[gmx-users] Subject: Constraint bonds
Bakary N'tji Diallo
diallobakary4 at gmail.com
Fri Sep 28 10:45:30 CEST 2018
Hi Rose
How should i define ffbonded.itp?
Kb is determined through force field parameterization.
If for example kb of Mn-O for another similar structures exists in
literatures can i use them?
You can
Here is a nice paper about parameters for manganese:
https://pubs.acs.org/doi/10.1021/ct400055v
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
You can restraint the bonds:
http://www.gromacs.org/Documentation/How-tos/Distance_Restraints
Le jeu. 27 sept. 2018 à 23:57, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> a écrit :
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> Today's Topics:
>
> 1. Constraint bonds (rose rahmani)
> 2. Re: atom types not found (Alex)
> 3. compiling 2018.3 ... problems with hwloc (Michael Brunsteiner)
> 4. gmp_distance VS VMD distance analysis VS snapshot
> (Antonio Carlesso)
> 5. e-mail (Antonio Carlesso)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 27 Sep 2018 23:09:41 +0330
> From: rose rahmani <rose.rhmn93 at gmail.com>
> To: Gromacs <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Constraint bonds
> Message-ID:
> <CAO6==5QrXrm2RzLwe=
> zxNUWJwQ4BDcdqwHktqMAAY6mobukZVQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond,
> Mn-O bond,... formed. Now i want to do MD simulation for this
> functionalized nanotube. (I use AMBER99SB ff)
>
> How should i define ffbonded.itp?I have bond length and angles but i don't
> know kb. If for example kb of Mn-O for another similar structures exists in
> literatures can i use them?
> If kb doesn't exist, can i freeze this BOND(not the whole AA) on known bond
> length, ANGLE on known dihedral angle and known partial charges charges(all
> achieved after functionalization of NT with AA by DFT) or maybe constraint
> it?
> Is it possible to freeze bond at all?! Is there any better choice?
>
>
> Would you please help and correct me?
>
> Best regards
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 27 Sep 2018 14:16:39 -0600
> From: Alex <nedomacho at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] atom types not found
> Message-ID: <1c8755c8-1c83-0e94-bcd6-fa8cba0050aa at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hi Paul,
>
> Glad x2top is working out for you. The rest of the things you're
> pointing out, I hope others could comment. I haven't simulated any
> proteins in a long time, but if you ever need to drop a protein on the
> surface of some sort of an insane molybdenum disulfide-graphene-boron
> nitride heterostructure, I could be of service. ;)
>
> Alex
>
>
> On 9/27/2018 10:44 AM, pbuscemi wrote:
> > Alex,
> > This pertains the prior correspondence to building a polymer and is the
> process I've been developing.
> >
> > To date I can obtain an ITP and pdb from ATB for a monomer. From there
> with information in those files, it is relatively easy to construct the n2t
> file to use in x2top. ( I?d be happy to provide an example as a
> 'tutorial' of sorts). X2top provides the monomer rtp for use in pdb2gmx.
> It has all the atom type information. Thanks for the guidance on that.
> >
> > The hangups are not associated with the rtp but of all things producing
> the pdb of the polymer specifically positioning along,say, the x axis but
> more importantly, producing the pdb of the polymer that uses the same atom
> labels as the original pdb of the monomer. In the PE example from gromacs
> there are 3 mers of 2 atoms so it is easy to manually keep track of the
> names, but not if you have 1000 mers. Avogadro renames the added mers.
> >
> > Since gromacs can build proteins, and I can tell gmx that the monomer is
> a protein ( it wants to think that it is anyway), I will try to use the
> same logic to build the polymer. More to come.
> >
> > Paul
> >
> >
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 27 Sep 2018 20:56:37 +0000 (UTC)
> From: Michael Brunsteiner <mbx0009 at yahoo.com>
> To: Gmx Users <gmx-users at gromacs.org>
> Subject: [gmx-users] compiling 2018.3 ... problems with hwloc
> Message-ID: <780561502.585894.1538081797022 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
>
> Hi,
>
> In the past I compiled gmx 2016.4 on our old cluster and this worked as
> expected.
> Now I just compiled 2018.3 only to find that the resulting binary was
> unexpectedly slow ...
> On each node I have a multi-core architecture with 12 logical threads,
> but htop shows that gmx uses only one thread.
> Google-ing i found that the problem is probably due to gmx not properly
> detecting my hardware as described here:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/117830.html
>
> So as suggested in the above post i tried to re-compile gmx with the
> flag? -DGMX_HWLOC=ON (after installing hwloc-2.0.2 locally).
> "cmake" reports no problem, but when i do "make" compilation stops with
> errors that are obviously related to hwloc ... see below.
>
> any ideas on how to resolve this so that 2018 runs as expected would be
> highly appreciated!
>
> cheers,
> Michael
>
>
> compiling gmx 2018:
>
> prompt> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF
> -DCMAKE_INSTALL_PREFIX=/home/micb/local/gromacs-2018.3-bin
> -DGMX_HWLOC=ON -DCMAKE_C_COMPILER=/home/micb/local/bin/gcc
> -DCMAKE_CXX_COMPILER=/home/micb/local/bin/g++
> -DCMAKE_LIBRARY_PATH=/home/micb/local/lib:/home/micb/local/lib64
>
> no complaints here
>
> prompt> make -j 4
> ...
> [ 96%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:
> In function ?int gmx::{anonymous}::parseHwLocNuma(hwloc_topology_t,
> gmx::HardwareTopology::Machine*)?:
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:354:64:
>
> error: ?struct hwloc_obj? has no member named ?memory?
> ????????????? machine->numa.nodes[i].memory =
> hwlocNumaNodes[i]->memory.total_memory;
> ???????????????????????????????????????????????????????????????? ^
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:378:101:
>
> error: ?hwloc_get_whole_distance_matrix_by_depth? was not declared in
> this scope
> ????????? const struct hwloc_distances_s * dist =
> hwloc_get_whole_distance_matrix_by_depth(topo, depth);
> ^
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:381:54:
>
> error: ?const struct hwloc_distances_s? has no member named ?latency_base?
> ????????????? machine->numa.baseLatency??????? = dist->latency_base;
> ?????????????????????????????????????????????????????? ^
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:382:54:
>
> error: ?const struct hwloc_distances_s? has no member named ?latency_max?
> ????????????? machine->numa.maxRelativeLatency = dist->latency_max;
> ?????????????????????????????????????????????????????? ^
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:389:65:
>
> error: ?const struct hwloc_distances_s? has no member named ?latency?
> ????????????????????? machine->numa.relativeLatency[i][j] =
> dist->latency[i*dist->nbobjs+j];
> ????????????????????????????????????????????????????????????????? ^
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:407:65:
>
> error: ?struct hwloc_obj? has no member named ?memory?
> ????????????? machine->numa.nodes[0].memory?????? =
> hwlocMachine->memory.total_memory;
> ????????????????????????????????????????????????????????????????? ^
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:
> In function ?void
> gmx::{anonymous}::parseHwLoc(gmx::HardwareTopology::Machine*,
> gmx::HardwareTopology::SupportLevel*, bool*)?:
> /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:507:36:
>
> error: ?HWLOC_TOPOLOGY_FLAG_IO_DEVICES? was not declared in this scope
> ????? hwloc_topology_set_flags(topo, HWLOC_TOPOLOGY_FLAG_IO_DEVICES);
> ???????????????????????????????????? ^
> [ 96%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 27 Sep 2018 23:23:46 +0200
> From: Antonio Carlesso <antonio.gromacs.carlesso at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] gmp_distance VS VMD distance analysis VS snapshot
> Message-ID:
> <
> CAGrzmXLbqpMDgJqyxsfyWbFWFn+m1mo7Y0-5ndAbLnPEwOgFxg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> I would like to take the distance over time between two pair of atoms.
>
> I used gmx distance.
>
> to check the value I download the snapshot every 100 ns..
>
> When the distance is within the unit cell everything should be fine.
>
> when the distance increase the value seems not to be correct ( comparison
> between snapshot and value returned using gmx distance.
>
> I also double check using VMD and the value seems in agreement with the
> snapshot and in disagreement with gmx distance output).
>
>
>
> Do you know how to rationalize this different distance values?
>
>
>
> I also find this thread
>
> https://www.researchgate.net/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs
> where they suggest to ask this question for clarification
>
>
>
> Thank you for your help!
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 27 Sep 2018 23:55:57 +0200
> From: Antonio Carlesso <antonio.gromacs.carlesso at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] e-mail
> Message-ID:
> <
> CAGrzmXLms9XNBYokbK8WALPcVN_+TaV8eE_WNoSDST3D20g2cw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> antonio.gromacs.carlesso at gmail.com
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 173, Issue 103
> *******************************************************
>
--
Bakary N’tji DIALLO
Pharm. D. / M.Sc. Student in Bioinformatics
<https://www.linkedin.com/in/bakaryntjidiallo>
Mail: diallobakary4 at gmail.com | Skype: diallobakary4
Tel: +27798233845 | +223 74 56 57 22 | +223 97 39 77 14
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