RE: [gmx-users] Calculate interaction energy dynamically
> Date: Fri, 26 Jul 2013 11:30:14 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/26/13 5:21 AM, Davit Hakobyan wrote: > >> From: davhak2...@hotmail.com > >> To: gmx-users@gromacs.org > >> Subject: RE: [gmx-users] Calculate interaction energy dynamically > >> Date: Thu, 25 Jul 2013 09:13:14 + > >> > >> > >> > >>> Date: Wed, 24 Jul 2013 09:35:26 -0400 > >>> From: jalem...@vt.edu > >>> To: gmx-users@gromacs.org > >>> Subject: Re: [gmx-users] Calculate interaction energy dynamically > >>> > >>> > >>> > >>> On 7/24/13 9:25 AM, Davit Hakobyan wrote: > >>>> Thank you again for your time and help. > >>>> > >>>> Performing "rerun" on the original system passes without warnings: > >>>> > >>>> The > >>>>subsequent g_energy also runs smoothly. One gets no warning also if > >>>> passing the ordered *ordered.tpr and the new index (*ordered.ndx) files > >>>> to the "mdrun -rerun" of the original system. This indeed leaves with > >>>> the ordered trajectory file as the only problematic point which might > >>>> cause the warnings. > >>>> > >>> > >>> Good to know. > >>> > >>>> Interestingly, the ordered *.trr file > >>>> (product of trjorder command) is nearly twice as small as the original > >>>> *.trr file. Since the coordinates in the ordered *.trr file look fine > >>>> then probably it is the velocities which might be missing in it. Can the > >>> > >>> There's no "might" about it - your gmxcheck output from before shows that > >>> velocities are definitely absent, which should account for the difference > >>> in > >>> file size. > >>> > >>>>warnings come from this issue ? In this case the g_energy should not > >>>> be > >>>>able to calculate the kinetic energy. If this is the case may one > >>>> still > >>>>rely on the numbers obtained by g_energy for the coulomb and vdw terms > >>>> (despite the warning messages) ? > >>>> > >>> > >>> This is a very weird issue. The .trr file clearly has step and time > >>> information > >>> (from your earlier post), but the resulting .edr file from mdrun -rerun > >>> does not > >>> have the correct step number (though it appears to have time). Your > >>> problem > >>> does not derive from anything to do with velocities, as far as I can tell. > >>> Proceed carefully and scrutinize the output to see if it indeed makes > >>> sense - > >>> you can verify energy values from snapshots that have not been ordered by > >>> creating index files that correspond to the same lipids, for instance. > >>> This is > >>> a very non-standard exercise, so it's probably never been tested and > >>> debugged. > >> > >> The energy calculation between the nearest neighbors at a given time frame > >> based on the original trajectory file (with help of new index file) indeed > >> gives the same values as for the ordered trajectory file. So one can > >> probably rely on the energy output from the ordered trajectory despite the > >> warnings. > >> > >> In case of more information about the warnings I will write in this thread. > >> > > > > It seems that the problem appears when for the trjorder command one > > indicates *.trr instead of *.xtc as an output. > > When *.xtc is mentioned like "trjorder ... -o output.xtc" both the "mdrun > > -rerun" and g_energy subsequently pass without warnings. > > > > Interesting. That leads me to suspect that there is something wrong with the > way trjorder writes .trr frames. It writes .xtc files correctly, but > incorrect > step information in .trr files. Thanks for following up. I'll look into it > and > probably file a bug report on it. What Gromacs version are you using? Maybe > you said that before, but I've forgotten. I use Gromacs 4.5.1. Thank you very much for your help and time. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow
RE: [gmx-users] Calculate interaction energy dynamically
> From: davhak2...@hotmail.com > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Calculate interaction energy dynamically > Date: Thu, 25 Jul 2013 09:13:14 + > > > > > Date: Wed, 24 Jul 2013 09:35:26 -0400 > > From: jalem...@vt.edu > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > > > > > On 7/24/13 9:25 AM, Davit Hakobyan wrote: > > > Thank you again for your time and help. > > > > > > Performing "rerun" on the original system passes without warnings: > > > > > > The > > > subsequent g_energy also runs smoothly. One gets no warning also if > > > passing the ordered *ordered.tpr and the new index (*ordered.ndx) files > > > to the "mdrun -rerun" of the original system. This indeed leaves with > > > the ordered trajectory file as the only problematic point which might > > > cause the warnings. > > > > > > > Good to know. > > > > > Interestingly, the ordered *.trr file > > > (product of trjorder command) is nearly twice as small as the original > > > *.trr file. Since the coordinates in the ordered *.trr file look fine > > > then probably it is the velocities which might be missing in it. Can the > > > > There's no "might" about it - your gmxcheck output from before shows that > > velocities are definitely absent, which should account for the difference > > in > > file size. > > > > > warnings come from this issue ? In this case the g_energy should not be > > > able to calculate the kinetic energy. If this is the case may one still > > > rely on the numbers obtained by g_energy for the coulomb and vdw terms > > > (despite the warning messages) ? > > > > > > > This is a very weird issue. The .trr file clearly has step and time > > information > > (from your earlier post), but the resulting .edr file from mdrun -rerun > > does not > > have the correct step number (though it appears to have time). Your > > problem > > does not derive from anything to do with velocities, as far as I can tell. > > Proceed carefully and scrutinize the output to see if it indeed makes sense > > - > > you can verify energy values from snapshots that have not been ordered by > > creating index files that correspond to the same lipids, for instance. > > This is > > a very non-standard exercise, so it's probably never been tested and > > debugged. > > The energy calculation between the nearest neighbors at a given time frame > based on the original trajectory file (with help of new index file) indeed > gives the same values as for the ordered trajectory file. So one can probably > rely on the energy output from the ordered trajectory despite the warnings. > > In case of more information about the warnings I will write in this thread. > It seems that the problem appears when for the trjorder command one indicates *.trr instead of *.xtc as an output. When *.xtc is mentioned like "trjorder ... -o output.xtc" both the "mdrun -rerun" and g_energy subsequently pass without warnings. > Thank you very much for all the help. > > > > > -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 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > == > > -- > > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Calculate interaction energy dynamically
> Date: Wed, 24 Jul 2013 09:35:26 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/24/13 9:25 AM, Davit Hakobyan wrote: > > Thank you again for your time and help. > > > > Performing "rerun" on the original system passes without warnings with the > > following output: > > > > > > > > Option Filename Type Description > > > >-s inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr InputRun input > > file: tpr tpb tpa > > > > -o > > /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_testrerun.trr > > Output Full precision trajectory: trr trj cpt > >-x traj.xtc Output, Opt. Compressed trajectory (portable xdr > > format) > > -cpi state.cpt Input, Opt. Checkpoint file > > -cpo state.cpt Output, Opt. Checkpoint file > >-c crd/dynmc_end/dppc_dupc_chol_034x051x015_295K_testrerun.gro Output > > Structure file: gro g96 pdb etc. > >-e dat/enr/dppc_dupc_chol_034x051x015_295K_testrerun.edr Output > > Energy file > >-g out/dppc_dupc_chol_034x051x015_295K_testrerun.log Output Log > > file > > -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file > > -fieldfield.xvg Output, Opt. xvgr/xmgr file > > -tabletable.xvg Input, Opt. xvgr/xmgr file > > -tablep tablep.xvg Input, Opt. xvgr/xmgr file > > -tableb table.xvg Input, Opt. xvgr/xmgr file > > -rerun > > /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K.trr > > Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt > > -tpitpi.xvg Output, Opt. xvgr/xmgr file > > -tpid tpidist.xvg Output, Opt. xvgr/xmgr file > > -eisam.edi Input, Opt. ED sampling input > > -eosam.edo Output, Opt. ED sampling output > >-j wham.gct Input, Opt. General coupling stuff > > -jobam.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 > > -px pullx.xvg Output, Opt. xvgr/xmgr file > > -pf pullf.xvg Output, Opt. xvgr/xmgr 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]version bool no Print version info and quit > > -niceint0 Set the nicelevel > > -deffnm string Set the default filename for all file options > > -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none > > -[no]pd bool no Use particle decompostion > > -dd vector 0 0 0 Domain decomposition grid, 0 is optimize > > -nt int0 Number of threads to start (0 is guess) > > -npmeint-1 Number of separate nodes to be used for PME, -1 > > is guess > > -ddorder enum interleave DD node order: interleave, pp_pme or > > cartesian > > -[no]ddcheck bool yes Check for all bonded interactions with DD > > -rdd real 0 The maximum distance for bonded interactions > > with > > DD (nm), 0 is determine from initial > > coordinates > > -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate > > -dlb enum autoDynamic load balancing (with DD): auto, no or > > yes > > -dds real 0.8 Minimum allowed dlb scaling of the DD cell size > > -gcomint-1 Global communication frequency > > -[no]v bool no Be loud and noisy > > -[no]compact bool yes Write a compact log file > > -[no]seppot bool no Write separate V and dVdl terms for each > > interaction type and node to the log file(s) > > -pforce real -1 Print all forces larger than this (kJ/mol nm) > > -[no]reprod bool no Try to avoid optimizations that affect binary > > rep
RE: [gmx-users] Calculate interaction energy dynamically
LAYER', reading coordinates from input trajectory '/scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K.trr' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Reading frame 1 time 1000.000 Reading frame 2 time 2000.000 Reading frame 3 time 3000.000 Reading frame 4 time 4000.000 Reading frame 5 time 5000.000 Reading frame 6 time 6000.000 Reading frame 7 time 7000.000 Reading frame 8 time 8000.000 Reading frame 9 time 9000.000 Reading frame 10 time 1.000 Reading frame 11 time 11000.000 Reading frame 12 time 12000.000 Reading frame 13 time 13000.000 Reading frame 14 time 14000.000 Reading frame 15 time 15000.000 Reading frame 16 time 16000.000 Reading frame 17 time 17000.000 Reading frame 18 time 18000.000 Reading frame 19 time 19000.000 Reading frame 20 time 2.000 Reading frame 30 time 3.000 Reading frame 40 time 4.000 Reading frame 50 time 5.000 Reading frame 60 time 6.000 Reading frame 70 time 7.000 Reading frame 80 time 8.000 Reading frame 90 time 9.000 Reading frame 100 time 10.000 Reading frame 110 time 11.000 Reading frame 120 time 12.000 Reading frame 130 time 13.000 Reading frame 140 time 14.000 Reading frame 150 time 15.000 Reading frame 160 time 16.000 Reading frame 170 time 17.000 Reading frame 180 time 18.000 Reading frame 190 time 19.000 Reading frame 200 time 20.000 Reading frame 300 time 30.000 Reading frame 400 time 40.000 Reading frame 500 time 50.000 Reading frame 600 time 60.000 Reading frame 700 time 70.000 Reading frame 800 time 80.000 Reading frame 900 time 90.000 Reading frame1000 time 100.000 Reading frame1100 time 110.000 Reading frame1200 time 120.000 Reading frame1300 time 130.000 Reading frame1400 time 140.000 Reading frame1500 time 150.000 Reading frame1600 time 160.000 Reading frame1700 time 170.000 Reading frame1800 time 180.000 Reading frame1900 time 190.000 Reading frame2000 time 200.000 Reading frame3000 time 300.000 Reading frame4000 time 400.000 Reading frame5000 time 500.000 Reading frame6000 time 600.000 Reading frame7000 time 700.000 Reading frame8000 time 800.000 Reading frame9000 time 900.000 Reading frame 1 time 1000.000 Reading frame 11000 time 1100.000 Reading frame 12000 time 1200.000 Last frame 12000 time 1200.000 Average load imbalance: 30.8 % Part of the total run time spent waiting due to load imbalance: 1.7 % NOTE: 6 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 1157.505 1157.505100.0 19:17 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 12.993 1.855 895719.837 0.000 The subsequent g_energy also runs smoothly. One gets no warning also if passing the ordered *ordered.tpr and the new index (*ordered.ndx) files to the "mdrun -rerun" of the original system. This indeed leaves with the ordered trajectory file as the only problematic point which might cause the warnings. Interestingly, the ordered *.trr file (product of trjorder command) is nearly twice as small as the original *.trr file. Since the coordinates in the ordered *.trr file look fine then probably it is the velocities which might be missing in it. Can the warnings come from this issue ? In this case the g_energy should not be able to calculate the kinetic energy. If this is the case may one still rely on the numbers obtained by g_energy for the coulomb and vdw terms (despite the warning messages) ? Thanks a lot for all the suggestions. > Date: Wed, 24 Jul 2013 07:12:54 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > On 7/24/13 5:49 AM, Davit Hakobyan wrote: > > This is smelling a bit buggy to me, but then too, I've never tried a rerun on > a > reordered trajectory. As a test, can you produce an .edr file from a rerun > of > the original trajectory (i.e. not manipulated by trjorder)? > > -Justin > > -- > =
RE: [gmx-users] Calculate interaction energy dynamically
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 0.141960 GL2 DPPC 164 0.14 0.1995 1960 1970 1980 1990 2000 2010 ... 5580 5590 5595 GL1 DPPC 467 0.145596 GL2 DPPC 467 0.14 0.2001 5600 5610 ... 7630 7640 7647 GL1 DUPC 638 0.147648 GL2 DUPC 638 0.14 0.2157 7650 7660 ... 7900 7910 7911 GL1 DUPC 660 0.147912 GL2 DUPC 660 0.14 0.2135 7920 7930 ... 8980 8990 8991 GL1 DUPC 750 0.148992 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 0.1413.2 15.4 6.87 1922 GL1 DPPC 161 0.1413.3 15.2 7.27 1923 GL2 DPPC 161 0.14 13 15 7.33 1924 C1A DPPC 161 0.1513.5 15.2 7.77 1925 C2A DPPC 161 0.1513.6 158.2 1926 C3A DPPC 161 0.1513.8 14.8 8.51 1927 C4A DPPC 161 0.1513.9 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 0.1512.7 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 FirstLast 0 System 30704 1 30704 1 Other 30704 1 30704 2 DPPC6480 16480 3 DUPC97206481 16200 4 CHOL1904 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: jalem...@vt.edu > To: gmx-users@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: jalem...@vt.edu > >> To: gmx-users@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. > >>> > >
RE: [gmx-users] Calculate interaction energy dynamically
Thank you very much for your continuous support. > Date: Tue, 23 Jul 2013 12:06:57 -0400 > From: jalem...@vt.edu > To: gmx-users@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. > >>From the generated energy file one optionally could select not only coulomb > >>and vdw terms between the goups lipid1, lipid2 and lipid3 but also between > >>lipid1 and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ > >>-30-40 kJ/mol. Since the latter is the vdw energy of a lipid with itself > >>should one understand this value as the interaction between different atoms > >>of one lipid? > > > > Yes. There are several intramolecular terms that can come into play here. > > > The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart > > from the feeling that these vdw numbers are ~ twice larger than they should > > does this procedure contain some obvious problems? > > > > Upon what do you base your feeling? In principle, this is a very simple > calculation to decompose the short-range nonbonded interactions in a pairwise > fashion. Note that these are not free energies and there is no reason to > believe that any given force field will be able to produce a physically > meaningful value here as the force field almost certainly wasn't > parameterized > to reproduce such a value. You should be right concerning the vdw values since my feeling was mistakenly based on resembling these absolute values with the difference of the interaction energies between the final and initial configuration (which is ~15-20 kJ/mol). Please let me know if you would have a suggestion about the above mdrun/g_energy warnings. Thanks very much again for your help and time. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > * Ca
RE: [gmx-users] Calculate interaction energy dynamically
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? >From the generated energy file one optionally could select not only coulomb >and vdw terms between the goups lipid1, lipid2 and lipid3 but also between >lipid1 and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ >-30-40 kJ/mol. Since the latter is the vdw energy of a lipid with itself >should one understand this value as the interaction between different atoms of >one lipid? The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart from the feeling that these vdw numbers are ~ twice larger than they should does this procedure contain some obvious problems? Thanks very much for all the help. > Date: Mon, 22 Jul 2013 08:39:27 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/22/13 8:37 AM, Davit Hakobyan wrote: > > Thanks very much for all your suggestions! > > > >> One way that you might approach it is to use mdrun -rerun. You could > >> order the > >> lipids with respect to the lipid of interest, such that the reference > >> lipid is > >> always molecule N and the nearest lipid is always written as N+1 in the > >> ordered > >> trajectory file. Then use normal index groups as your energygrps in the > >> .mdp > >> file and recalculate the energies with mdrun -rerun. > > > > Do I understand correctly that in the ordered trajectory each frame should > > have lipids ordered is such a way that in any two frames N and M the lipids > > with n and n + 1 indices should be neighbors but these need not necessarily > > be the same lipids in two frames ? > > > > Yes. > > > Could you also please inform what command may one use to reorder lipids in > > a trajectory per frame? > > > > Start by reading trjorder -h. The exact approach depends on what you're > dealing > with. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Calculate interaction energy dynamically
Thanks very much for all your suggestions! > One way that you might approach it is to use mdrun -rerun. You could order > the > lipids with respect to the lipid of interest, such that the reference lipid > is > always molecule N and the nearest lipid is always written as N+1 in the > ordered > trajectory file. Then use normal index groups as your energygrps in the .mdp > file and recalculate the energies with mdrun -rerun. Do I understand correctly that in the ordered trajectory each frame should have lipids ordered is such a way that in any two frames N and M the lipids with n and n + 1 indices should be neighbors but these need not necessarily be the same lipids in two frames ? Could you also please inform what command may one use to reorder lipids in a trajectory per frame? Thanks very much for all the help. > Date: Mon, 22 Jul 2013 08:04:27 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/22/13 6:20 AM, Davit Hakobyan wrote: > > Dear Gromacs Users, > > > > Is there a way in Gromacs to calculate the interaction energy between any > > two neighbor lipids dynamically? Since the neighbor lipids change over time > > in the trajectory file specifying a static energy groups in the input > > script will not help. > > > > Is there a way to accomplish this? > > > > One could use the g_select tool to define dynamic groups but again the > > energy file needs a predefined groups which probably makes the g_select > > tool useless in this case? > > > > One way that you might approach it is to use mdrun -rerun. You could order > the > lipids with respect to the lipid of interest, such that the reference lipid > is > always molecule N and the nearest lipid is always written as N+1 in the > ordered > trajectory file. Then use normal index groups as your energygrps in the .mdp > file and recalculate the energies with mdrun -rerun. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Calculate interaction energy dynamically
Dear Gromacs Users, Is there a way in Gromacs to calculate the interaction energy between any two neighbor lipids dynamically? Since the neighbor lipids change over time in the trajectory file specifying a static energy groups in the input script will not help. Is there a way to accomplish this? One could use the g_select tool to define dynamic groups but again the energy file needs a predefined groups which probably makes the g_select tool useless in this case? Any advice is greatly appreciated. Thanks a lot in advance. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Restart a run with different files
Dear Gromacs users,
I use Gromacs 4.5.1. The problem relates to the restarting procedure of a run.
Usually I restart the run with the "-append" option and now I need to move the
".trr" and ".xtc" files to another directory since they got too big for the
directory quota where they were located by now. So, previously the restart line
looked like the following:
mdrun -append -s system.tpr -c system.gro -g system.log -e system.edr -cpi
system.cpt -cpo system.cpt -o system.trr -x system.xtc
and now after copying (or just moving) the ".trr" and ".xtc" files to a new
directory the restart line looks like:
dir=new_dir
mdrun -append -s system.tpr -c system.gro -g system.log -e
system.edr -cpi system.cpt -cpo system.cpt -o ${dir}/system.trr -x
${dir}/system.xtc
However, in the latter case Gromacs gives the error "output files not present
or named differently:..." complaining that the ".trr" and ".xtc" files could
not be found in the location pointed by the checkpoint ".cpt" file. This is
even when the copy of the original ".trr" and ".xtc" files were left in their
original directory.
Could anybody point to a solution or a workaround ?
Thanks a lot in advance.
--
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