[gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 112
Raag Saluja
saluja.raag at gmail.com
Tue Apr 25 19:47:50 CEST 2017
Thank you, Justin! I will definitely try this out. However, I can't find
anyone or any paper where they have done a similar thing... Could you
please suggest which force field should be the best to try first?
On Tue, 25 Apr 2017 at 2:08 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: HBond for F and S (Justin Lemkul) (Marcelo Dep?lo)
> 2. User Defined Potentials (Ommair Ishaque)
> 3. Most suitable intervals of temperature in REMD (????? ?????????)
> 4. Hbond residence time (Marcelo Dep?lo)
> 5. addition of an isopeptide bond and its simulation (Raag Saluja)
> 6. CG Graphene - dihedral problem/parameter (Sajjad Kavyani)
> 7. Re: User Defined Potentials (Vytautas Rakeviius)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 24 Apr 2017 17:59:28 -0300
> From: Marcelo Dep?lo <marcelodepolo at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] HBond for F and S (Justin Lemkul)
> Message-ID:
> <
> CAFAAhpbgfZNomPkFtoWGJREPO86_wrAWugstz-PkPtYEb9jrdw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks, Justin!
>
>
> It worked just fine.
>
> I guess using a flag to include different atomtypes into the analyses would
> be a nice feature for next GROMACS versions.
>
> Cheers!
> --
> Marcelo Dep?lo Pol?to
> DSc. Cell and Molecular Biology - UFRGS (Brazil)
> Group of Structural Bioinformatics - Room 202
> Center of Biotechnology - UFRGS
> Phone: + 55 51 3308-7770
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 24 Apr 2017 17:58:05 -0400
> From: Ommair Ishaque <ommair at udel.edu>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] User Defined Potentials
> Message-ID:
> <
> CAJmqV+b-VL-GdwyikrDBwbuKdz6cSztUXLpfjSKPcaWBX+YK1A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I am Phd physics phd student at University of Delaware. I am using GROMACS
> for calculation of solvation energy of argon or methane in water. But Our
> water model has additional interaction terms other than already define in
> GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*
>
> And one of my senior colleagues was telling me in past, GROMACS had no
> quaternion algorithm for rigid molecules. It handles rigid molecules using
> SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
> we will be able to use it for our water model (CC-5spol) which has at least
> 25 sites. *If there is now a means of truly propagating the motion of rigid
> molecules without SHAKE/RATTLE/LINCS, this will be great.*
>
> I am looking forward for your positive reply. Thanks
>
> Ommair Ishaque
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 25 Apr 2017 08:09:42 +0900
> From: ????? ????????? <b.mijiddorj at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Most suitable intervals of temperature in REMD
> Message-ID:
> <CABgRApvdCMYtNiMa8J8JsonWD6Gq0dqiFARvqV==
> Wz4vrHatwA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gmx users,
>
> Do you have a suggestions and discussions about most suitable temperature
> intervals for REMD simulations of the peptides?
>
> Best regards,
> Mijee
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 24 Apr 2017 22:45:01 -0300
> From: Marcelo Dep?lo <marcelodepolo at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Hbond residence time
> Message-ID:
> <CAFAAhpao6fnJFv2cS5re08j5LbBbXUtk+EnRf9hXX9w=
> Wjf8Lg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all!
>
>
> I have been looking into the autocorrelation function outputs of 'gmx
> hbond' in order to calculate the residence time for my water hbond to a
> specific heteroatom. It turns out that I couldn't find any detailed
> explanation about each 'type' outputted. In my case:
>
> Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
> Forward 3.384 0.296 1.506 0.0290557
> Backward -0.183 -5.477 -666.000
> One-way 8.291 0.121 -0.716
> Integral 0.802 1.247 5.075
> Relaxation 0.767 1.303 5.185
>
> Does anyone have a suggestion of what each of these types mean?
>
> Thanks in advance!
> --
> Marcelo Dep?lo Pol?to
> DSc. Cell and Molecular Biology - UFRGS (Brazil)
> Group of Structural Bioinformatics - Room 202
> Center of Biotechnology - UFRGS
> Phone: + 55 51 3308-7770
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 25 Apr 2017 10:12:24 +0530
> From: Raag Saluja <saluja.raag at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] addition of an isopeptide bond and its simulation
> Message-ID:
> <CALwqOC5BF_d++d2QeZHDyz2-qVrvb8Hp-K84VSkhWpV1hKR=
> mQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi!
>
> I need to study the effect of post-translational modifications on the
> biophysical properties of my protein. This involves the addition of an
> isopeptide bond to the primary chain of the C-terminal tail.
>
> How may I add this isopeptide bond? And then which force field can I use to
> simulate it?
>
> Looking forward to your kind help!
> Regards,
> Raag
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 25 Apr 2017 12:57:03 +0430
> From: Sajjad Kavyani <kavyani.sajjad at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] CG Graphene - dihedral problem/parameter
> Message-ID:
> <CAMns7=
> 5NJ2mhT_txKCdFnF5TCysBwQWNj_TKQ53q_OOeLwdqRA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear experts,
> I want to simulate a graphene sheet with MARTINI force field. (In MARTINI
> FF, the banzene is represented with 3 beads)
> The problem I encountered with is the dihedral parameter.
> I searched papers and found that the dihedral parameters for the sheet are
> K=3.1, n=2 and phi =180. just that
>
> The parameter (itp) and the gro I used is in the zip-file below:
>
> https://drive.google.com/open?id=0B8rMZ-61IzIWQS0tTTE1Qk9aM28
>
> It is noteworthy that I tried both dihedral type
> 3 4.000 0.000 -4.000 0.000 0.000 0.000
> and
> 1 180.00 2.0 2
>
> but in every EM run, the forces are high.
>
> Could you please help me how to place the parameter in the topology? and
> what should order of indices be? Is they correct?
>
> Regards
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 25 Apr 2017 07:46:22 +0000 (UTC)
> From: Vytautas Rakeviius <vytautas1987 at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>,
> "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] User Defined Potentials
> Message-ID: <523284338.986381.1493106382145 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Inside GROMACS folder go share/top/ you will find folders for force fileds
> like gromos53a5.ff/ there are files with water topology like tip3p.itp you
> can write your own using them as examples.
>
>
> On Tuesday, April 25, 2017 12:58 AM, Ommair Ishaque <ommair at udel.edu>
> wrote:
>
>
> Hi,
>
> I am Phd physics phd student at University of Delaware. I am using GROMACS
> for calculation of solvation energy of argon or methane in water. But Our
> water model has additional interaction terms other than already define in
> GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*
>
> And one of my senior colleagues was telling me in past, GROMACS had no
> quaternion algorithm for rigid molecules. It handles rigid molecules using
> SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
> we will be able to use it for our water model (CC-5spol) which has at least
> 25 sites. *If there is now a means of truly propagating the motion of rigid
> molecules without SHAKE/RATTLE/LINCS, this will be great.*
>
> I am looking forward for your positive reply. Thanks
>
> Ommair Ishaque
> --
> Gromacs Users mailing list
>
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>
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