[gmx-users] atoms are not part of any of the T-Coupling groups
Nidhi Katyal
nidhikatyal1989 at gmail.com
Thu Aug 7 08:16:23 CEST 2014
gmxcheck of my index file gives:
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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