compatible with the 43A1 force field, I think) from: http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used either so have no idea which might be better. The ones that Binpin suggested look like they work with the newer GROMOS 54A7 force field, so they might be the ones to use. On your other question, I am not sure about the protein-zinc parameters with a GROMOS force field. I would say, is there any particular need for using one of the GROMOS protein force fields? There are definitely parameters out there for some of the all-atom protein force fields (e.g. AMBER ones) which are probably also better in terms of protein parameters. Cheers Tom PS: Hope things are good in the (relatively) new job! From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Michael Carter [michael.car...@icr.ac.uk] Sent: 20 August 2014 12:56 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, "bipin singh" wrote: >This might help. > >http://vienna-ptm.univie.ac.at/ > > > >*Thanks and Regards,Bipin Singh* > > > >On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter >wrote: > >> Hi, >> >> I have two questions regarding the parameterisation of Zinc ions and a >> phosphorylated TYR residue within two different protein systems. >> >> >> 1. Zinc parameters: >> >> I have three zinc ions within one protein system. I want to use a bonded >> model so that they do not fly out of my protein upon simulation. Is >>there >> any documentation on the parameters for such a model in the GROMOS >> forcefield? >> >> 2. Phosphorylated TYR >> >> In another system I have a phosphorylated TYR residue. PDB2GMX does not >> like this and after looking inot the manual I have found that you can >>add >> parameters for this to the existing forcefields. Much like the previous >> question, is there any documentation on the addition of parameters for >> phosphorylated residues in the GROMOS forcefield? >> >> Any pointers for these questions would be greatly appreciated. >> >> Cheers, >> Mike Carter >> >> The Institute of Cancer Research: Royal Cancer Hospital, a charitable >> Company Limited by Guarantee, Registered in England under Company No. >> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 >>3RP. >> >> This e-mail message is confidential and for use by the addressee only. >>If >> the message is received by anyone other than the addressee, please >>return >> the message to the sender by replying to it and then delete the message >> from your computer and network. >> -- >> 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. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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] Hydrogen bonds between new residue and protein.
Dear Gromacs experts, This time I would like to use g_hbond to calculate hydrogen bonds between one residue of the protein and all other residues in the protein. The thing is that the former residue is a new one, defined by me from scratch. Now when I run g_hbond and choose CH6 and Protein index groups (CH6 is my new residue and Protein also includes this CH6 residue) I got 0.0 for every time step although I strongly believe there are couple of hydrogen bonds. I was thinking that the issue may be that CH6 is built of atomtypes which are not recognised by g_hbond as ones able to form hydrogen bonds. Is it possible explanation? If yes, what can I do? Is recompiling what I need to do? Thanks, Dawid Grabarek -- 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] Hydrogen bonds between new residue and protein.
I found one problem. If I create new group in index.ndx file which contains protein without CH6 residue then some h-bonds are detected but actually I wouldn't expect it the way it looks. So again, how does actually g_hbond calculate hydrogen bonds except the distance and angle restraints. Does it recognize donors and acceptors by the atom types? If so, how can I force it to recognize MO3 as h-bond acceptor for instance? 2014-08-20 16:44 GMT+01:00 Dawid das : > Dear Gromacs experts, > > This time I would like to use g_hbond to calculate hydrogen bonds between > one residue of the protein and all other residues in the protein. The thing > is that the former residue is a new one, defined by me from scratch. Now > when I run g_hbond and choose CH6 and Protein index groups (CH6 is my new > residue and Protein also includes this CH6 residue) I got 0.0 for every > time step although I strongly believe there are couple of hydrogen bonds. > > I was thinking that the issue may be that CH6 is built of atomtypes which > are not recognised by g_hbond as ones able to form hydrogen bonds. Is it > possible explanation? If yes, what can I do? Is recompiling what I need to > do? > > Thanks, > > Dawid Grabarek > -- 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] Regarding error in NPT SIMULATION in VACUM
On 2014-08-20 17:03, vidhya sankar wrote: Dear Justin Thank you for your previous reply When I run NPT equlibiriation for My CNT CNCASSED CYCLICPETIDE in VACUM I have Got the Following error after 3 lacs steps out of 10 lacs What do you *think* will happen when you do pressure coupling in vacuum? The X-size of the box (7.750338) times the triclinic skew factor (1.00) is smaller than the number of DD cells (8) times the smallest allowed cell size (0.969134) My Box size is 10.83680 10.88700 10.19300 MY NPT parameters are title= NPT Equilibration for KALP15-DPPC define= -DPOSRES ; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 100; 2 * 50 = 1000 ps (1 ns) dt = 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= yes; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 0.9; short-range neighborlist cutoff (in nm) rcoulomb= 0.9; short-range electrostatic cutoff (in nm) rvdw= 1.4; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= Nose-Hoover; More accurate thermostat tc-grps= Protein CNTCL; three coupling groups - more accurate tau_t= 0.5 0.50.5; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CNT_protein CL ; Scale COM of reference coordinates refcoord_scaling = com How to Solve this error? Please Help me Which Parameter Shoul I Cahnge in . mdp file? Thanks in Advance -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Increase the box size or decrease rlist
Thank you Mark for ur reply. In the generated POPC.top from POPC.pdb and POPC.psf using VMD, the charges have become to zero. Here are few lines of my POPC.top [ atomtypes ] ; name bond_type mass charge ptype sigma epsilon C1 C 1.0 0.0 A 0.0 0.0 C11 C 1.0 0.0 A 0.0 0.0 C12 C 1.0 0.0 A 0.0 0.0 C13 C 1.0 0.0 A 0.0 0.0 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 N 1 POPC N 1 0.14.0070 2 C11 1 POPCC11 2 0.12.0110 3 C12 1 POPCC12 2 0.12.0110 4 C13 1 POPCC13 3 0.12.0110 My question is whether this could be the reason for not having the charges over the atoms. If it is so, could you please suggest me the proper way of getting parameters for POPC (charmm36 ff). Thanking You, On Wed, Aug 20, 2014 at 8:37 PM, Mark Abraham wrote: > You can't have a sensible bilayer with atomistic water and have no charged > atoms! Please reconsider however you are generating that input. > > Mark > > > On Wed, Aug 20, 2014 at 4:33 PM, pragna lakshmi > wrote: > > > I could solve the fatal error by giving box vectors 4.84331 4.84331 > 6.69130 > > while generating .gro file from .pdb using editconf. > > Then, the following warning: > > WARNING 1 [file minim.mdp]: > > You are using full electrostatics treatment PME for a system without > > charges. > > This costs a lot of performance for just processing zeros, consider > using > > Cut-off instead. > > > > > > So, should i give -maxwarn 1 or change the electrostatics from 'PME' to > > 'Cut-off'. Can anyone please suggest? > > > > Thanking You, > > > > > > > > On Wed, Aug 20, 2014 at 8:55 AM, pragna lakshmi > > wrote: > > > > > Thank u Justin for your reply. > > > I have realized that stockholm lipids are derived from Amber ff. But i > am > > > unable to get parameters for POPC derived from charmm ff. Is there any > > > source for that? > > > The box vectors that are listed in POPC.gro are0.0 0.0 > > > 0.0 > > > > > > > > > > > > On Tue, Aug 19, 2014 at 11:50 PM, Justin Lemkul > wrote: > > > > > >> > > >> > > >> On 8/19/14, 2:14 PM, pragna lakshmi wrote: > > >> > > >>> Dear all, > > >>> I am trying to do MD simulation of POPC membrane simulation with > > >>> peripheral > > >>> attachment of protein ligand complex. Steps that i have performed so > > far > > >>> are: > > >>> > > >>> 1. orienting the protein with editcong -princ command > > >>> 2. rotating it along the y-axis with editconf -rotate 0 40 0 command > > >>> 3. separation of protein ligand files into individual files and > > >>> generation > > >>> of topology file of protein from pdb2gmx and ligand from swissparam. > > >>> (charmm 36ff was used for protein topology generation. source: > > >>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs ) > > >>> 4. The protein and ligand files were merged followed by necessary > > changes > > >>> in topology file. > > >>> 5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's > > website > > >>> whereas its itp file was taken from Stockholm_Lipids website. > > >>> > > >> > > >> The Stockholm lipids are derived from Amber force fields. You can't > > >> combine them with CHARMM protein parameters and expect anything > > physically > > >> meaningful. If you're using the CHARMM protein force field, use the > > CHARMM > > >> lipid parameters. > > >> > > >> > > >> 6. After this, when i am running the command > > >>> grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr > > >>> i am facing the fatal error: > > >>> ERROR: The cut-off length is longer than half the shortest box vector > > or > > >>>longer than the smallest box diagonal element. Increase the box > size > > >>> or > > >>>decrease rlist. > > >>> > > >> > > >> What are the box vectors listed in POPC.gro? > > >> > > >> > > >> As it is suggesting, I have decreased rlist, rcoulomb and rvdw from > 1.2 > > >>> to > > >>> 1.0. But still the same error is raising. > > >>> > > >> > > >> Don't mess with these settings just to make an error message go away. > > >> The nonbonded setup is a fixed feature of the force field, and lipids > > are > > >> especially sensitive to changes here. I just posted the proper > settings > > >> for the CHARMM force field a few days ago; use those settings and > don't > > >> deviate unless you have proof that what you're doing is superior. > > >> > > >> -Justin > > >> > > >> -- > > >> == > > >> > > >> Justin A. Lemkul, Ph.D. > > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > >> > > >> Department of Pharmaceutical Sciences > > >> School of Pharmacy > > >> Health Sciences Facility II, Room 601 > > >> University of Maryland, Baltimore > > >> 20 Penn St. > > >> Baltimore, MD 21201 > > >> > > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > >> http://mackerell.umaryland.edu/~jalemkul > > >> > > >> ==
Re: [gmx-users] Increase the box size or decrease rlist
On 8/20/14, 12:56 PM, pragna lakshmi wrote: Thank you Mark for ur reply. In the generated POPC.top from POPC.pdb and POPC.psf using VMD, the charges have become to zero. Here are few lines of my POPC.top [ atomtypes ] ; name bond_type mass charge ptype sigma epsilon C1 C 1.0 0.0 A 0.0 0.0 C11 C 1.0 0.0 A 0.0 0.0 C12 C 1.0 0.0 A 0.0 0.0 C13 C 1.0 0.0 A 0.0 0.0 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 N 1 POPC N 1 0.14.0070 2 C11 1 POPCC11 2 0.12.0110 3 C12 1 POPCC12 2 0.12.0110 4 C13 1 POPCC13 3 0.12.0110 My question is whether this could be the reason for not having the charges over the atoms. If it is so, could you please suggest me the proper way of getting parameters for POPC (charmm36 ff). The proper parameters are published and are included in the .rtp file for CHARMM36 that our lab produced. There is no reason to run anything through VMD; it looks like it produces a shell of a topology that is totally nonfunctional. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Hydrogen bonds between new residue and protein.
On 8/20/14, 12:02 PM, Dawid das wrote: I found one problem. If I create new group in index.ndx file which contains protein without CH6 residue then some h-bonds are detected but actually I wouldn't expect it the way it looks. So again, how does actually g_hbond calculate hydrogen bonds except the distance and angle restraints. Does it recognize donors and acceptors by the atom types? If so, how can I force it to recognize MO3 as h-bond acceptor for instance? It reads the first character of atom names, nothing more. The best bet is to name atoms more conventionally, such that the first letter is the actual elemental symbol. You can do this after the simulation by editing the .top and producing a new .tpr file with new names. It doesn't affect the simulation in any way. -Justin 2014-08-20 16:44 GMT+01:00 Dawid das : Dear Gromacs experts, This time I would like to use g_hbond to calculate hydrogen bonds between one residue of the protein and all other residues in the protein. The thing is that the former residue is a new one, defined by me from scratch. Now when I run g_hbond and choose CH6 and Protein index groups (CH6 is my new residue and Protein also includes this CH6 residue) I got 0.0 for every time step although I strongly believe there are couple of hydrogen bonds. I was thinking that the issue may be that CH6 is built of atomtypes which are not recognised by g_hbond as ones able to form hydrogen bonds. Is it possible explanation? If yes, what can I do? Is recompiling what I need to do? Thanks, Dawid Grabarek -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] too many lincs warnings
On 8/20/14, 3:59 AM, Meenakshi Rajput wrote: hello users I had done energy minimisation of protein-ligand complex and i got negative potential. Also the ligand was at right place after EM run but when I tried the positional restrained run, too many lincs warnings came and md run stopped suddenly. I am using charmm force field and mdp file settings for position restrined run are:- define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 5; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 500; save coordinates every 0.2 ps nstvout= 500; save velocities every 0.2 ps nstenergy= 500; save energies every 0.2 ps nstlog= 500; update log file every 0.2 ps ; Bond parameters continuation= yes; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) rvdw-switch = 1.0 You need the force-switch method as your vdw-modifier if you are using CHARMM. ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 300; temperature for Maxwell distribution gen_seed= -1; generate a random seed Please tell me if there is something wrong with mdp settings or is it some other problem? Usual diagnostics apply: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System The ligand is the first place I'd start. Simplify the system - put the ligand in vacuum and run it to see if it is stable, if it is put it in water and run, etc. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] delete molecule with command line?
On 8/20/14, 5:27 AM, Albert wrote: Hello: I am just wondering is it possible to delet water molecules within 4A of a ligand through Gromacs command line? Everytime I have to do this in VMD which is a little bit complecated. g_select can do this. It can give you an index group of atoms that can be passed to trjconv for coordinate extraction. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Extending simulation problem.
On 8/20/14, 6:33 AM, Dawid das wrote: Dear Gromacs experts, I googled for answer and I found these: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_1_ps but still I am confused about what happens in my simulation. I did 5 ns simulation and I would like to add extra 5 ns on top of that so that new results (energies, temperature, trajectory, etc.) will be appended to already existing files after first 5 ns simulation. Now I used this command to run MD simulation for the first time: \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1 After this in the same directory I run: tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr \$MDRUN -s npt-md-ext.tpr -cpi state.cpt I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of previous simulation. What can cause that? Is it because of used files names or I did something else wrong? What does the .log file say? It should clearly indicate if the restart was done by reading in the checkpoint file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Energy drift
Hi, Mark. I tested my system today with NVE and time step =1fs and 0.5fs. The drift still exists. I didn't test the system by double precision GROMACS yet. Thank you. _ Xiaobin Cao Dept of Geology & Geophysics E235, Howe-Russell Geosciences Complex, Louisiana State University, Baton Rouge, LA 70803, U.S.A. -- 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 invoke hamiltonian replica exchange in 4.6.3
Dear gmx users: I got a problem that I could not invoke hamiltonian replica exchange in version 4.6.3. I've different lambda value for each replica ( free_energy = yes; init-lambda = 0.X ) however I got error "the properties of the 4 systems arre all the same..." I've tried the method suggested in https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083425.html , however after add fep-lambdas = 0.X I still get same error. I'm checking src/kernel/repl_ex.c and found if my systems are assigned as hamiltonian replica exchange, it should report "Replica exchange in lambda" to log file ( aroundl299), and in my log file it has "Replica exchange in temperature" so it shows I failed at invoke hamiltonian replica exchange. I just wonder would any one like to tell me how to invoke hamiltonian replica exchange in 4.6.3? Yhank you! Yours Guang -- 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] Time evolution of distance of Hydrogen bond
Dear Users, I am working on protein-ligand MD simulation. I have managed to get the number of H-bonds formed between the protein and ligand throughout my simulation period. I noticed three important residue participate in the formation of this H-bonding network. I need to determine the *time evolution* of the specific H-bond *distance* throughout my simulation. How do I go about this? -- 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] Time evolution of distance of Hydrogen bond
On 8/20/14, 8:54 PM, MUSYOKA THOMMAS wrote: Dear Users, I am working on protein-ligand MD simulation. I have managed to get the number of H-bonds formed between the protein and ligand throughout my simulation period. I noticed three important residue participate in the formation of this H-bonding network. I need to determine the *time evolution* of the specific H-bond *distance* throughout my simulation. How do I go about this? Distances are measured with g_dist/gmx distance. Create index groups for each of the heavy atoms that participate as donor and acceptor and measure the distance between each relevant pair. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Energy drift
Hi, Repeating: how small a step is small enough to suppress the drift? Mark On Wed, Aug 20, 2014 at 10:42 PM, Xiaobin Cao wrote: > Hi, Mark. I tested my system today with NVE and time step =1fs and 0.5fs. > The drift still exists. I didn't test the system by double precision > GROMACS yet. > > Thank you. > > _ > Xiaobin Cao > Dept of Geology & Geophysics > E235, Howe-Russell Geosciences Complex, > Louisiana State University, Baton Rouge, LA 70803, U.S.A. > > -- > 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] Simulating different pH values of water
Dear all, This might not be relevant to MD technicalities, but I guess I should give it a shot. I would like to simulate water droplets at different pH values. However, knowing that a realistic system would need 180k water molecules to mimic a pH of 7.Is there another viable approach that I can use to simulate water droplets from low to high pH values?The original question was posted here: https://www.researchgate.net/post/How_can_I_calculate_the_number_of_molecules_with_respect_to_the_pH-value_in_solution?_tpcectx=subscription_feed#53f576d7d4c11805568b469cRegards,Kester -- 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] Simulating different pH values of water
Hi Kester, You do realize that water is odd quantum stuff, with oxygens going about in a sea of protons? The main way to move a free proton is to rewire the O-H bonds. What effects do you want investigate with your simulations? That determines what setup you need. Cheers, Tsjerk On Aug 21, 2014 6:46 AM, "Kester Wong" wrote: > Dear all, > > > This might not be relevant to MD technicalities, but I guess I should give > it a shot. > > > I would like to simulate water droplets at different pH values. > > However, knowing that a realistic system would need 180k water molecules > to mimic a pH of 7. > > Is there another viable approach that I can use to simulate water droplets > from low to high pH values? > > > The original question was posted here: > > > https://www.researchgate.net/post/How_can_I_calculate_the_number_of_molecules_with_respect_to_the_pH-value_in_solution?_tpcectx=subscription_feed#53f576d7d4c11805568b469c > > > > Regards, > > Kester > > -- > 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] Several questions about log file.
Hi, 1. Does "force" in the R E A L C Y C L E A N D T I M E A C C O U N T I N G table mean the time spent on short-range force calculation? 2. Does "Comm. coord" mean the communication of atom positions when calculating short-range force interaction? 3. What forces are waited and communicated in "Wait + Comm. F"? Each node of our cluster has two Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, each has 8 cores. When we are using 2 nodes, that is 2nodes * 2 cpus * 8 cores = 32 cores, we will be Using 32 MPI processes Using 1 OpenMP thread per MPI proces and Comm. coord. 241 19200 1.483 92.327 1.0 1.483s are spent on the coordinate communication When we are using 32 nodes, that is 32nodes * 2 cpus * 8 cores = 32 cores, we will be Using 512 MPI processes Using 1 OpenMP thread per MPI proces and Comm. coord. 3841 19200 2.094 2086.377 5.2 2.094s are spent on the coordinate communication 4. Why the time spent on communication of coordinate doesn't scale up as the cores are increasing? BR, Theo -- 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] REMD tutorial
Dear Mark Before, in following address you said: Google knows about two GROMACS REMD tutorials. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-January/086563.html Unfortunately, I could not find tutorials you mentioned. Also, in following address you said: I've added a section on replica-exchange to http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2007-December/031188.html . Is this link active, now? I have no access to this link. - I want to know Is there a tutorial for REMD like what is in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/. 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.
Re: [gmx-users] Simulating different pH values of water
Hi Tsjerk, Thanks for your reply. I want to study the effect of pH on the wetting behaviour of water nanodroplet on graphene, the contact angle especially.For acidic solution, H and Cl ions are included in the water model, whereas for a high pH solution, there will be Na and OH ions, for instance.I am aware that a lot of quantum mechanics studies have been put into obtaining the H2O-carbon interaction properties with MP2 level accuracy.Using polarisable force field in this case might capture the properties of the charged ions, however, I am concerned if this approach is appropriate.Any feedback is greatly appreciated.Regards,Kester- 원본 메일 -보낸사람 : Tsjerk Wassenaar 받는사람 : Discussion list for GROMACS us 받은날짜 : 2014년 8월 21일(목) 14:37:55제목 : Re: [gmx-users] Simulating different pH values of waterHi Kester, You do realize that water is odd quantum stuff, with oxygens going about in a sea of protons? The main way to move a free proton is to rewire the O-H bonds. What effects do you want investigate with your simulations? That determines what setup you need. Cheers, Tsjerk On Aug 21, 2014 6:46 AM, "Kester Wong" wrote: > Dear all, > > > This might not be relevant to MD technicalities, but I guess I should give > it a shot. > > > I would like to simulate water droplets at different pH values. > > However, knowing that a realistic system would need 180k water molecules > to mimic a pH of 7. > > Is there another viable approach that I can use to simulate water droplets > from low to high pH values? > > > The original question was posted here: > > > https://www.researchgate.net/post/How_can_I_calculate_the_number_of_molecules_with_respect_to_the_pH-value_in_solution?_tpcectx=subscription_feed#53f576d7d4c11805568b469c > > > > Regards, > > Kester > > -- > 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.
