[gmx-users] g_select

Wed Mar 26 18:40:36 CET 2014

On 3/26/14, 11:57 AM, Josip Lovrić wrote:
> 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

Are you sure this is the value you want?  Your PME grid is going to be about 5x 
coarser than the default settings, so your run will be much faster, but less 
accurate...

> ; 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
>

You can't use groups across two index files.  I assume you are supplying 
index.ndx to grompp (showing the actual command you're using helps), which 
leaves "notattached" out in the cold and undefined.  You need all necessary 
index groups in a single index file.

-Justin

>
>
>
> 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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-- 
==================================================

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

==================================================