On 9/18/18 11:55 AM, Mario Andres Rodriguez Pineda wrote:
when i try to run mdrun they start showing this:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= -2.46652e+06 Fmax= 6.62812e+05, atom=
2881
Step= 1, Dmax= 1.0e-02 nm, Epot= -2.48761e+06 Fmax= 6.51531e+05, atom=
2881
Step= 2, Dmax= 1.2e-02 nm, Epot= -2.51019e+06 Fmax= 6.38455e+05, atom=
2881
Step= 3, Dmax= 1.4e-02 nm, Epot= -2.53494e+06 Fmax= 6.23418e+05, atom=
2881
Step= 4, Dmax= 1.7e-02 nm, Epot= -2.56238e+06 Fmax= 6.06180e+05, atom=
2881
Step= 5, Dmax= 2.1e-02 nm, Epot= -2.59295e+06 Fmax= 5.86164e+05, atom=
2881
Step= 6, Dmax= 2.5e-02 nm, Epot= -2.62704e+06 Fmax= 5.62063e+05, atom=
2881
Step= 7, Dmax= 3.0e-02 nm, Epot= -2.66494e+06 Fmax= 5.31531e+05, atom=
2881
Step= 8, Dmax= 3.6e-02 nm, Epot= -2.70684e+06 Fmax= 4.91124e+05, atom=
2881
Step= 9, Dmax= 4.3e-02 nm, Epot= -2.75366e+06 Fmax= 4.36752e+05, atom=
2881
Step= 10, Dmax= 5.2e-02 nm, Epot= -2.80104e+06 Fmax= 3.67647e+05, atom=
2881
Step= 11, Dmax= 6.2e-02 nm, Epot= -2.84787e+06 Fmax= 4.16988e+05, atom=
2883
Step= 12, Dmax= 7.4e-02 nm, Epot= -2.86654e+06 Fmax= 2.20175e+06, atom=
2903
Step= 13, Dmax= 8.9e-02 nm, Epot= -2.88894e+06 Fmax= 2.80767e+05, atom=
2883
Step= 14, Dmax= 1.1e-01 nm, Epot= -2.95328e+06 Fmax= 1.33061e+05, atom=
2883
Step= 15, Dmax= 1.3e-01 nm, Epot= -3.03044e+06 Fmax= 2.52114e+05, atom=
2881
step 16: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
tMPI error: Receive buffer size too small for transmission (in valid comm)
Abort (core dumped)
I don't understand what happend. Please can you help me? How i can reduce
timestep?
You're stuck at a huge force on atom 2881. Check on what that is, what's
around it, etc.
If necessary, you can reduce emstep (energy minimization step size, not
dt which is the time step in MD) to a smaller value. I don't think
that's going to be an effective fix here. EM is clearly stuck trying to
resolve something bad in your structure and it can't do it.
-Justin
Em ter, 18 de set de 2018 às 08:36, Justin Lemkul <jalem...@vt.edu>
escreveu:
On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote:
These were the errors until the moment of executing the minimization:
After adding ions grompp:
NOTE 1 [file topol.top, line 37566]:
System has non-zero total charge: -18.999999
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
minimization mdrun
step 16: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
tMPI error: Receive buffer size too small for transmission (in valid
comm)
Abort (core dumped)
In attach send you the mdp archive for minimization run.
The mailing list does not allow attachments.
Use the -v flag of mdrun to track the energy and forces at every step
until the crash to see what's going on and where the maximum force is
acting. There's probably a bad contact somewhere that can't be relaxed
and you need to investigate why that's happening.
-Justin
Thanks for your help
Em seg, 17 de set de 2018 às 19:56, Justin Lemkul <jalem...@vt.edu>
escreveu:
On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote:
Hi everyone.
I'm trying simulate a protein in water followin lysozyme tutorial using
gromacs 2016.3. When triying minimize the system after make the box and
insert a salt concentration the minimization has been stoped sendingme
the
following error:
step 16: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
tMPI error: Receive buffer size too small for transmission (in valid
comm)
Abort (core dumped)
Water SETTLE problems are not unusual in energy minimization and are
often resolved. If, however, such a message immediately precedes a
failure, then you have a serious problem with either the coordinates or
topology. mdrun prints out which atom is experiencing the maximum force,
so start by looking there, as well as reviewing your notes about what
warnings pdb2gmx or grompp may have issued (but surely you wouldn't have
ignored any, right? :).
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
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Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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