On 1/8/16 12:50 AM, shagun krishna wrote:
Hiii Justin,
Thank you very much for your help. After changing my settings according to
your suggestions I am not getting the previous errors. :) The grompp
command ran successfully, but when I am evoking the mdrun using rerun
option I am getting a fatal error. Please have a look at my terminal
window. And let me know how to solve this. What I guess that probably I
should increase my box size. My ligand has almost 55 atom.
You're post-processing an existing system; you can't increase the box size and
make anything work. The error is related to domain decomposition, which you
don't need during a rerun anyway, so just do the rerun on a single core (or
maybe via OpenMP, but I don't know if that works). Just avoid MPI, which
triggers DD.
-Justin
cbb@cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ grompp -f
md_SOL_rerun.mdp -c equil.gro -o md_sol_rerun.tpr
:-) G R O M A C S (-:
:-) VERSION 4.6.5 (-:
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
NOTE 1 [file md_SOL_rerun.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 168 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'M_R'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
NOTE 2 [file topol.top]:
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
Analysing residue names:
There are: 1 Other residues
There are: 859 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group M_R is 106.94
Number of degrees of freedom in T-Coupling group SOL is 5151.06
Largest charge group radii for Van der Waals: 0.370, 0.293 nm
Largest charge group radii for Coulomb: 0.370, 0.307 nm
NOTE 3 [file md_SOL_rerun.mdp]:
The sum of the two largest charge group radii (0.676770) is larger than
rlistlong (1.400000) - rcoulomb (0.900000).
With exact cut-offs, better performance can be obtained with
cutoff-scheme = Verlet, because it does not use charge groups at all.
This run will generate roughly 199 Mb of data
There were 3 notes
Back Off! I just backed up md_sol_rerun.tpr to ./#md_sol_rerun.tpr.2#
gcq#139: "We All Get the Flu, We All Get Aids" (LIVE)
cbb@cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ mdrun -s
md_sol_rerun.tpr -rerun md_sol.xtc
:-) G R O M A C S (-:
Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
:-) VERSION 4.6.5 (-:
:-) mdrun (-:
Back Off! I just backed up md.log to ./#md.log.2#
Reading file md_sol_rerun.tpr, VERSION 4.6.5 (single precision)
Using 4 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine,
which is better)
Back Off! I just backed up traj.trr to ./#traj.trr.2#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting md rerun 'M_R in water', reading coordinates from input trajectory
'md_sol.xtc'
Reading frame 0 time 0.000
WARNING: Some frames do not contain velocities.
Ekin, temperature and pressure are incorrect,
the virial will be incorrect when constraints are present.
Reading frame 140 time 280.000
DD cell 0 0 0: Neighboring cells do not have atoms: 45
DD cell 2 0 0: Neighboring cells do not have atoms: 32
-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/domdec_con.c, line:
722
Fatal error:
DD cell 0 0 0 could only obtain 11 of the 12 atoms that are connected via
constraints from the neighboring cells. This probably means your constraint
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or lincs-order.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thanks a ton...I am really very thankful to you... :)
Best regards,
Shagun
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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