[gmx-users] Calculate interaction energy dynamically

Davit Hakobyan davhak2000 at hotmail.com
Wed Jul 24 11:49:45 CEST 2013


Please find below the gmxcheck output. Opposite to what I said earlier it does contain warning messages.
Thanks a lot for any suggestion.

gmxcheck output:

Option     Filename  Type         Description
------------------------------------------------------------
 
 -f 
/scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_r1_ordered.trr 
 Input, Opt!  Trajectory: xtc trr trj gro g96 pdb cpt
 -f2       traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
 -s1       top1.tpr  Input, Opt.  Run input file: tpr tpb tpa
 -s2       top2.tpr  Input, Opt.  Run input file: tpr tpb tpa
  -c inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr  Input, Opt! 
                                   Structure+mass(db): tpr tpb tpa gro g96 pdb
  -e dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr  Input, Opt! 
                                   Energy file
 -e2      ener2.edr  Input, Opt.  Energy file
  -n inp/analysis/dppc_dupc_chol_034x051x015_295K_r1_ordered.ndx  Input, Opt!
                                   Index file
  -m        doc.tex  Output, Opt. LaTeX file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-vdwfac      real   0.8     Fraction of sum of VdW radii used as warning
                            cutoff
-bonlo       real   0.4     Min. fract. of sum of VdW radii for bonded atoms
-bonhi       real   0.7     Max. fract. of sum of VdW radii for bonded atoms
-[no]rmsd    bool   no      Print RMSD for x, v and f
-tol         real   0.001   Relative tolerance for comparing real values
                            defined as 2*(a-b)/(|a|+|b|)
-abstol      real   0.001   Absolute tolerance, useful when sums are close to
                            zero.
-[no]ab      bool   no      Compare the A and B topology from one file
-lastener    string         Last energy term to compare (if not given all are
                            tested). It makes sense to go up until the
                            Pressure.

trn version: GMX_trn_file (single precision)

Reading frame       0 time    0.000   
# Atoms  30704

Reading frame       1 time 1000.000   
Reading frame       2 time 2000.000   
Reading frame       3 time 3000.000   
...
Reading frame   12000 time 12000000.000   
Last frame      12000 time 12000000.000   


Item        #frames Timestep (ps)
Step         12001    1000
Time         12001    1000
Lambda       12001    1000
Coords       12001    1000
Velocities       0
Forces           0
Box          12001    1000
Checking energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr

Opened dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr as single precision energy file
68 groups in energy file
Reading energy frame      0 time    0.000         
WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr
Found: step=-1, nre=68, nblock=0, time=0.
Trying to skip frame expect a crash though

frame:     -1 (index      0), t:      0.000

Reading energy frame      1 time 1000.000         
WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr
Found: step=-1, nre=68, nblock=0, time=1000.
Trying to skip frame expect a crash though

Reading energy frame      2 time 2000.000         
WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr
Found: step=-1, nre=68, nblock=0, time=2000.
Trying to skip frame expect a crash though

...

WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr
Found: step=-1, nre=68, nblock=0, time=1.1998e+07.
Trying to skip frame expect a crash though

WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr
Found: step=-1, nre=68, nblock=0, time=1.1999e+07.
Trying to skip frame expect a crash though

Reading energy frame  12000 time 12000000.000         
WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr
Found: step=-1, nre=68, nblock=0, time=1.2e+07.
Trying to skip frame expect a crash though

Last energy frame read 12000 time 12000000.000         

Found 12001 frames with a timestep of 1000 ps.
Checking coordinate file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr
Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr, VERSION 4.5.1 (single precision)
Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr, VERSION 4.5.1 (single precision)
30704 atoms in file
coordinates found
box         found
velocities  found

Kinetic energy: 112959 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 294.983 K or 442.474 K respectively.

Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
relative to sum of Van der Waals distance:

   10
   20
   30
   40
   50
   60
   70
   80
   90
  100
  110
  120
...
 1930
 1940
 1950
atom# name  residue r_vdw  atom# name  residue r_vdw  distance

 1959  GL1 DPPC 164 0.14    1960  GL2 DPPC 164 0.14   0.1995

 1960
 1970
 1980
 1990
 2000
 2010
...
 5580
 5590
 5595  GL1 DPPC 467 0.14    5596  GL2 DPPC 467 0.14   0.2001

 5600
 5610
...
 7630
 7640
 7647  GL1 DUPC 638 0.14    7648  GL2 DUPC 638 0.14   0.2157

 7650
 7660
...
 7900
 7910
 7911  GL1 DUPC 660 0.14    7912  GL2 DUPC 660 0.14   0.2135

 7920
 7930
...
 8980
 8990
 8991  GL1 DUPC 750 0.14    8992  GL2 DUPC 750 0.14   0.2007

 9000
 9010
...
12640
12650
12651  GL1 DUPC1055 0.14   12652  GL2 DUPC1055 0.14   0.2102

12660
12670
...
15280
15290
15291  GL1 DUPC1275 0.14   15292  GL2 DUPC1275 0.14   0.2186

15300
15310
15315  GL1 DUPC1277 0.14   15316  GL2 DUPC1277 0.14   0.1977

15320
15330
...
16190
16200
16205   R4 CHOL1351 0.14   16206   R5 CHOL1351 0.14   0.2032
... Some more of such messages
18080
18085   R4 CHOL1586 0.14   18086   R5 CHOL1586 0.14   0.2111

18090
18092   R3 CHOL1587 0.14   18094   R5 CHOL1587 0.14   0.2036

18093   R4 CHOL1587 0.14   18094   R5 CHOL1587 0.14   0.2114

18100
18110
18120
...
30680
30690
30700

Atoms outside box ( 23.4746 23.6402 6.35814 ):
(These may occur often and are normally not a problem)
atom# name  residue r_vdw  coordinate
 1921  PO4 DPPC 161 0.14    13.2   15.4   6.87
 1922  GL1 DPPC 161 0.14    13.3   15.2   7.27
 1923  GL2 DPPC 161 0.14      13     15   7.33
 1924  C1A DPPC 161 0.15    13.5   15.2   7.77
 1925  C2A DPPC 161 0.15    13.6     15    8.2
 1926  C3A DPPC 161 0.15    13.8   14.8   8.51
 1927  C4A DPPC 161 0.15    13.9   14.6   8.79
 1928  C1B DPPC 161 0.15      13   15.1   7.75
 1929  C2B DPPC 161 0.15      13   14.9   8.15
 1930  C3B DPPC 161 0.15    12.7   14.8   8.46
(maybe more)


gcq#134: "Push It Real Good" (Salt 'n' Pepa)

                         :-)  G  R  O  M  A  C  S  (-:

                   Good gRace! Old Maple Actually Chews Slate

                            :-)  VERSION 4.5.1  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
        Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, 
          Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz, 
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            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.

                         :-)  gmxcheck_4.5.1_intel  (-:

Checking file /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_r1_ordered.trr

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

Contents of index file inp/analysis/dppc_dupc_chol_034x051x015_295K_r1_ordered.ndx
--------------------------------------------------
Nr.   Group               #Entries   First    Last
   0  System                 30704       1   30704
   1  Other                  30704       1   30704
   2  DPPC                    6480       1    6480
   3  DUPC                    9720    6481   16200
   4  CHOL                    1904   16201   18104
   5  W                      12600   18105   30704
   6  DPPC_DUPC_CHOL         18104       1   18104
   7  DPPC_r1                   12       1      12
   8  DPPC_r2                   12      13      24
   9  DPPC_r3                   12      25      36


> Date: Tue, 23 Jul 2013 17:07:09 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
> 
> 
> 
> On 7/23/13 1:54 PM, Davit Hakobyan wrote:
> > Thank you very much for your continuous support.
> >
> >> Date: Tue, 23 Jul 2013 12:06:57 -0400
> >> From: jalemkul at vt.edu
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Calculate interaction energy dynamically
> >>
> >>
> >>
> >> On 7/23/13 11:05 AM, Davit Hakobyan wrote:
> >>> Thanks so much for the suggestion.
> >>>
> >>> By using the command:
> >>>
> >>> trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr
> >>>
> >>> the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm).
> >>>
> >>> Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the "rerun" flag:
> >>>
> >>> mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr  -c system_ordered.gro  -e system_ordered.edr
> >>>
> >>> many warnings were shown like:
> >>>
> >>> WARNING: there may be something wrong with energy file system_ordered.edr
> >>> Found: step=-1, nre=68, nblock=0, time=31000.
> >>> Trying to skip frame expect a crash though
> >>>
> >>> WARNING: there may be something wrong with energy file system_ordered.edr
> >>> Found: step=-1, nre=68, nblock=0, time=32000.
> >>> Trying to skip frame expect a crash though
> >>>
> >>> WARNING: there may be something wrong with energy file system_ordered.edr
> >>> Found: step=-1, nre=68, nblock=0, time=33000.
> >>> Trying to skip frame expect a crash though
> >>>
> >>> Do these warnings point to some error?
> >>>
> >>
> >> Where do they come from - mdrun? g_energy? gmxcheck?  If you haven't run
> >> gmxcheck on the .edr file, please do.
> >>
> >
> > The above warnings are issued by mdrun. The g_energy generates similar warnings like:
> >
> > WARNING: there may be something wrong with energy file system_ordered.edr
> > Found: step=-1, nre=68, nblock=0, time=74000.
> > Trying to skip frame expect a crash though
> >
> > WARNING: there may be something wrong with energy file system_ordered.edr
> > Found: step=-1, nre=68, nblock=0, time=75000.
> > Trying to skip frame expect a crash though
> > Last energy frame read 75 time 75000.000
> > ...
> >
> > The gmxcheck command:
> >
> > gmxcheck -f system_ordered.trr -c system_ordered.tpr -n system_ordered.ndx -e system_ordered.edr
> >
> > does not give any warning/error.
> >
> 
> Can you please provide the actual gmxcheck output?
> 
> -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
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> 
> ==================================================
> -- 
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