[gmx-users] ./mdrun

[lin hen]

 constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
#nsteps              =  -1
nsteps              =  100
nstlist             =  0
ns_type             =  grid
rlist               =  0
coulombtype         =  cut-off
vdwtype             =  cut-off
rcoulomb            =  0
rvdw                =  0
pbc                 =  no
epsilon_rf          =  0
rgbradii            =  0
comm_mode           = angular
implicit_solvent    = GBSA
gb_algorithm        = OBC
gb_epsilon_solvent  = 78.3
sa_surface_tension  = 2.25936
nstxout             = 0
nstfout             = 0
nstvout             = 0
nstxtcout           = 0
nstlog              = 0
nstcalcenergy       = -1
nstenergy           = 0
tcoupl              = berendsen
tc-grps             = system
tau-t               = 0.1
ref-t               = 300

This is the .mdf file, even I modified the nsteps, it still comes with the same error:
 

Back Off! I just backed up ener.edr to ./#ener.edr.1#
 
WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator.
 

WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.
 

WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" option.
 

WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in OpenMM with the default Gromacs values.
 

Pre-simulation ~15s memtest in progress...done, no errors detected
starting mdrun 'Protein'
-1 steps, infinite ps.

 
the log file:
Input Parameters:
   integrator           = md
   nsteps               = -1
   init_step            = 0
   ns_type              = Grid
   nstlist              = 0
   ndelta               = 2
   nstcomm              = 10
   comm_mode            = Angular
   nstlog               = 0
   nstxout              = 0
   nstvout              = 0
   nstfout              = 0
   nstcalcenergy        = 10
   nstenergy            = 0

 
the nsteps is still -1, did I do something wrong?
 
Thanks a lot
 
YY



From: roland at utk.edu
Date: Tue, 9 Nov 2010 21:34:34 -0500
Subject: Re: [gmx-users] ./mdrun
To: gmx-users at gromacs.org

Hi,


as you output says. It infinite long trajectory. Either set a number of steps (in mdp file or with tpbconf) or set a maximum time with (mdrun -maxh)


Roland


On Tue, Nov 9, 2010 at 9:03 PM, lin hen <cuteyy83 at live.com> wrote:


Hi,
 
I am using the dhfr gpu benchmark with mdrun-gpu:dhfr-solv-RF-2nm.bench.
export LD_LIBRARY_PATH=/path to OPENMM lib and cuda lib/
export OPENMM_PLUGIN=/path to OPENMM lib plugins/
it shows:
Back Off! I just backed up md.log to ./#md.log.1#
Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
Back Off! I just backed up ener.edr to ./#ener.edr.1#
WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator.

WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.

WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" option.

Pre-simulation ~15s memtest in progress...done, no errors detected
starting mdrun 'Protein in water'
-1 steps, infinite ps.

 
and keeps this status for at least one hour, did I miss something? or do somthing wrong?
 
thanks,
 
yy

--
gmx-users mailing list    gmx-users at 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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309

-- gmx-users mailing list gmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101111/7f9a4659/attachment.html>