[gmx-users] Freezing problem
Dr. Vitaly Chaban
vvchaban at gmail.com
Fri Nov 22 14:18:54 CET 2013
probably there should be three "freeze values" standing for Cartesions
directions. What I see below is "YYY" with no spaces between.
Dr. Vitaly V. Chaban
On Fri, Nov 22, 2013 at 1:56 PM, Debashis Sahu
<debashis.sahu87 at gmail.com> wrote:
> Dear all,
> I can not freeze a group in mdrun in gas phase. Actually the
> following error is coming in the grompp step................
>
> Program grompp, VERSION 4.6.3
> Source code file: /compile/gromacs-4.6.3/src/kernel/readir.c, line: 3192
>
> Fatal error:
> Invalid Freezing input: 1 groups and 1 freeze values
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I have tried also by taking the index file in grompp step, but same error
> coming. My index file and mdp file are listed below. I want to freeze ABC
> group while DDD will be free. In the topology I have inserted the molecule
> DDD as DDD.itp..........If any mistake in the files there, plz help me.
>
> *index.ndx file:*
>
> [ System ]
> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
> 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
> 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
> 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
> 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
> 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
> 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
> 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
> 121 122 123 124 125 126 127 128 129
> [ Other ]
> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
> 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
> 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
> 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
> 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
> 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
> 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
> 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
> 121 122 123 124 125 126 127 128 129
> [ ABC ]
> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
> 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
> 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
> 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
> 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
> 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
> 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
> 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
> 121 122 123 124 125 126
> [ DDD ]
> 127 128 129
>
> *mdp file:*
>
> title = NVT equilibration
> define = -DPOSRES ; position restrain the solute
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 50000 ; 2 * 50000 = 100 ps
> 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 = no ; 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
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; 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
> freezegrps = ABC
> freezedim =YYY
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = ABC DDD ; two coupling groups - more accurate
> tau_t = 0.1 0.1 ; 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
> --
> *Debashis Sahu*
> *Central Salt and Marine Chemical Research Institute*
> *Bhavnagar, Gujarat*
> *India, 364002.*
> --
> 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-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list