[gmx-users] atoms are not part of any of the T-Coupling groups
Justin Lemkul
jalemkul at vt.edu
Thu Aug 7 14:58:24 CEST 2014
On 8/7/14, 12:16 AM, Nidhi Katyal wrote:
> gmxcheck of my index file gives:
>
It looks like you have created the index file before adding any solvent. Hence
you have 215000+ atoms that are not accounted for. You need to generate index
files after the system is complete. You can, of course, re-use your custom
groups, but they need to be used in addition to sensible groups for everything else.
-Justin
> Contents of index file index.ndx
> --------------------------------------------------
> Nr. Group #Entries First Last
> 0 System 2230 1 2230
> 1 Protein 2226 1 2226
> 2 Protein-H 2226 1 2226
> 3 C-alpha 308 3 2218
> 4 Backbone 922 1 2219
> 5 MainChain 1232 1 2226
> 6 MainChain+Cb 1488 1 2226
> 7 MainChain+H 1232 1 2226
> 8 SideChain 994 8 2225
> 9 SideChain-H 994 8 2225
> 10 Prot-Masses 2226 1 2226
> 11 non-Protein 4 2227 2230
> 12 Ion 4 2227 2230
> 13 CU 2 2227 2229
> 14 ZN 2 2228 2230
> 15 r_131_&_chA 8 956 963
> 16 r_131_&_chB 8 2069 2076
> 17 r_132 11 1207 1217
> 18 r_286 11 2611 2621
> 19 CA_chA_r131 1 1209 1209
> 20 CA_chB_r131 1 2613 2613
>
> and following are the contents of my .mdp file:
>
> title = Umbrella pulling simulation
> define = -DPOSRES_CA_chA_r131
> ; Run parameters
> integrator = md
> dt = 0.002
> tinit = 0
> nsteps = 250000 ; 500 ps
> nstcomm = 10
> ; Output parameters
> nstxout = 5000 ; every 10 ps
> nstvout = 5000
> nstfout = 500
> nstxtcout = 500 ; every 1 ps
> nstenergy = 500
> ; Bond parameters
> constraint_algorithm = lincs
> constraints = all-bonds
> continuation = yes ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist = 5
> ns_type = grid
> rlist = 1.4
> rcoulomb = 1.4
> rvdw = 1.4
> ; PME electrostatics parameters
> coulombtype = PME
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = Nose-Hoover
> tc_grps = Protein Non-Protein
> tau_t = 0.5 0.5
> ref_t = 310 310
> ; Pressure coupling is on
> Pcoupl = Parrinello-Rahman
> pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
> ; Long-range dispersion correction
> DispCorr = EnerPres
> ; Pull code
> pull = umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim = Y N N
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group0 = CA_chA_r131
> pull_group1 = CA_chB_r131
> pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 4200 ; kJ mol^-1 nm^-2
>
> Thanks in advance.
>
> Nidhi
>
>
>
>
> On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/6/14, 3:46 AM, Nidhi Katyal wrote:
>>
>>> Hello all,
>>>
>>> I am working on protein with two chains. I would like to restrain one atom
>>> of one chain while doing steered MD. For the same reason, I have created
>>> an
>>> index file that includes that atom, then created its posre.itp file and
>>> finally included following lines at the end of topol_Protein_chainA.itp:
>>>
>>> ; Include Position restraint file
>>> #ifdef POSRES_CA_chA_r131
>>> #include "posre.itp"
>>> #endif
>>>
>>> I am also pasting a small section of my topol.top file:
>>>
>>>
>>> ; Include forcefield parameters
>>> #include "gromos53a6.ff/forcefield.itp"
>>>
>>> ; Include chain topologies
>>> #include "topol_Protein_chain_A.itp"
>>> #include "topol_Protein_chain_B.itp"
>>> #include "topol_Ion_chain_A2.itp"
>>> #include "topol_Ion_chain_B2.itp"
>>>
>>> ; Include water topology
>>> #include "gromos53a6.ff/spc.itp"
>>>
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ; i funct fcx fcy fcz
>>> 1 1 1000 1000 1000
>>> #endif
>>>
>>> After carrying out NPT equilibration, when I run following command:
>>>
>>> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
>>> -o pull.tpr
>>>
>>> as given in tutorial:
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>> gmx-tutorials/umbrella/05_pull.html
>>>
>>> I am getting following error:
>>> 215400 atoms are not part of any of the T-Coupling groups
>>>
>>> Since my pull.mdp file as the same as given in tutorial, my coupling
>>> groups are Protein and Non-Protein.
>>> I suspect there is something wrong while adding restraints using
>>> include file mechanism. Please help me resolve the problem.
>>>
>>>
>> The error is not a result of the #include mechanism; it's a problem in the
>> group definitions, either in the .mdp file or in the index file. Without
>> the full text of the .mdp and the gmxcheck output of the index.ndx file,
>> there's little to suggest.
>>
>> -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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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--
==================================================
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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