[gmx-users] Re: Energy minimization has stopped....

2013-11-05 Thread Kalyanashis 
I have given my .mdp file,
; title =  trp_drg
warning =  10
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002 ; ps !
nsteps  =  100 ; total 2000.0 ps.
nstcomm =  100
nstxout =  250 ; ouput coordinates every 0.5 ps
nstvout =  1000 ; output velocities every 2.0 ps
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  100
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdwtype =  cut-off
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes
; Berendsen temparature coupling is on
Tcoupl  =  berendsen
tau_t   =  1.01.0-0.1  1.0   1.0
tc_grps =  SOLNA protein   OMP   CL
ref_t   =  300300300   300   300
; Pressure coupling is on
pcoupl  =  berendsen ; Use Parrinello-Rahman for research work
pcoupltype  =  isotropic ; Use semiisotropic when working with
membranes
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
refcoord-scaling=  all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529


And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.
Thank you so much..



On Tue, Nov 5, 2013 at 5:29 PM, jkrie...@mrc-lmb.cam.ac.uk [via GROMACS] <
ml-node+s5086n5012256...@n6.nabble.com> wrote:

> What does your curve look like? What parameters are you using in the mdp?
> How big is your system and what kind of molecules are in there? Providing
> this kind of information would help people work out what the problem is.
>
> Then again it may be ok that the minimisation has converged without
> reaching the Fmax cutoff. 2 is a large number of steps.
>
> > Hi,
> >   Whenever I am trying to do position retrained MD run, It has been
> > stopped
> > at middle of the MD run. I have given the following error. Can you
> please
> > suggest me something to resolve this error?
> > Energy minimization has stopped, but the forces havenot converged to the
> > requested precision Fmax < 100 (whichmay not be possible for your
> system).
> > It
> > stoppedbecause the algorithm tried to make a new step whose sizewas too
> > small, or there was no change in the energy sincelast step. Either way,
> we
> > regard the minimization asconverged to within the available machine
> > precision,given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, butthis is often
> not
> > needed for preparing to run moleculardynamics.
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 20514 steps,
> > but did not reach the requested Fmax < 100.
> > Potential Energy  = -9.9811250e+06
> > Maximum force =  6.1228135e+03 on atom 15461
> > Norm of force =  1.4393512e+01
> >
> > gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)
> >
> > --
> > Kalyanashis Jana
> > email: [hidden email]
> > --
> > gmx-users mailing list[hidden 
> > email]
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Re: [gmx-users] Re: Energy minimization has stopped....

2013-11-05 Thread Justin Lemkul 



On 11/5/13 7:19 AM, Kalyanashis wrote:

I have given my .mdp file,
; title =  trp_drg
warning =  10
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002 ; ps !
nsteps  =  100 ; total 2000.0 ps.
nstcomm =  100
nstxout =  250 ; ouput coordinates every 0.5 ps
nstvout =  1000 ; output velocities every 2.0 ps
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  100
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdwtype =  cut-off
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes
; Berendsen temparature coupling is on
Tcoupl  =  berendsen
tau_t   =  1.01.0-0.1  1.0   1.0
tc_grps =  SOLNA protein   OMP   CL
ref_t   =  300300300   300   300


These settings make no sense.  Please read 
http://www.gromacs.org/Documentation/Terminology/Thermostats.



; Pressure coupling is on
pcoupl  =  berendsen ; Use Parrinello-Rahman for research work
pcoupltype  =  isotropic ; Use semiisotropic when working with
membranes
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
refcoord-scaling=  all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529


And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.


The run crashes because your energy minimization effectively failed.

-Justin

--
==

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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