[gmx-users] segmentation fault in gmx hbond
Dr. D. H. Dagade
dhd_chem at unishivaji.ac.in
Wed Mar 1 12:17:34 CET 2017
Dear Prof David van der Spoel and all others,
Thank you very much for the reply. I will wait for the release of GROMACS
2016.2 version. Could the version 2016.2 will be used to analyse the
simulation data from previous version i.e. of 2016.1?
With Best Reagrds,
Dr Dilip H Dagade,
Department of Chemistry,
Shivaji University,
Kolhapur - 416004 (INDIA)
On Wed, Mar 1, 2017 at 1:53 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: segmentation fault in gmx hbond (Tasneem Kausar)
> 2. Re: Cohesive Energy Density (CED) Calculation in Gromacs
> simulations (David van der Spoel)
> 3. Re: segmentation fault in gmx hbond (David van der Spoel)
> 4. Charmm topologies for DHF/NADPH (Nicolas Cheron)
> 5. Re: PDB2GMX Fatal Error (Syed Azeem)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Mar 2017 12:30:24 +0530
> From: Tasneem Kausar <tasneemkausar12 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] segmentation fault in gmx hbond
> Message-ID:
> <CAFaK4UbakNohkcRy6sAvz1i4pDijQgEieOjQER3sToBsvvtW=A at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Check your hbnum.xvg file. Probably you calculation has been completed
> successfully.
>
>
> On Wed, Mar 1, 2017 at 12:21 PM, Dr. D. H. Dagade <
> dhd_chem at unishivaji.ac.in
> > wrote:
>
> > Dear Gromacs users,
> > I am doing hbond analysis of various organic anions after
> doing
> > successful free energy calculations with timestep of 2fs using GROMACS
> > 2016.1 version. While using -ac option for autocorrelation, I got
> following
> > error.
> > Doing autocorrelation according to the theory of Luzar and Chandler.
> > Segmentation fault (core dumped)
> > Is it a bug or some mistake in calculations? I searched the gmx-mailing
> > archive as well as on google for the solution but not got any clue. Can
> > anyone help me?
> > The details are given below:
> >
> > gmx hbond -f /run/media/dhd/Datadisk/dd/Free_energy/bimgly/ace/coul/
> > Lambda_20/Production_MD/md20.trr -s /run/media/dhd/Datadisk/dd/
> > Free_energy/bimgly/ace/coul/Lambda_20/Production_MD/md20.tpr -num -g
> -dist
> > -ang -hx -hbn -hbm -don -dan -life -nhbdist -ac
> >
> > Reading file /run/media/dhd/Datadisk/dd/Free_energy/bimgly/ace/coul/
> > Lambda_20/Production_MD/md20.tpr, VERSION 2016 (single precision)
> > Specify 2 groups to analyze:
> > Group 0 ( System) has 3010 elements
> > Group 1 ( Other) has 7 elements
> > Group 2 ( ACEA) has 7 elements
> > Group 3 ( Water) has 3003 elements
> > Group 4 ( SOL) has 3003 elements
> > Group 5 ( non-Water) has 7 elements
> > Select a group: 2
> > Selected 2: 'ACEA'
> > Select a group: 3
> > Selected 3: 'Water'
> > Checking for overlap in atoms between ACEA and Water
> > Calculating hydrogen bonds between ACEA (7 atoms) and Water (3003 atoms)
> > Found 1001 donors and 1003 acceptors
> > Making hbmap structure...done.
> > trr version: GMX_trn_file (single precision)
> > Reading frame 0 time 0.000
> > Will do grid-seach on 8x8x5 grid, rcut=0.35
> > Frame loop parallelized with OpenMP using 32 threads.
> > Last frame 2000 time 2000.000
> > WARNING: Incomplete header: nr 2001 time 2000
> > Found 825 different hydrogen bonds in trajectory
> > Found 745 different atom-pairs within hydrogen bonding distance
> > Merging hbonds with Acceptor and Donor swapped
> > 1001/1001
> > - Reduced number of hbonds from 825 to 825
> > - Reduced number of distances from 745 to 745
> > Average number of hbonds per timeframe 6.671 out of 502002 possible
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
> > Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
> > J. Phys. Chem. B 110 (2006) pp. 4393-4398
> > -------- -------- --- Thank You --- -------- --------
> >
> > Doing autocorrelation according to the theory of Luzar and Chandler.
> > Segmentation fault (core dumped)
> >
> > Is it a bug or some mistake in calculations? I searched the gmx-mailing
> > archive as well as on google for the solution but not got any clue.
> >
> > With Warm Regards,
> >
> > Dr Dilip H Dagade,
> > Department of Chemistry,
> > Shivaji University,
> > Kolhapur 416004
> >
> > --
> > This email and any files transmitted with it are confidential and
> intended
> > solely for the use of the individual or entity to whom they are
> addressed.
> > If you have received this email in error please notify the system
> manager.
> > Please note that any views or opinions presented in this email are solely
> > those of the author and do not necessarily represent those of the Shivaji
> > University. Finally, the recipient should check this email and any
> > attachments for the presence of viruses. Shivaji University accepts no
> > liability for any damage caused by any virus transmitted by this email.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 1 Mar 2017 08:34:44 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Cohesive Energy Density (CED) Calculation in
> Gromacs simulations
> Message-ID: <ed240cb0-889f-b34a-bf50-156e85617d3e at xray.bmc.uu.se>
> Content-Type: text/plain; charset=gbk; format=flowed
>
> On 01/03/17 07:30, ZUO Taisen wrote:
> > Hi guys:
> >
> > Recently, I'm simulation a protein in the mixture of water and
> ethanol. And I want to know the interaction energy among the three items
> and also the Cohesive Energy Density of the whole system.
> >
> Never old enough to learn something new, I had never heard of Cohesive
> Energy Density but I found this:
> https://en.wikipedia.org/wiki/Hildebrand_solubility_parameter
> this parameter has a non-physical unit of sqrt(kg/m)/s
>
> It is important to realize that this kind of chemical engineering
> properties do not have any fundamental information, although they may be
> practically applied.
>
> Interaction energy is only a valid concept in the limit of pure pair
> potentials, which is what we use in classical non-polarizable
> simulations (but in e.g. quantum chemistry there is no real equivalent).
> You can decompose the reciprocal part of the Coulomb energy according to
> the supporting information of
> http://pubs.acs.org/doi/abs/10.1021/ct400404q
>
> If you want to study a more meaningful property like the enthalpy of
> mixing you would have to do a concentration series, like here:
> http://folding.bmc.uu.se/david/oldpapers/wensink2003a.pdf
>
> > In order to calculate the cohesive energy I only added up LJ (SR)
> Disper. corr. Coulomb (SR) and Coul. recip. from the log file of
> Gromacs. But someone pointed out that Disper. corr.and Coul. recip.are
> correction of cutoff of the nonbonded interaction namely LJ and Coulomb
> interaction.It also contain the energy inside the molecules namely long
> range correction of LJ-14 and Coulomb-14?I don't know whether he is correct
> or not, but I can never find anywhere a lenthy description of the Disper.
> corr.and Coul. recip. in the manual of Gromacs.
> >
> > Could soneone explain the meaning of Disper. corr.and Coul. recip.
> and offer me the methods of calculating the correct CED of the system and
> individual interaction energy like Protein-SOL and SOL-SOL?
> >
>
> >
> > --
> > Taisen Zuo
> >
> > China Spallation Neutron Source?Institute of High Energy Physics?
> Chinese Academy of Science
> > A1-510, Zhongziyuan road NO.1, Dongguan, Guangdong, PR China. 523770
> > Tel: 86-0769-89156495
> > Cell: 13650469795
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 1 Mar 2017 08:35:07 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] segmentation fault in gmx hbond
> Message-ID: <7cad00a8-76d6-a7a8-c9cf-ac602572508a at xray.bmc.uu.se>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 01/03/17 07:51, Dr. D. H. Dagade wrote:
> > Dear Gromacs users,
> > I am doing hbond analysis of various organic anions after
> doing
> > successful free energy calculations with timestep of 2fs using GROMACS
> > 2016.1 version. While using -ac option for autocorrelation, I got
> following
> > error.
>
> This has been fixed in 2016.2
>
>
> > Doing autocorrelation according to the theory of Luzar and Chandler.
> > Segmentation fault (core dumped)
> > Is it a bug or some mistake in calculations? I searched the gmx-mailing
> > archive as well as on google for the solution but not got any clue. Can
> > anyone help me?
> > The details are given below:
> >
> > gmx hbond -f /run/media/dhd/Datadisk/dd/Free_energy/bimgly/ace/coul/
> > Lambda_20/Production_MD/md20.trr -s /run/media/dhd/Datadisk/dd/
> > Free_energy/bimgly/ace/coul/Lambda_20/Production_MD/md20.tpr -num -g
> -dist
> > -ang -hx -hbn -hbm -don -dan -life -nhbdist -ac
> >
> > Reading file /run/media/dhd/Datadisk/dd/Free_energy/bimgly/ace/coul/
> > Lambda_20/Production_MD/md20.tpr, VERSION 2016 (single precision)
> > Specify 2 groups to analyze:
> > Group 0 ( System) has 3010 elements
> > Group 1 ( Other) has 7 elements
> > Group 2 ( ACEA) has 7 elements
> > Group 3 ( Water) has 3003 elements
> > Group 4 ( SOL) has 3003 elements
> > Group 5 ( non-Water) has 7 elements
> > Select a group: 2
> > Selected 2: 'ACEA'
> > Select a group: 3
> > Selected 3: 'Water'
> > Checking for overlap in atoms between ACEA and Water
> > Calculating hydrogen bonds between ACEA (7 atoms) and Water (3003 atoms)
> > Found 1001 donors and 1003 acceptors
> > Making hbmap structure...done.
> > trr version: GMX_trn_file (single precision)
> > Reading frame 0 time 0.000
> > Will do grid-seach on 8x8x5 grid, rcut=0.35
> > Frame loop parallelized with OpenMP using 32 threads.
> > Last frame 2000 time 2000.000
> > WARNING: Incomplete header: nr 2001 time 2000
> > Found 825 different hydrogen bonds in trajectory
> > Found 745 different atom-pairs within hydrogen bonding distance
> > Merging hbonds with Acceptor and Donor swapped
> > 1001/1001
> > - Reduced number of hbonds from 825 to 825
> > - Reduced number of distances from 745 to 745
> > Average number of hbonds per timeframe 6.671 out of 502002 possible
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
> > Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
> > J. Phys. Chem. B 110 (2006) pp. 4393-4398
> > -------- -------- --- Thank You --- -------- --------
> >
> > Doing autocorrelation according to the theory of Luzar and Chandler.
> > Segmentation fault (core dumped)
> >
> > Is it a bug or some mistake in calculations? I searched the gmx-mailing
> > archive as well as on google for the solution but not got any clue.
> >
> > With Warm Regards,
> >
> > Dr Dilip H Dagade,
> > Department of Chemistry,
> > Shivaji University,
> > Kolhapur 416004
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 1 Mar 2017 09:14:22 +0100
> From: Nicolas Cheron <nicolas.cheron.boulot at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Charmm topologies for DHF/NADPH
> Message-ID:
> <CAA5k+evEiGagqvG9fiXrx_UEwrH7JzmjYaNLDfsk3gCxVkaF7g@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
>
> I am searching for topology files in Gromacs format for the NADPH cofactor
> and the dihydrofolate (DHF) ligand that would be compatible with the
> Charmm27 force field.
>
> Does anyone here have them and woud kindly accept to send them to me? If
> you have them in another format than Gromacs, I am also interested.
>
> Thanks a lot.
>
> Nicolas
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 1 Mar 2017 13:53:02 +0530
> From: Syed Azeem <syedazeemullah186 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] PDB2GMX Fatal Error
> Message-ID:
> <CAJnO2SAscLyidf7+u_AgBhR496_UcZ256rQ3M54xtGe96Tkg_A at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> >
> > Use -ignh in pdb2gmx.
> Hi Reza,
>
> I tried -ignh, it's working fine.
>
> But i need to calculate H-bonds after docking the same peptide. Then
> the same error will crop up and I won't be able to calculate H-bonds.
>
> >> On Mar 1, 2017, at 10:22, Syed Azeem <syedazeemullah186 at gmail.com>
> wrote:
> >>
> >> Hi all,
> >>
> >> I tried passing a predicted peptide (16-mer) into GMX and ended up
> >> with a fatal error regarding hydrogen. I tried ignoring the hydrogens
> >> using -ignh command. But I'll need to calculate H-bonds for the next
> >> analysis, as I'll dock this peptide into a target protein.
> >>
> >> Fatal error:
> >> Atom HB3 in residue ASN 1 was not found in rtp entry NASN with 16 atoms
> >> while sorting atoms.
> >>
> >> For a hydrogen, this can be a different protonation state, or it
> >> might have had a different number in the PDB file and was rebuilt
> >> (it might for instance have been H3, and we only expected H1 & H2).
> >> Note that hydrogens might have been added to the entry for the
> >> N-terminus.
> >> Remove this hydrogen or choose a different protonation state to solve
> it.
> >> Option -ignh will ignore all hydrogens in the input.
> >>
> >> How to solve this issue?
> >>
> >> Thanks in advance
> >>
> >> Azeem
>
>
> ------------------------------
>
> --
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> *****************************************************
>
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Please note that any views or opinions presented in this email are solely
those of the author and do not necessarily represent those of the Shivaji
University. Finally, the recipient should check this email and any
attachments for the presence of viruses. Shivaji University accepts no
liability for any damage caused by any virus transmitted by this email.
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