[gmx-users] Hydrogen bonding pair selection (Erik Marklund)
Binwu Zhao
bzhao at ncsu.edu
Fri Mar 18 16:00:55 CET 2016
Dear Eric,
You are right, it doesn’t cause any problems with the results!
Thanks a lot!
Binwu
> On Mar 17, 2016, at 5:18 PM, gromacs.org_gmx-users-request at maillist.sys.kth.se wrote:
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> Today's Topics:
>
> 1. Re: creating representative structures (Tsjerk Wassenaar)
> 2. pull code for Gromacs 5 (Nash, Anthony)
> 3. Volume and boundary Questions (ANAND AMITKUMAR DHARIA)
> 4. Hydrogen bonding pair selection (Binwu Zhao)
> 5. Re: Hydrogen bonding pair selection (Erik Marklund)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Mar 2016 18:36:02 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] creating representative structures
> Message-ID:
> <CABzE1SgH8HwohSNskpQ0zPOTniQHfJCkiK3xmjseb264RzjVSA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Shyno,
>
> Is there a difference in mass-weighting? Can you try on C- alphas only?
>
> Cheers,
>
> Tsjerk
> On Mar 16, 2016 15:55, "Shyno Mathew" <sm3334 at columbia.edu> wrote:
>
>> Dear all,
>>
>>
>> I wrote a tcl script to do cluster analysis, using gromos method. My
>> results are slightly different from the g_cluster results. I see the
>> difference is coming from RMSD values. For example, with g_cluster, ?The
>> RMSD ranges from 0.149614 to 0.220387 nm?
>>
>>
>> However with the tcl script, and after converting RMSD from ? to nm, the
>> value ranges from 0.173347 to 0.234409 nm! I am using the same selection in
>> both cases for RMSD calculations.
>>
>>
>> I use g_cluster the following way:
>>
>> g_cluster_mpi ?s ../PRO0.gro -f ../comb6.xtc -method gromos -sz
>> clustsize.xvg -o clusters.xpm -g cluster.log -clid clusidovertime.xvg -cl
>> -av out.pdb -cutoff 0.20 -dist rmsd-dist.xvg
>>
>>
>> For vmd, I use PRO0.gro, comb6.xtc and I am not considering the 0th frame,
>> so the RMSD values from both cases has to be identical.
>>
>>
>> thanks,
>>
>> Shyno
>>
>> On Mon, Feb 29, 2016 at 6:52 PM, Shyno Mathew <sm3334 at columbia.edu> wrote:
>>
>>> Dear all,
>>>
>>> I was able to write a tcl script to do cluster analysis, here I am using
>>> the gromos method.
>>> However, my script is giving slightly different results! I am testing my
>>> script on a smaller trajectory (8 frames).
>>> In the gromos method, the structure with the greatest number of neighbors
>>> is considered as the center of the cluster.
>>> What if more than one structure has the highest number of neighbors. For
>>> example, in my calculation, both frames 4 and 6 has 6 neighbors (maximum
>>> neighbor count).
>>> When I used g_cluster, the output file shows cluster center as frame 6.
>>> That means if I have more than one structure that has the maximum number
>> of
>>> neighbors, I can randomly choose the cluster center?
>>>
>>> thanks,
>>> Shyno
>>>
>>>
>>> On Fri, Feb 26, 2016 at 11:47 AM, Shyno Mathew <sm3334 at columbia.edu>
>>> wrote:
>>>
>>>> Dear Prof. Mark and Prof. Stephane,
>>>>
>>>> Thanks so much for your suggestions.
>>>>
>>>> thanks,
>>>> Shyno
>>>>
>>>> On Mon, Feb 8, 2016 at 12:23 PM, Shyno Mathew <sm3334 at columbia.edu>
>>>> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>>
>>>>> I have few questions regarding creating representative structures. For
>>>>> simplicity, let?s say I have a trajectory of 5 frames:
>>>>>
>>>>> 1. g_rmsf: After reading previous posts, here is what I
>>>>> understood. The average structures calculated using g_rmsf (by
>> specifying
>>>>> ?ox) is literally the average of x, y, z co-ordinates of each atom
>> over all
>>>>> the 5 frames in my case. Energy minimizing this averaged structure
>> might
>>>>> give a meaningful structure?
>>>>>
>>>>> 2. g_cluster: Here I am using the gromos method. I read the
>>>>> reference paper (Daura et al.). Using gromos method and by just
>> specifying
>>>>> ?cl (not ?av) I get the middle structures for each cluster. Let?s say
>> I get
>>>>> 2 clusters using rmsd 0.16. Now the representative structures of these
>> two
>>>>> clusters (obtained in the out.pdb) should exactly correspond to two
>> frames
>>>>> in my original trajectory (the one with 5 frames)?
>>>>>
>>>>> 3. My final question is regarding how exactly g_cluster works,
>>>>> here is what I understand from Daura et al.
>>>>>
>>>>> If I use g_cluster with gromos method, the code will look for neighbors
>>>>> of each frame within specified cutoff.
>>>>>
>>>>> Assume the first time the code finds the following:
>>>>>
>>>>> frame 0 has two neighbors: frames 2,3 within cutoff
>>>>>
>>>>> frame 1 has three neighbors: frames 2, 3, 4 within cutoff
>>>>>
>>>>> frame 2 has four neighbors: frames 0, 1, 3, 4 within cutoff
>>>>>
>>>>> frame 3 has three neighbors: frames 0,1, 2 within cutoff
>>>>>
>>>>> frame 4 has two neighbors: frames 1,2 within cutoff
>>>>>
>>>>>
>>>>>
>>>>> Since frame 2 has the highest number of neighbors, it's considered the
>>>>> center cluster and this frame along with neighbors are removed. The
>> same
>>>>> calculation is performed on the remaining frames if I had more frames.
>>>>>
>>>>>
>>>>>
>>>>> Thanks in advance for your help,
>>>>>
>>>>> Sincerely,
>>>>>
>>>>> Shyno
>>>>>
>>>>> --
>>>>> Shyno Mathew
>>>>> PhD Candidate
>>>>> Department of Chemical Engineering
>>>>> Graduate Assistant
>>>>> Office of Graduate Student Affairs
>>>>> The Fu Foundation School Of Engineering and Applied Science
>>>>> Columbia University
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Shyno Mathew
>>>> PhD Candidate
>>>> Department of Chemical Engineering
>>>> Graduate Assistant
>>>> Office of Graduate Student Affairs
>>>> The Fu Foundation School Of Engineering and Applied Science
>>>> Columbia University
>>>>
>>>
>>>
>>>
>>> --
>>> Shyno Mathew
>>> PhD Candidate
>>> Department of Chemical Engineering
>>> Graduate Assistant
>>> Office of Graduate Student Affairs
>>> The Fu Foundation School Of Engineering and Applied Science
>>> Columbia University
>>>
>>
>>
>>
>> --
>> Shyno Mathew
>> PhD Candidate
>> Department of Chemical Engineering
>> Graduate Assistant
>> Office of Graduate Student Affairs
>> The Fu Foundation School Of Engineering and Applied Science
>> Columbia University
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
>>
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>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 17 Mar 2016 17:40:26 +0000
> From: "Nash, Anthony" <a.nash at ucl.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] pull code for Gromacs 5
> Message-ID: <D3109B4A.D1C3%uccaja0 at ucl.ac.uk>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi all,
>
> I?m very unfamiliar with the pull code as of Gromacs 5. Unfortunately my
> system is not experiencing any noticeable ?pull?. From the options below,
> which is the group experiencing the pull and which is the reference group?
> Would applying a set of position restraints on the reference group
> prevent (in theory) the pulling group to move? From someone only having
> ran pull code on earlier versions of gromacs, am I missing anything
> blindingly obvious?
>
>
> pull = umbrella
> pull-geometry = direction-periodic
> pull-dim = N N Y
> pull-start = yes
> pull-ncoords = 1
> pull-ngroups = 2
> pull-group1-name = fix_collagen
> pull-group1-pbcatom = 0
> pull-group2-name = pull_group
> pull-coord1-groups = 1 2
> pull-coord1-rate = 0.1
> pull-coord1-k = 1000
>
>
>
> Context: I am pulling an explicit collagen molecule away from its
> neighbour. They are in a very tight ?rectangle?, thus they are
> experiencing a pseudo fibril environment. The need for direction-periodic
> is due to the length I am pulling the molecule (past half the box size).
>
> Thanks
> Anthony
>
>
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 17 Mar 2016 12:01:33 -0700
> From: ANAND AMITKUMAR DHARIA <adharia at berkeley.edu>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Volume and boundary Questions
> Message-ID:
> <CAH65dVJnyqhtUXvo5W5L9WGqMeWhy7zSMPOmGxuX4_py343DKg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
> I have two questions about setting up my box for simulation. Thank you for
> any and all input in advance.
>
> 1. Is the simulation box dimensions and volume fixed throughout the
> simulation (or are they allowed to fluctuate around the set dimensions)?
>
> 2. Is it possible to make custom box shapes (hexagonal) for a simulation
> run instead of using the gromacs supported box types?
>
> Context on my questions is that I would like to simulate proteins in
> restrained nanotubes, where the tubes are the dimensions of the simulation
> box (this way the entire system will look continuous with no space, when
> periodic boundaries are applied).
>
> Please let me know if I need to clarify further.
>
> Thanks,
> AD
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 17 Mar 2016 16:10:42 -0400
> From: Binwu Zhao <bzhao at ncsu.edu>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Hydrogen bonding pair selection
> Message-ID: <3BFB416B-0B6C-451D-93FB-6C06D2A3FBF2 at ncsu.edu>
> Content-Type: text/plain; charset=utf-8
>
> Dear Gromacs Users,
>
> I was trying to calculate the number of hydrogen bonds between the ?O? on Proline (acceptor) and the ?N-H? on Glycine (donor) in my system. There are 16 Proline residues and 32 Glycine residues.
>
> I first used command ?make_ndx" to create two groups, PRO_&_O and N_H_&GLY, corresponding to 16 ?O? on Proline, and 32 ?N-H? on Glycine, separately. Then I tried to calculate the number of H-bonds between these two groups.
>
> However, I encountered the following issue
>
> Select a group: 15
> Selected 15: 'N_H_&_GLY'
> Select a group: 17
> Selected 17: 'PRO_&_O'
> Checking for overlap in atoms between N_H_&_GLY and PRO_&_O
> Calculating hydrogen bonds between N_H_&_GLY (64 atoms) and PRO_&_O (16 atoms)
> Found 32 donors and 48 acceptors
>
> The ?hbond? command is actually picking up the ?N-H? on Glycine as acceptors as well. May I ask if there is any way I can let just the ?O? on Proline be the acceptor and ?N-H? on Glycine be the donor? In other words, I would like to have 32 donors and 16 acceptors.
>
> Is there any way to do that?
>
> Thanks in advance!
>
> Binwu
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 17 Mar 2016 21:18:35 +0000
> From: Erik Marklund <erik.marklund at chem.ox.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Hydrogen bonding pair selection
> Message-ID: <1627FD42-19B4-4576-8C00-4F5E4A8E40A1 at chem.ox.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Binwu,
>
> Is there really a problem? With your selections you will not register any hbonds with N_H_&GLY as the acceptor, since the other group contains no donors.
>
> Kind regards,
> Erik
>
>> On 17 Mar 2016, at 20:10, Binwu Zhao <bzhao at ncsu.edu> wrote:
>>
>> Dear Gromacs Users,
>>
>> I was trying to calculate the number of hydrogen bonds between the ?O? on Proline (acceptor) and the ?N-H? on Glycine (donor) in my system. There are 16 Proline residues and 32 Glycine residues.
>>
>> I first used command ?make_ndx" to create two groups, PRO_&_O and N_H_&GLY, corresponding to 16 ?O? on Proline, and 32 ?N-H? on Glycine, separately. Then I tried to calculate the number of H-bonds between these two groups.
>>
>> However, I encountered the following issue
>>
>> Select a group: 15
>> Selected 15: 'N_H_&_GLY'
>> Select a group: 17
>> Selected 17: 'PRO_&_O'
>> Checking for overlap in atoms between N_H_&_GLY and PRO_&_O
>> Calculating hydrogen bonds between N_H_&_GLY (64 atoms) and PRO_&_O (16 atoms)
>> Found 32 donors and 48 acceptors
>>
>> The ?hbond? command is actually picking up the ?N-H? on Glycine as acceptors as well. May I ask if there is any way I can let just the ?O? on Proline be the acceptor and ?N-H? on Glycine be the donor? In other words, I would like to have 32 donors and 16 acceptors.
>>
>> Is there any way to do that?
>>
>> Thanks in advance!
>>
>> Binwu
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
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>
>
> ------------------------------
>
> --
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>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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