[gmx-users] gromacs.org_gmx-users Digest, Vol 136, Issue 133
Raag Saluja
saluja.raag at gmail.com
Fri Aug 28 08:01:49 CEST 2015
Yes,I did, Mark. Thanks! But I don't need GTP. The pdb file just shows a
GTP-binding site. So, how do I proceed?
On Thu, Aug 27, 2015 at 2:52 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Comparing various MD packages (Mark Abraham)
> 2. Re: Probable bug in 5.0.4 gmx enemat (Mark Abraham)
> 3. Re: Probable bug in 5.0.4 gmx enemat (Mark Abraham)
> 4. Fatal error: Residue 'GTP' not found in residue topology
> database" (Raag Saluja)
> 5. Re: Fatal error: Residue 'GTP' not found in residue topology
> database" (Mark Abraham)
> 6. Re: Fatal error: Residue 'GTP' not found in residue topology
> database" (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 27 Aug 2015 07:45:46 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Comparing various MD packages
> Message-ID:
> <CAMNuMASBVS7W4xpNDMbSkm7SGPQt7FC0=
> CKygu1jR8e_OmmO5Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> On Tue, Aug 25, 2015 at 8:16 PM Sabyasachi Sahoo <ssahoo.iisc at gmail.com>
> wrote:
>
> > Hello all,
> > I am interested in comparing various MD packages like LAMMPS, GROMACS,
> > DESMOND, NWChem, RedMD. I was looking through literature to find any
> > relevant papers regarding the same and found a paper or two that do so.
> But
> > they used different set of bench-marking problem sets, and no single
> common
> > benchmark was used to compare all of them.
> >
> > However I fail to understand, how to draw any common conclusion amongst
> the
> > molecular dynamics packages, since they have used different benchmark
> > problems for every package that they tested on. Though we know that every
> > molecular dynamics package has different objective and each of them try
> to
> > meet different goals, but shouldn't we compare all MD packages w.r.t.
> same
> > benchmark problem rather than taking different benchmark problem suitable
> > to individual MD package. Because at the end of the day, along
> > with optimizations being done for specific subset of MD problems, all
> > MD packages are implementing same (or rather similar) set of mechanics
> > equations with the goal of simulation molecules.
> >
>
> This sounds reasonable, but will generate more heat than light.
> * As soon as you have a standard benchmark, then people are tempted to
> engineer for the benchmark rather than for actual usefulness (e.g. the use
> of LINPACK to measure Top500 place).
> * There may be a sufficiently similar subset of functionality common to all
> packages, but very few users of any of the packages run in that mode, so
> the comparison doesn't mean anything.
> * Then you have the problem of choosing test hardware - some MD code that
> runs only the CUDA GPUs on a single node is not going to be comparable with
> one that runs over MPI+CUDA using both CPU and GPU.
> * Then there's the qualities that you might actually compare - ideally
> you'd want a metric of simulation rate for given simulation quality, but
> the quality required for different kinds of actual science is probably
> different and isn't well understood anyway.
> * If you have to buy your own hardware, then the cost analysis will be
> different from whether you can win free time on a big national computing
> resources (and does it matter that such a code might be "scaleable" to lots
> of nodes because it is slow?).
> * Then there's the choice of date you do the comparison on, and how that
> lines up with simulation packages' development trajectories (and if you
> published such a comparison in a journal, it would be out of date before it
> saw press).
>
> If we were to select any one or two benchmark problem for comparing MD
> > packages, can anyone please suggest some such good benchmark problems,
> > since it will be harder for me to narrow down the set of such benchmark
> > problems, owing to my non-biological sciences background. Any material
> > related to this topic throwing more light in this direction will be of
> > great help to me. More insight for its better understanding is also
> hugely
> > appreciated.
> >
> > P.S.: If it is already asked question, or something similar was
> previously
> > asked, can you please give me the link for same?
> >
>
> You can see results of previous such efforts online, e.g.
> http://www.hecbiosim.ac.uk/benchmarks/BioMolBenchIII.pdf
>
> Mark
>
>
> > Thanks in advance
> >
> > --
> > Yours sincerely,
> > Saby
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 27 Aug 2015 07:47:17 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Probable bug in 5.0.4 gmx enemat
> Message-ID:
> <
> CAMNuMARbuJzK7OnYhzjsfV52EG7Xi781tjyiUDzXU3OeKbP1ew at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> So you've concluded that there's no implementation of gmx enemat that ever
> worked for your use case? What command line is that?
>
> Mark
>
> On Fri, Aug 21, 2015 at 5:13 PM Tushar Ranjan Moharana <
> tusharranjanmoharana at gmail.com> wrote:
>
> > Hi Mark,
> > As per your suggestion I have tried 4.6.7 version and also installed
> > gromacs in debug mode. However that didn't help. I got the same error as
> > follows;
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *Opened FOA2_lip_pull.edr as single precision energy file Will read
> > groupnames from inputfile Read 2 groups group 0WARNING! could not find
> > group Coul-SR:Protein-Protein (0,0)in energy file WARNING! could not
> find
> > group LJ-SR:Protein-Protein (0,0)in energy file WARNING! could not find
> > group Coul-SR:Protein-Non-protein (0,1)in energy file WARNING! could
> not
> > find group LJ-SR:Protein-Non-protein (0,1)in energy file group 1WARNING!
> > could not find group Coul-SR:Non-protein-Non-*
> >
> >
> >
> >
> >
> >
> >
> > *protein (1,1)in energy file WARNING! could not find group
> > LJ-SR:Non-protein-Non-protein (1,1)in energy file Will select
> half-matrix
> > of energies with 0 elements Last energy frame read 1400 time 1400.000
> > Will build energy half-matrix of 2 groups, 0 elements, over 1401 frames
> > Segmentation fault (core dumped)*
> >
> > When I use g_energy I was prompt to choose which energy I want as shown
> > below
> >
> > 2505 LJ-SR:MET24-THR177 2506
> > Coul-14:MET24-THR177
> > 2507 LJ-14:MET24-THR177 2508
> > Coul-SR:MET24-ASP178
> > 2509 LJ-SR:MET24-ASP178 2510
> > Coul-14:MET24-ASP178
> > 2511 LJ-14:MET24-ASP178 2512
> > Coul-SR:MET24-GLN184
> > 2513 LJ-SR:MET24-GLN184 2514
> > Coul-14:MET24-GLN184
> > 2515 LJ-14:MET24-GLN184 2516
> > Coul-SR:MET24-ALA190
> > 2517 LJ-SR:MET24-ALA190 2518
> > Coul-14:MET24-ALA190
> > 2519 LJ-14:MET24-ALA190 2520
> > Coul-SR:MET24-ALA191
> > 2521 LJ-SR:MET24-ALA191 2522
> > Coul-14:MET24-ALA191
> > 2523 LJ-14:MET24-ALA191 2524 Coul-SR:MET24-ALA194
> >
> > and when I choose a number and 0 it shows
> >
> >
> >
> >
> >
> >
> >
> > *Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 1 data
> > setsAll statistics are over 10001 pointsEnergy
> > Average Err.Est. RMSD
> >
> >
> Tot-Drift-------------------------------------------------------------------------------LJ-SR:LEU244-ODA
> > -0.150913 0.11 0.43633 0.017812 (kJ/mol)*
> >
> > Which seems to be correct. But then my question is why gmx enemat is
> giving
> > error and what is the solution for that. I want to calculate the average
> > non-bonded energy between various energy groups. gmx energy is giving me
> a
> > particular energy between 2 group as a function of time.
> >
> > Thanks a lot in advance.
> >
> >
> > "A society with free knowledge is better than a society with free food"
> >
> > Tushar Ranjan Moharana
> > B. Tech, NIT Warangal
> > Ph D Student, CCMB
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 27 Aug 2015 07:47:17 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Probable bug in 5.0.4 gmx enemat
> Message-ID:
> <
> CAMNuMARbuJzK7OnYhzjsfV52EG7Xi781tjyiUDzXU3OeKbP1ew at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> So you've concluded that there's no implementation of gmx enemat that ever
> worked for your use case? What command line is that?
>
> Mark
>
> On Fri, Aug 21, 2015 at 5:13 PM Tushar Ranjan Moharana <
> tusharranjanmoharana at gmail.com> wrote:
>
> > Hi Mark,
> > As per your suggestion I have tried 4.6.7 version and also installed
> > gromacs in debug mode. However that didn't help. I got the same error as
> > follows;
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *Opened FOA2_lip_pull.edr as single precision energy file Will read
> > groupnames from inputfile Read 2 groups group 0WARNING! could not find
> > group Coul-SR:Protein-Protein (0,0)in energy file WARNING! could not
> find
> > group LJ-SR:Protein-Protein (0,0)in energy file WARNING! could not find
> > group Coul-SR:Protein-Non-protein (0,1)in energy file WARNING! could
> not
> > find group LJ-SR:Protein-Non-protein (0,1)in energy file group 1WARNING!
> > could not find group Coul-SR:Non-protein-Non-*
> >
> >
> >
> >
> >
> >
> >
> > *protein (1,1)in energy file WARNING! could not find group
> > LJ-SR:Non-protein-Non-protein (1,1)in energy file Will select
> half-matrix
> > of energies with 0 elements Last energy frame read 1400 time 1400.000
> > Will build energy half-matrix of 2 groups, 0 elements, over 1401 frames
> > Segmentation fault (core dumped)*
> >
> > When I use g_energy I was prompt to choose which energy I want as shown
> > below
> >
> > 2505 LJ-SR:MET24-THR177 2506
> > Coul-14:MET24-THR177
> > 2507 LJ-14:MET24-THR177 2508
> > Coul-SR:MET24-ASP178
> > 2509 LJ-SR:MET24-ASP178 2510
> > Coul-14:MET24-ASP178
> > 2511 LJ-14:MET24-ASP178 2512
> > Coul-SR:MET24-GLN184
> > 2513 LJ-SR:MET24-GLN184 2514
> > Coul-14:MET24-GLN184
> > 2515 LJ-14:MET24-GLN184 2516
> > Coul-SR:MET24-ALA190
> > 2517 LJ-SR:MET24-ALA190 2518
> > Coul-14:MET24-ALA190
> > 2519 LJ-14:MET24-ALA190 2520
> > Coul-SR:MET24-ALA191
> > 2521 LJ-SR:MET24-ALA191 2522
> > Coul-14:MET24-ALA191
> > 2523 LJ-14:MET24-ALA191 2524 Coul-SR:MET24-ALA194
> >
> > and when I choose a number and 0 it shows
> >
> >
> >
> >
> >
> >
> >
> > *Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 1 data
> > setsAll statistics are over 10001 pointsEnergy
> > Average Err.Est. RMSD
> >
> >
> Tot-Drift-------------------------------------------------------------------------------LJ-SR:LEU244-ODA
> > -0.150913 0.11 0.43633 0.017812 (kJ/mol)*
> >
> > Which seems to be correct. But then my question is why gmx enemat is
> giving
> > error and what is the solution for that. I want to calculate the average
> > non-bonded energy between various energy groups. gmx energy is giving me
> a
> > particular energy between 2 group as a function of time.
> >
> > Thanks a lot in advance.
> >
> >
> > "A society with free knowledge is better than a society with free food"
> >
> > Tushar Ranjan Moharana
> > B. Tech, NIT Warangal
> > Ph D Student, CCMB
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 27 Aug 2015 14:23:13 +0530
> From: Raag Saluja <saluja.raag at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Fatal error: Residue 'GTP' not found in residue
> topology database"
> Message-ID:
> <
> CALwqOC5idtZ0oYJfMyJPZTHoaJv-6MNg5+MXDV6bocMyCunCAw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi!
>
> I was trying to simulate tubular (1TUB.pdb). I could run the pdb.gmx step.
> I added the water molecules. But when I defined the force field (I chose
> 15), it gave an error. It said, "
>
>
> Fatal error:
>
> Residue 'GTP' not found in residue topology database"
>
>
> Please guide!
>
> --
> Regards,
> Raag
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 27 Aug 2015 09:22:29 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Fatal error: Residue 'GTP' not found in
> residue topology database"
> Message-ID:
> <CAMNuMASDo916=22V849n2=
> zWbjpASszm8bnkom3kbUf-uy6x2g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Did you follow the link it gave?
>
> http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
>
> Mark
>
> On Thu, Aug 27, 2015 at 10:53 AM Raag Saluja <saluja.raag at gmail.com>
> wrote:
>
> > Hi!
> >
> > I was trying to simulate tubular (1TUB.pdb). I could run the pdb.gmx
> step.
> > I added the water molecules. But when I defined the force field (I chose
> > 15), it gave an error. It said, "
> >
> >
> > Fatal error:
> >
> > Residue 'GTP' not found in residue topology database"
> >
> >
> > Please guide!
> >
> > --
> > Regards,
> > Raag
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 27 Aug 2015 09:22:29 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Fatal error: Residue 'GTP' not found in
> residue topology database"
> Message-ID:
> <CAMNuMASDo916=22V849n2=
> zWbjpASszm8bnkom3kbUf-uy6x2g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Did you follow the link it gave?
>
> http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
>
> Mark
>
> On Thu, Aug 27, 2015 at 10:53 AM Raag Saluja <saluja.raag at gmail.com>
> wrote:
>
> > Hi!
> >
> > I was trying to simulate tubular (1TUB.pdb). I could run the pdb.gmx
> step.
> > I added the water molecules. But when I defined the force field (I chose
> > 15), it gave an error. It said, "
> >
> >
> > Fatal error:
> >
> > Residue 'GTP' not found in residue topology database"
> >
> >
> > Please guide!
> >
> > --
> > Regards,
> > Raag
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 136, Issue 133
> *******************************************************
>
--
Regards,
Raag
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