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 < [email protected]> wrote: > Send gromacs.org_gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > 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 <[email protected]> > To: [email protected] > Subject: [gmx-users] query regarding center of mass removal > Message-ID: > <CAEScH66GPJ2cmUJPTAh0m2U=nhCmaG4HmTisXiR_sfv11Zr0= > [email protected]> > 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 <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] query regarding center of mass removal > Message-ID: <[email protected]> > 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 > > [email protected] | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 3 > Date: Sat, 4 Jan 2020 02:11:21 +0000 > From: Neena Susan Eappen <[email protected]> > To: "[email protected]" > <[email protected]> > Subject: Re: [gmx-users] What is the "gen-vel" used for? > Message-ID: > < > yt1pr01mb37234d43c1489f79c11faeadcd...@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 <[email protected]> > To: "[email protected]" > <[email protected]> > Subject: Re: [gmx-users] amide-capped C-terminus; OPLS force field > Message-ID: > < > yt1pr01mb3723bf41d44ed7648364e666cd...@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 <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] nrexcl value for ions > Message-ID: > <CACrPy4BsEr0AK9Nt-Tb= > [email protected]> > 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 <[email protected]> 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 > > > > [email protected] | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > 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 [email protected]. > > > > > ------------------------------ > > -- > 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 [email protected]. > > End of gromacs.org_gmx-users Digest, Vol 189, Issue 7 > ***************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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