On 8/22/18 2:26 AM, RAHUL SURESH wrote:
Dear Bratin,
See documentation for installation of gromacs with double precision. You
can always have gromacs installed with various versions. There is no need
to recompile, just have another source with double precision. Try it if it
doesn’t work better you will other good advices too. Hope gromacs don’t
suggest if it’s unlikely useful.
Thank you
More, I think here everyone suggest based on their own experiences.
Yes, but great care is needed to not tell someone to do something
unproductive. The magnitude of forces the OP reports are not going to be
resolved by double precision code. GROMACS programs can't think for the
user, so error messages often include generic advice that *might* be
relevant. For mdrun, if convergence criteria aren't met, that suggestion
is printed. But forces of 10^7 clearly indicate something pathological
with the system.
-Justin
On Wed, 22 Aug 2018 at 11:26 AM, Alex <nedoma...@gmail.com> wrote:
Before you go on to listen to bad advice and recompile Gromacs in double
precision, the errors you're getting during minimization are _much_ more
likely to come from a bad initial state of your system.
Alex
On 8/21/2018 11:51 PM, Bratin Kumar Das wrote:
Dear Rahul,
Thinking you for your suggestion. I don't know how to
use double precision. can you please share some link for that
On Wed, Aug 22, 2018 at 11:02 AM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:
Hi.
As gromacs suggested try double precision.
Thank you
On Wed, 22 Aug 2018 at 10:36 AM, Bratin Kumar Das <
177cy500.bra...@nitk.edu.in> wrote:
Dear All,
I am simulating a membrane protein which have
extracellular
domain, TMD(trans membrane domain) and a extracellular domain. After
packing the POPC molecules around the protein, I solvated the system.
I
removed all the waters from the POPC portion and added ions to
neutralise
the system. During the energy minimisation the following errors are
coming
GROMACS is written by:
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Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit
Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios
Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per
Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik
Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland
Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2016.5
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir:
/home/workstation/Documents/GROMACS_projects/g_protein_
class_b_sim_gromacs
Command line:
gmx mdrun -v -s energy_minim.tpr -deffnm energy_minim
Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
Hardware topology: Basic
Reading file energy_minim.tpr, VERSION 2016.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+02
Number of steps = 50000
WARNING: Listed nonbonded interaction between particles 6334 and 6358
at distance 4.241 which is larger than the table limit 2.200 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the
table-extension
distance in the mdp file if you are really sure that is the reason.
Step= 0, Dmax= 1.0e-02 nm, Epot= 7.97855e+11 Fmax= 2.74610e+14,
atom=
3647
Step= 1, Dmax= 1.0e-02 nm, Epot= 4.26666e+09 Fmax= 7.52956e+11,
atom=
3647
Step= 2, Dmax= 1.2e-02 nm, Epot= 1.33982e+08 Fmax= 1.49946e+10,
atom=
2036
Step= 3, Dmax= 1.4e-02 nm, Epot= 2.28974e+07 Fmax= 9.37337e+08,
atom=
3647
Step= 4, Dmax= 1.7e-02 nm, Epot= 4.48769e+06 Fmax= 3.34151e+07,
atom=
13662
Step= 5, Dmax= 2.1e-02 nm, Epot= 3.37628e+06 Fmax= 3.28448e+06,
atom=
3645
Step= 6, Dmax= 2.5e-02 nm, Epot= 3.10830e+06 Fmax= 1.71706e+06,
atom=
6356
Step= 7, Dmax= 3.0e-02 nm, Epot= 2.96689e+06 Fmax= 1.68266e+06,
atom=
6356
Step= 8, Dmax= 3.6e-02 nm, Epot= 2.83736e+06 Fmax= 1.63442e+06,
atom=
6356
Step= 9, Dmax= 4.3e-02 nm, Epot= 2.70582e+06 Fmax= 1.59406e+06,
atom=
6356
Step= 10, Dmax= 5.2e-02 nm, Epot= 2.57016e+06 Fmax= 6.10145e+06,
atom=
68387
step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step11b.pdb to ./#step11b.pdb.3#
Back Off! I just backed up step11c.pdb to ./#step11c.pdb.3#
Wrote pdb files with previous and current coordinates
Step= 12, Dmax= 3.1e-02 nm, Epot= 2.52760e+06 Fmax= 1.57824e+06,
atom=
6356
Step= 13, Dmax= 3.7e-02 nm, Epot= 2.41877e+06 Fmax= 3.20637e+06,
atom=
68387
Step= 14, Dmax= 4.5e-02 nm, Epot= 2.39232e+06 Fmax= 1.51717e+06,
atom=
6356
Step= 15, Dmax= 5.3e-02 nm, Epot= 2.25380e+06 Fmax= 5.76014e+06,
atom=
6358
Step= 16, Dmax= 6.4e-02 nm, Epot= 2.23708e+06 Fmax= 1.48175e+06,
atom=
6358
Step= 17, Dmax= 7.7e-02 nm, Epot= 2.00861e+06 Fmax= 1.06806e+06,
atom=
6358
Step= 18, Dmax= 9.2e-02 nm, Epot= 1.89692e+06 Fmax= 3.69159e+06,
atom=
6358
Step= 19, Dmax= 1.1e-01 nm, Epot= 1.75521e+06 Fmax= 1.19996e+06,
atom=
6358
Step= 20, Dmax= 1.3e-01 nm, Epot= 1.47811e+06 Fmax= 3.67398e+06,
atom=
8027
Step= 22, Dmax= 8.0e-02 nm, Epot= 1.45234e+06 Fmax= 2.18802e+06,
atom=
6356
Step= 23, Dmax= 9.6e-02 nm, Epot= 1.42778e+06 Fmax= 1.22861e+07,
atom=
6285
Step= 24, Dmax= 1.2e-01 nm, Epot= 1.39384e+06 Fmax= 1.16780e+06,
atom=
6358
Step= 26, Dmax= 6.9e-02 nm, Epot= 1.22389e+06 Fmax= 1.01826e+06,
atom=
6356
Step= 27, Dmax= 8.3e-02 nm, Epot= 1.05663e+06 Fmax= 8.23676e+05,
atom=
6358
Step= 28, Dmax= 9.9e-02 nm, Epot= 9.00862e+05 Fmax= 4.41513e+06,
atom=
6285
Step= 30, Dmax= 6.0e-02 nm, Epot= 8.78491e+05 Fmax= 9.03216e+05,
atom=
6356
Step= 31, Dmax= 7.2e-02 nm, Epot= 7.32139e+05 Fmax= 8.20015e+05,
atom=
6285
Step= 32, Dmax= 8.6e-02 nm, Epot= 6.90801e+05 Fmax= 7.16405e+06,
atom=
6285
Step= 33, Dmax= 1.0e-01 nm, Epot= 6.01138e+05 Fmax= 7.02733e+05,
atom=
6358
Step= 34, Dmax= 1.2e-01 nm, Epot= 4.08422e+05 Fmax= 6.19177e+05,
atom=
6356
Step= 35, Dmax= 1.5e-01 nm, Epot= 2.39180e+05 Fmax= 8.93953e+06,
atom=
6356
Step= 36, Dmax= 1.8e-01 nm, Epot= 1.77754e+05 Fmax= 4.65642e+05,
atom=
6356
Step= 37, Dmax= 2.1e-01 nm, Epot= 9.49342e+03 Fmax= 7.65517e+06,
atom=
6356
Step= 39, Dmax= 1.3e-01 nm, Epot= -1.01297e+05 Fmax= 3.21496e+05,
atom=
6357
step 40: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step40b.pdb to ./#step40b.pdb.2#
Back Off! I just backed up step40c.pdb to ./#step40c.pdb.2#
Wrote pdb files with previous and current coordinates
Step= 41, Dmax= 7.7e-02 nm, Epot= -1.70370e+05 Fmax= 1.79323e+06,
atom=
6532
Step= 43, Dmax= 4.6e-02 nm, Epot= -1.94365e+05 Fmax= 2.98882e+05,
atom=
6357
Step= 44, Dmax= 5.5e-02 nm, Epot= -2.50520e+05 Fmax= 1.07420e+06,
atom=
6551
Step= 45, Dmax= 6.6e-02 nm, Epot= -2.65915e+05 Fmax= 2.73365e+05,
atom=
6357
Step= 46, Dmax= 8.0e-02 nm, Epot= -3.58321e+05 Fmax= 2.46276e+05,
atom=
6357
Step= 47, Dmax= 9.6e-02 nm, Epot= -4.33618e+05 Fmax= 6.66792e+05,
atom=
6285
Step= 48, Dmax= 1.1e-01 nm, Epot= -4.45739e+05 Fmax= 6.65627e+05,
atom=
6285
step 49: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step49b.pdb to ./#step49b.pdb.2#
Back Off! I just backed up step49c.pdb to ./#step49c.pdb.2#
Wrote pdb files with previous and current coordinates
Step= 50, Dmax= 6.9e-02 nm, Epot= -4.86014e+05 Fmax= 3.28474e+05,
atom=
6285
Step= 51, Dmax= 8.3e-02 nm, Epot= -5.04696e+05 Fmax= 2.93639e+06,
atom=
6272
Step= 52, Dmax= 9.9e-02 nm, Epot= -5.45904e+05 Fmax= 1.87021e+05,
atom=
6357
Step= 53, Dmax= 1.2e-01 nm, Epot= -6.52906e+05 Fmax= 2.72180e+05,
atom=
6357
Step= 55, Dmax= 7.1e-02 nm, Epot= -7.07692e+05 Fmax= 1.08267e+07,
atom=
3569
Step= 62, Dmax= 1.3e-03 nm, Epot= -7.60656e+05 Fmax= 1.19350e+08,
atom=
11335
Step= 65, Dmax= 4.0e-04 nm, Epot= -7.60669e+05 Fmax= 3.94493e+07,
atom=
3569
Step= 69, Dmax= 6.0e-05 nm, Epot= -7.60669e+05 Fmax= 1.55572e+07,
atom=
35695
Step= 70, Dmax= 7.2e-05 nm, Epot= -7.60670e+05 Fmax= 1.30303e+07,
atom=
11335
Step= 71, Dmax= 8.7e-05 nm, Epot= -7.60677e+05 Fmax= 2.11985e+07,
atom=
3569
Step= 72, Dmax= 1.0e-04 nm, Epot= -7.60678e+05 Fmax= 1.99492e+07,
atom=
11335
Step= 73, Dmax= 1.2e-04 nm, Epot= -7.60686e+05 Fmax= 2.93949e+07,
atom=
3569
Step= 74, Dmax= 1.5e-04 nm, Epot= -7.60686e+05 Fmax= 2.98387e+07,
atom=
11335
Step= 75, Dmax= 1.8e-04 nm, Epot= -7.60696e+05 Fmax= 4.12585e+07,
atom=
3569
Step= 83, Dmax= 1.7e-06 nm, Epot= -7.60696e+05 Fmax= 4.05617e+07,
atom=
35695
Energy minimization has stopped, but the forces have not converged to
the
requested precision Fmax < 100 (which may not be possible for your
system).
It stopped because the algorithm tried to make a new step whose size
was
too
small, or there was no change in the energy since last step. Either
way,
we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often
not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 84 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -7.6069581e+05
Maximum force = 4.1258524e+07 on atom 3569
Norm of force = 1.6956947e+05
GROMACS reminds you: "If you want to destroy my sweater, hold this
thread
as I walk away." (Weezer)
I can't understand what is the problem inside the system. Because of
this
reason I can't proceed to equilibration step. please help me.
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*Rahul *
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