[gmx-users] Error in Umbrella sampling command

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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