[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
>
> ==================================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users
mailing list