[gmx-users] g_select

[Josip Lovrić]

Thank you for the tips!

This is my .mdp file:

title = nacl
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 2000000 ; 2 * 500000 = 1000 ps, 1 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = no ; Restarting after NPT
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 = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.6 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = system ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 335 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Berendsen;Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-6 ; isothermal compressibility of NaCl, bar^-1
; 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 = 335 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed

energygrps = Na Cl MOL notattached

Contents of index file index.ndx
--------------------------------------------------
Nr.   Group               #Entries   First    Last
   0  System                 16800       1   16800
   1  Ion                     5600       1    5600
   2  Na                      2800       1    2800
   3  Cl                      2800    2801    5600
   4  MOL                    11200    5601   16800
   5  Other                  11200    5601   16800
   6  Na                      2800       1    2800
   7  Cl                      2800    2801    5600
   8  MOL                    11200    5601   16800

Contents of index file select.ndx
--------------------------------------------------
Nr.   Group               #Entries   First    Last
   0  notattached_0.000       3050    5901   16800




2014-03-26 16:36 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 3/26/14, 11:30 AM, Josip Lovrić wrote:
>
>> Hello,
>>
>> I managed to create notattached group but now it is not recognizing system
>> group when I compile it with gromp.
>> I get this answer:
>>
>> Fatal error:
>> Group system referenced in the .mdp file was not found in the index file.
>> Group names must match either [moleculetype] names or custom index group
>> names, in which case you must supply an index file to the '-n' option
>> of grompp.
>>
>> This is my grompp line:
>> grompp_mpi -f md.mdp -c nacl_palm_md_224.gro -p topol_nc.top -o
>> nacl_palm_md_224_na.tpr -n select.ndx
>>
>> group system is defined like this in .top file:
>>
>> [ system ]
>> ; Name
>> NaCl
>>
>> P.S.
>> Feel free to ask me more information, I am quite new in gromacs and I am
>> not sure if I am giving you all the information.
>>
>>
> The [system] directive just gives a name for output coordinate files and
> such. It is not equivalent to the "System" index group.
>
> When reporting errors with groups, index files, etc, you need to provide
> the text of the .mdp file and, at minimum, a listing of the groups in the
> index file, e.g. from gmxcheck.
>
>
> -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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