[gmx-users] Re: Energy Minimization
Gia Maisuradze
gia at chem.unr.edu
Wed Jan 12 22:03:23 CET 2005
David,
Thanks for your reply. Below I have attached the files for energy
minimization of Ribonuclease S-peptide, which is given in tutorial and I
followed exactly the tutrial "getting started". I have attached the file how
I got the number of waters, it is 850:
genbox -cp out -cs -p speptide -o b4em
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) genbox (-:
Option Filename Type Description
------------------------------------------------------------
-cp out.gro Input, Opt! Generic structure: gro g96 pdb tpr tpb tpa
xml
-cs spc216.gro Input, Opt!, Lib. Generic structure: gro g96 pdb tpr
tpb
tpa xml
-ci insert.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-o b4em.gro Output Generic structure: gro g96 pdb xml
-p speptide.top In/Out, Opt! Topology file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-box vector 0 0 0 box size
-nmol int 0 no of extra molecules to insert
-try int 10 try inserting -nmol*-try times
-seed int 1997 random generator seed
-vdwd real 0.105 default vdwaals distance
-shell real 0 thickness of optional water layer around solute
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
In case you use free energy of solvation predictions:
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
GROwing Monsters And Cloning Shrimps
Containing 191 atoms in 19 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 2x3x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 2592 residues
Calculating Overlap...
box_margin = 0.315
Removed 4047 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
Generated table with 0 data points for COUL.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 7967 charge groups and 7967 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 11 x 18 x 9 cells
Succesfully made neighbourlist
nri = 15852, nrj = 638633
Checking Protein-Solvent overlap: tested 5166 pairs, removed 318 atoms.
Checking Solvent-Solvent overlap: tested 56725 pairs, removed 861 atoms.
Added 850 molecules
Generated solvent containing 2550 atoms in 850 residues
Writing generated configuration to b4em.gro
GROwing Monsters And Cloning Shrimps
Output configuration contains 2741 atoms in 869 residues
Volume : 28.7068 (nm^3)
Density : 1006.98 (g/l)
Number of SOL molecules: 850
Processing topology
Adding line for 850 solute molecules to topology file (speptide.top)
Back Off! I just backed up speptide.top to ./#speptide.top.1#
gcq#119: "Bring Out the Gimp" (Pulp Fiction)
For energy minimization I used following em.mdp file (as given in tutorial
"getting started"):
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 100
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
The result of minimization is following:
mdrun -v -s em -o em -c after_em -g emlog
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s em.tpr Input Generic run input: tpr tpb tpa xml
-o em.trr Output Full precision trajectory: trr trj
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-c after_em.gro Output Generic structure: gro g96 pdb xml
-e ener.edr Output Generic energy: edr ene
-g emlog.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
pdb
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-pi pull.ppa Input, Opt. Pull parameters
-po pullout.ppa Output, Opt. Pull parameters
-pd pull.pdo Output, Opt. Pull data output
-pn pull.ndx Input, Opt. Index file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-deffnm string Set the default filename for all file options
-np int 1 Number of nodes, must be the same as used for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]multi bool no Do multiple simulations in parallel (only with
-np > 1)
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file em.tpr, VERSION 3.2.1 (single precision)
Loaded with Money
Steepest Descents:
Tolerance (Fmax) = 2.00000e+03
Number of steps = 100
Step= 0, Dmax= 1.0e-02 nm, Epot= -1.58854e+04 Fmax= 2.32306e+04, atom=
1854
Step= 1, Dmax= 1.0e-02 nm, Epot= -1.97858e+04 Fmax= 9.80772e+03, atom=
372
Step= 2, Dmax= 1.2e-02 nm, Epot= -2.33927e+04 Fmax= 4.17653e+03, atom=
1026
Step= 3, Dmax= 1.4e-02 nm, Epot= -2.64625e+04 Fmax= 5.17623e+03, atom= 10
Step= 4, Dmax= 1.7e-02 nm, Epot= -2.66158e+04 Fmax= 1.35947e+04, atom=
120
Step= 5, Dmax= 2.1e-02 nm, Epot= -2.71794e+04 Fmax= 1.39224e+04, atom=
120
Step= 7, Dmax= 1.2e-02 nm, Epot= -2.83565e+04 Fmax= 3.17368e+03, atom=
120
Step= 9, Dmax= 7.5e-03 nm, Epot= -2.86437e+04 Fmax= 8.12602e+03, atom=
120
Step= 10, Dmax= 9.0e-03 nm, Epot= -2.89633e+04 Fmax= 3.75650e+03, atom=
120
Step= 12, Dmax= 5.4e-03 nm, Epot= -2.91623e+04 Fmax= 4.08285e+03, atom=
120
Step= 13, Dmax= 6.4e-03 nm, Epot= -2.93300e+04 Fmax= 4.17672e+03, atom=
120
Step= 14, Dmax= 7.7e-03 nm, Epot= -2.94109e+04 Fmax= 7.12510e+03, atom=
120
Step= 15, Dmax= 9.3e-03 nm, Epot= -2.95755e+04 Fmax= 5.34043e+03, atom=
120
Step= 17, Dmax= 5.6e-03 nm, Epot= -2.97351e+04 Fmax= 2.55527e+03, atom=
120
Step= 18, Dmax= 6.7e-03 nm, Epot= -2.97518e+04 Fmax= 6.13042e+03, atom= 81
Step= 19, Dmax= 8.0e-03 nm, Epot= -2.98587e+04 Fmax= 5.12232e+03, atom=
120
Step= 21, Dmax= 4.8e-03 nm, Epot= -2.99705e+04 Fmax= 1.99691e+03, atom=
2437
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 2000 in 22 steps
Potential Energy = -2.9970463e+04
Maximum force = 1.9969060e+03 on atom 2437
Norm of force = 4.9306812e+04
gcq#270: "Live for Liposuction" (Robbie Williams)
According to the tutorial the potential energy should be lower than -35700
kJ/mol (-42 x 850), but my result is higher.
The same kind of problem I had for lambda repressor.
How can I fix this problem?
With best wishes,
Gia Maisuradze
----- Original Message -----
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Tuesday, January 11, 2005 11:54 PM
Subject: Re: [gmx-users] Re: Energy Minimization
> On Tue, 2005-01-11 at 16:42 -0800, Gia Maisuradze wrote:
> > Hi,
> >
> > I am a new user of GROMACS. I have sent this message one week ago but
> > did not get any answer. I am trying to run MD simulation of one of the
> > proteins. I followed the "getting started" tutorial. My question is
> > about minimization of my system in solvent. According to the tutorial
> > the minimization should be finished when either the minimization has
> > converged or a fixed number of steps has been performed. In my case
> > the minimization has converged before it reached the fixed number of
> > steps. But the potential energy after minimization IS NOT lower than
> > potential energy calculated by formula: -42(kJ/mole)xN (N is a number
> > of SPC water molecules). What is the problem? How can I fix it? The
> > same problem I had for Ribonuclease S-peptide given in tutorial. As I
> > heard the problem might be a precision. Am I correct? My calculations
> > run in single precision, so I may need a double precision. But I don't
> > know how to change the precision. Can anyone help me to change a
> > single precission to double precision? Is there any other ways to fix
> > this problem?
> Is the number of waters correct? It is not in the tutorial.
> >
> > My second question is about short and full MD run. According to the
> > tutorial to generate the input for the position restrained mdrun we
> > have the following command:
> >
> > grompp -f pr -o pr -c after_em -r after_em -p speptide
> >
> > for full md to do the same thing we have the following command:
> >
> > grompp -v -f full -o full -c after_pr -p speptide
> >
> > We can see that full MD is quite similar to the restrained MD, but
> > there is a difference which makes impossible to run full MD without
> > restrained MD. In full MD we have "-c after_pr" which is an input file
> > and "after_pr" can be obtained from short MD run. Is it correct that
> > we can't run full MD run without short MD or is there any other way to
> > run directly full MD (for example, use the same files for full MD as
> > used for short MD)?
> If you don't do the PR you may end up with large forces due to the newly
> added solvent which may disrupt your original structure. This is usually
> not what you want, but that is for you to decide of course.
> >
> > I look forward to hearing your reply,
> >
> > With best wishes,
> >
> > Gia Maisuradze
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
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