On 2/27/13 8:53 AM, jesmin jahan wrote:
Thanks Crasten for your reply.
Even after removing comment, I am getting the same error message.
You need to re-create the .tpr file after modifying the .mdp file. If you're
getting the same error, you're using the wrong .tpr file.
Do you have any sample .mdp file that can be used while using MPI+OPENMP?
I am trying to compute the GB energy (implicit solvent based).
Note that implicit solvent calculations can be run on no more than 2 processors.
You'll get a fatal error if you try to use more.
-Justin
On Wed, Feb 27, 2013 at 2:59 AM, Carsten Kutzner <ckut...@gwdg.de> wrote:
Hi,
On Feb 27, 2013, at 6:55 AM, jesmin jahan <shraba...@gmail.com> wrote:
Dear Gromacs Users,
I am trying to run the following command on gromacs 4.6
mdrun -ntmpi 2 -ntomp 6 -s imd.tpr
But I am getting the following error
OpenMP threads have been requested with cut-off scheme Group, but
these are only supported with cut-off scheme Verlet
Does any one know a solution to the problem?
I am using the following .mdp file
constraints = none
integrator = md
;cutoff-scheme = Verlet
yes, as the note says, use the verlet cutoff scheme (by deleting the ";")
Carsten
pbc = no
dt = 0.001
nsteps = 0
rcoulomb = 300
rvdw = 300
rlist = 300
nstgbradii = 300
rgbradii = 300
implicit_solvent = GBSA
gb_algorithm = HCT ;
sa_algorithm = None
gb_dielectric_offset = 0.02
;optimize_fft = yes
energygrps = protein
Please let me know what to change so that it runs perfectly!
Thanks,
Jesmin
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
