Re: [gmx-users] how to make molecular model with both ion channel and lipid bilayer?
Charmm-gui.org could help you. Bests, Hadi On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong" wrote: Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I can find the 'pdb' files of ion channels, but I have no idea how to combine them. Thanks all, Tong -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List (http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List) before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists (http://www.gromacs.org/Support/Mailing_Lists) * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users (https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users) or send a mail to gmx-users-requ...@gromacs.org (mailto: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] bend angles of a kink motif
Dear Users Can we calculate the bend angle of a kink motif in an alpha helix from a .xtc file? Thanks a lot. H.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] cpu gpu performance
Dear Users, I'm simulating a membrane protein system with approximately 185000 atoms with an Intel Corei7 cpu. I have two questions: 1. Performance of my simulations is about 1.8ns/day. Is this performance normal for such a system? Or my simulations are suffering from lack of performance? 2. when I use mdrun command with -nb gpu, the performance reduces to 1.3ns/day!! How can I resolve this problem? my mdp file parameters are: integrator = md dt = 0.002 nsteps = 1500 nstlog = 1000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstcalcenergy = 100 nstenergy = 1000 nstxtcout= 2000; xtc compressed trajectory output every 2 ps ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 0.9 rvdw= 1.0 ; tcoupl = berendsen tc_grps = PROT NPROT SOL_ION tau_t = 1.01.0 1.0 ref_t = 303.15 303.15 303.15 ; pcoupl = berendsen pcoupltype = semiisotropic tau_p = 5.0 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = PROT NPROT SOL_ION ; refcoord_scaling= com and at the end of log file when I use gpu I have: NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - NB VdW [VF]65.721780 65.722 0.0 Pair Search distance check 354.0956963186.861 0.1 NxN QSTab Elec. + LJ [F] 78361.108992 4153138.77792.2 NxN QSTab Elec. + LJ [VF]1094.086656 88621.019 2.0 1,4 nonbonded interactions 92.3662448312.962 0.2 Calc Weights 273.4639389844.702 0.2 Spread Q Bspline 5833.897344 11667.795 0.3 Gather F Bspline 5833.897344 35003.384 0.8 3D-FFT 19866.277292 158930.218 3.5 Solve PME5.271904 337.402 0.0 Shift-X 2.625854 15.755 0.0 Bonds 14.647068 864.177 0.0 Propers106.938468 24488.909 0.5 Impropers1.961496 407.991 0.0 Virial 4.877756 87.800 0.0 Stop-CM 1.125366 11.254 0.0 Calc-Ekin9.753172 263.336 0.0 Lincs 20.1621961209.732 0.0 Lincs-Mat 129.913632 519.655 0.0 Constraint-V96.517170 772.137 0.0 Constraint-Vir 4.084834 98.036 0.0 Settle 18.7309266050.089 0.1 (null) 0.653184 0.000 0.0 - Total 4503897.712 100.0 - 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 On 1 MPI rank, each using 8 OpenMP threads Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Neighbor search18 14 0.301 8.175 0.4 Launch GPU ops.18486 0.063 1.719 0.1 Force 18486 4.351118.334 6.3 PME mesh 18486 8.685236.229 12.5 Wait GPU local 18486 52.321 1423.144 75.5 NB X/F buffer ops. 18958 0.389 10.571 0.6 Write traj.18 1 0.265 7.221 0.4 Update 18486
[gmx-users] -vsite hydrogen
Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option? Best wishes, H.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] POPC with CHARMM
Dear Users, I want to simulate POPC membrane with CHARMM ff using GROMACS 4.6.5. but in CHARMM ff directory, there is no popc itp file. How can I proceed? Best, H.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] potassium ion in GROMOS
Dear users, How can we define potassium ion in GROMOS ions.itp file? Best, H.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] Electrostatic energy between two groups of atoms
Dear users, Can we calculate electrostatic energy between two groups of atoms in GROMACS? Best wishes, H.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] distance tracking
Dear GROMACS users, Is it possible to track H-bonding or distance between two certain atoms in GROMACS? Best wishes, Hadi -- 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] Atom was not found
Dear Users, I want to simulate a protein by GROMACS. When I use pdb2gmx command, topology and other files are produced from my pdb file. But when I define a box for my protein by editconf before pdb2gmx, I face with this fatal error: Atom OXT in residue VAL 226 was not found in rtp entry VAL with 8 atoms while sorting atoms of course as I said, without defining a box, pdb2gmx is ok!! Thanks for any help, Hadi -- 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
Dear all, In one of my simulations when I use the command mdrun -v -deffnm nvt I face with this fatal error: Too many LINCS warnings (1056) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I dont know what does it mean and how can I fix it! Best wishes, Hadi -- 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_membed itp file
Dear GROMACS users, I'm a new GROMACS user and I would like to apologize for my basic question. I want to use g_membed to insert protein in membrane according to Wolf's paper manual. I have the pdb, mdp and top files in my directory, but when I enter the command grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr I face with this fatal error: Fatal error: Topology include file ffoplsaalipid.itp not found Now I want to know how can I create this itp file? 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] g_membed itp file
Dear GROMACS users, I'm a new GROMACS user and I would like to apologize for my basic question. I want to use g_membed to insert protein in membrane according to Wolf's paper manual. I have the pdb, mdp and top files in my directory, but when I enter the command grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr I face with this fatal error: Fatal error: Topology include file ffoplsaalipid.itp not found Now I want to know how can I create this itp file? 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.
