[gmx-users] Freezing problem
Debashis Sahu
debashis.sahu87 at gmail.com
Sat Nov 23 11:38:18 CET 2013
Thanks Dr. Chaban, I got the point.
On Fri, Nov 22, 2013 at 6:47 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:
> 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.*
> > --
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--
*Debashis Sahu*
*Central Salt and Marine Chemical Research Institute*
*Bhavnagar, Gujarat*
*India, 364002.*
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