[gmx-users] g_select
Josip Lovrić
josip7lovric at gmail.com
Thu Mar 27 09:44:04 CET 2014
Hello,
for the PME gromacs was giving me warnings about PME load so I putted that
values to fix warnings. I did not know this could affect accuracy.
For the .ndx file, actually I was supplying select.ndx and it can be seen
in previous mail.
I was trying to put both select.ndx and index.ndx in -n flag but it is not
possible so I need to put it both in one .ndx file.
Thank you very much, you deserve chocolate :-).
2014-03-26 18:38 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list