[gmx-users] query regarding center of mass removal

Sat Jan 4 07:38:28 CET 2020

Thank you Prof. Lemkul for your kind reply. In mdp file, I will set
comm_grps to "system". But in tc-grps, can I couple capsid with Ca2+ ions?
240 Ca2+ ions are non-covalently attached with the capsid and have
important role in maintaining capsid stability.

I am also planing to run another set of simulation, where RNA is
non-covalently attached with the capsid. In tc-grps, I can couple capsid,
RNA and Ca2+ ions together. I am looking forward for your reply.

-Snehasis

On Sat, Jan 4, 2020 at 12:02 AM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. query regarding center of mass removal (Snehasis Chatterjee)
>    2. Re: query regarding center of mass removal (Justin Lemkul)
>    3. Re: What is the "gen-vel" used for? (Neena Susan Eappen)
>    4. Re: amide-capped C-terminus; OPLS force field (Neena Susan Eappen)
>    5. Re: nrexcl value for ions (Dhrubajyoti Maji)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 3 Jan 2020 15:29:49 -0500
> From: Snehasis Chatterjee <snehasis.chatterjee18 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] query regarding center of mass removal
> Message-ID:
>         <CAEScH66GPJ2cmUJPTAh0m2U=nhCmaG4HmTisXiR_sfv11Zr0=
> w at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Gromacs users,
>
> I am trying to perform a virus capsid simulation using GROMACS 2018. 240
> Calcium ions bound to specific regions of the capsid and have important
> role in maintaining capsid stability. In this context, I had a query
> regarding the correct Center-of-Mass removal settings. I usually run
> protein simulation in aqueous environment using following mdp options:
>
>
>
> *nstcomm= 100comm_mode= linearcomm_grps= Protein Non-Protein*
>
> In aqueous environment, I typically use "Protein Non-Protein," with
> Non-Protein containing solvent and ions. Since, 240 Ca2+ ions are
> non-covalently attached with the capsid, I am planing to couple  capsid
> with Ca2+ ions. I am bit confused regarding this issue. Any kind of advice/
> suggestions will be deeply appreciated.
>
> Thanks in advance,
> Snehasis Chatterjee
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 3 Jan 2020 17:22:01 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] query regarding center of mass removal
> Message-ID: <0087bf32-f571-8dc4-0fc5-2e73c65af126 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/3/20 3:29 PM, Snehasis Chatterjee wrote:
> > Dear Gromacs users,
> >
> > I am trying to perform a virus capsid simulation using GROMACS 2018. 240
> > Calcium ions bound to specific regions of the capsid and have important
> > role in maintaining capsid stability. In this context, I had a query
> > regarding the correct Center-of-Mass removal settings. I usually run
> > protein simulation in aqueous environment using following mdp options:
> >
> >
> >
> > *nstcomm= 100comm_mode= linearcomm_grps= Protein Non-Protein*
> >
> > In aqueous environment, I typically use "Protein Non-Protein," with
> > Non-Protein containing solvent and ions. Since, 240 Ca2+ ions are
> > non-covalently attached with the capsid, I am planing to couple  capsid
> > with Ca2+ ions. I am bit confused regarding this issue. Any kind of
> advice/
> > suggestions will be deeply appreciated.
>
> For any system in an isotropic medium (i.e. water), comm-grps should be
> set to "system" because there are not multiple phases that may diffuse
> differently. You shouldn't use Protein/Non-Protein here; that's for
> tc-grps.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 4 Jan 2020 02:11:21 +0000
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] What is the "gen-vel" used for?
> Message-ID:
>         <
> YT1PR01MB37234D43C1489F79C11FAEADCD220 at YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yeping Sun,
>
> Quoting Justin's answer for a similar question I had on how to repeat a
> simulation say 10 times
>  " To run 10 independent simulations, I would run minimization once and
> start from 10 new equilibration runs, each with a different set of initial
> velocities (change gen_seed or simply set to -1).That approach may not be
> as robust as starting from 10 different configurations, but the exact
> approach depends on the system in question".
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 4 Jan 2020 02:36:39 +0000
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] amide-capped C-terminus; OPLS force field
> Message-ID:
>         <
> YT1PR01MB3723BF41D44ED7648364E666CD220 at YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I do this by adding amide group at the C-terminus on Pymol, use -ter flag
> during gmx pdb2gmx command, select None (for C-terminus), N and H in that
> amide group are automatically recognized as atom types opls 237 and opls
> 240 respectively. The net charge of system remains neutral.
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 4 Jan 2020 10:31:21 +0530
> From: Dhrubajyoti Maji <dmaji43 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] nrexcl value for ions
> Message-ID:
>         <CACrPy4BsEr0AK9Nt-Tb=
> h8-feY+4DyypaS-TgRqg_ZBsK6fO5g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you Prof. Lemkul for your kind reply.
>
> Dhrubajyoti
>
> On Sat, 4 Jan 2020 at 01:01, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 1/3/20 12:10 AM, Dhrubajyoti Maji wrote:
> > > Dear gromacs users,
> > >       A very happy new year to all of you. I an trying to simulate LiBr
> > and
> > > LiNO3. What will be the value of nrexcl in OPLS itp file for respective
> > > cation and anions? I found nrexcl=1 for atomic ions in ions.itp file in
> > > gromacs. Again in a tutorial of simulation of Choline Chloride + urea,
> > they
> > > have used nrecxl=3 for chloride ion. Here, I am confused about this.
> Any
> > > kind of help will be highly appreciated.
> >
> > There are no covalent bonds in monoatomic ions, so any value of nrexcl
> > can be used. NO3 has a maximum of two contiguous covalent bonds so
> > nrexcl = 2. Or you can set nrexcl = 3 for everything, which has the
> > exact same effect.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
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> End of gromacs.org_gmx-users Digest, Vol 189, Issue 7
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