On 11/7/13 6:27 AM, Arunima Shilpi wrote:
Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.
While running the following command
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
I got the following error. How to debug this error.
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
NOTE 1 [file npt_umbrella.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file npt_umbrella.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
WARNING 1 [file npt_umbrella.mdp]:
You are generating velocities so I am assuming you are equilibrating a
system. You are using Parrinello-Rahman pressure coupling, but this can
be unstable for equilibration. If your system crashes, try equilibrating
first with Berendsen pressure coupling. If you are not equilibrating the
system, you can probably ignore this warning.
ERROR 1 [file npt_umbrella.mdp]:
Generating velocities is inconsistent with attempting to continue a
previous run. Choose only one of gen-vel = yes and continuation = yes.
Either the run is starting for the first time (gen_vel = yes and continuation =
no) or it is a continuation (gen_vel = no and continuation = yes). In this
case, set continuation = no since it is the first run.
-Justin
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_E'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Velocities were taken from a Maxwell distribution at 300 K
There were 2 notes
There was 1 warning
-------------------------------------------------------
Program grompp_mpi_d, VERSION 4.6.3
Source code file:
/opt/apps/GROMACS/GROMACS-SOURCE/gromacs-4.6.3/src/kernel/gromp
p.c, line: 1593
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I request you to kindly help me to debug the error
Regards
Arunima
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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