[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 63
Faez Iqbal Khan
khanfaezkhan at gmail.com
Mon Aug 14 15:51:55 CEST 2017
Dear Justin,
I talk to administrator
They said:
"Dear Faez,
I picked this up in your error file:
There is no domain decomposition for 105 ranks that is compatible with the
given box and a minimum cell size of 1.025 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition"
Can you please suggest, how to use thes commands.
Thanks
On Sun, Aug 13, 2017 at 10:31 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: NVT error (Justin Lemkul)
> 2. Re: Magic Number Error in XTC file (read 0, should be 1995)
> (Justin Lemkul)
> 3. Re: ligand (farial tavakoli)
> 4. Re: ligand (Justin Lemkul)
> 5. Difference in omega angles!! (Seera Suryanarayana)
> 6. Re: Difference in omega angles!! (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 13 Aug 2017 13:11:39 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] NVT error
> Message-ID: <5b2aa8f8-1873-3983-0be3-143eb12e593b at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/13/17 12:45 PM, Faez Iqbal Khan wrote:
> > Hi
> > I am running MD simulation of Pro-Lig complex using protocol provided by
> Justin
> > Lemkul.
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/complex/06_equil.html
> > <https://www.researchgate.net/deref/http%3A%2F%2Fwww.
> bevanlab.biochem.vt.edu%2FPages%2FPersonal%2Fjustin%
> 2Fgmx-tutorials%2Fcomplex%2F06_equil.html>
> >
> > I am getting error at NVT stage.
> >
> > I am attaching my log files. Please suggest. Many many Thanks
>
> I don't see any error message, it just looks like your run hung. Talk to
> your
> system administrator about proper usage and/or compilation.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 13 Aug 2017 13:12:43 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Magic Number Error in XTC file (read 0,
> should be 1995)
> Message-ID: <2af71571-a1cc-0ee9-cd45-7a86d4ae0a3f at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/13/17 12:47 PM, ZHANG Cheng wrote:
> > Hi Justin,
> > Thank you for explaining that.
> >
> >
> > You said "a more reliable system", what does this mean? It is my first
> time adding glycines to my protein using OPLS-AA/L force field. Do you
> think this might be the reason, and should I switch to another force field?
> >
>
> I'm talking about hardware. Failure to write a valid frame is usually due
> to a
> filesystem problem (i.e. hard disk). It doesn't matter what your force
> field is
> or what your system contents are.
>
> >
> > My procedure is as follows:
> > 1) I get the glycine and protein pdb, convert them to .gro files using
> > gmx pdb2gmx -f glycine/protein.pdb -o glycine/protein.gro -water spce
> -inter
> > 2) then I add the protein.gro into a box, get the protein_newbox.gro:
> > gmx editconf -f protein.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
> > 3) then I add glycines to this box:
> > gmx insert-molecules -ci glycine.gro -nmol 203 -f protein_newbox.gro -o
> protein_203_glycine.gro
> > 4) then I do the exactly the same thing according to your tutorial, i.e.
> solvent with water, add ions, energy minimization, NVT, NPT, and finally
> the MD.
> >
> >
> > Can I ask if the procedure is correct? Would you please recommend some
> tutorial for prepare a system with protein and excipients (e.g. glycine,
> sorbitol, etc)?
> >
>
> It's fine.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 13 Aug 2017 16:29:33 +0000 (UTC)
> From: farial tavakoli <farial.tavakoli at ymail.com>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] ligand
> Message-ID: <1556367219.1034652.1502641773209 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
> #715FFA solid !important; padding-left:1ex !important;
> background-color:white !important; } Dear justin
> Thank you for your replyI thought that topology file obtained from ATB
> needs to be changed like PRODRG
>
>
> Sent from Yahoo Mail for iPhone
>
>
> On Sunday, August 13, 2017, 8:43 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
>
>
>
> On 8/13/17 3:13 AM, ?farial tavakoli? ? wrote:
> > Dear GROMACS users
> >
> > I noticed my ligand has some broken bonds and changes in atoms
> arrengement after md simulation was done. I have read before that no bond
> is broken and created in simulation . So why have been ligand changed ?
> > I think, i have to notice that when i wanted to create a ligand topology
> , i used ATB server to create topology and pdb files. and when wanted to
> reassign the charges and charge groups, noticed that some of the atoms of
> ligand that have to be in a charge group, were not successive? , so decided
> to rearrange them and replaced them to place them in a charge group.
>
> Why did you modify the topology?? Usually ATB topologies require no
> modification.? If you "rearranged" atoms in any way, then you irreparably
> broke
> the topology because no all of the bonded interactions are nonsense.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
> --
> 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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>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 13 Aug 2017 13:15:29 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] ligand
> Message-ID: <8bf679fa-1ee3-f677-74f0-f5d4ff64e171 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/13/17 12:29 PM, farial tavakoli wrote:
> > blockquote, div.yahoo_quoted { margin-left: 0 !important;
> border-left:1px #715FFA solid !important; padding-left:1ex !important;
> background-color:white !important; } Dear justin
> > Thank you for your replyI thought that topology file obtained from ATB
> needs to be changed like PRODRG
> >
>
> No, they generally should not. ATB is a much better topology source than
> PRODRG. That doesn't necessarily mean you should always trust a black box
> without some validation, but you shouldn't just blindly go messing with
> things
> because some other program is known to be problematic.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 14 Aug 2017 02:00:06 +0530
> From: Seera Suryanarayana <palusoori at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Difference in omega angles!!
> Message-ID:
> <CAAr94NOw68kNBUU9QU06fULcd-20K_64qm_=smjETQpHj3+x+w at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gromacs users
>
> First I have done simulations of peptide for 100ns. And then I have
> generated the .pdb file after energy minimization by following commands
> executed.
>
> gmx trjconv -s em.tpr -f em.trr -o em.pdb
>
> After generation of PDB file, I did mutation at one position in em.pdb file
> and named it em_mt.pdb. Then generated topology file, created box, solvated
> and added the counter ions to em_mt.pdb's simulation system to neutralize
> the system. After this I have done energy minimization with complete
> protein restrained. As I restrained the peptide during energy minimization,
> I expected the same torsion and omega angles in em_mt.pdb after energy
> minimization. But I got some different omega angles when I compared with
> the omega angles of em.pdb. The maximum difference is 5. what could be the
> reason in difference of omega angles between em.pdb and em_mt.pdb, even
> though the later one is restrained?
>
> Thanks in advance
> Surya
> Graduate student
> India.
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 13 Aug 2017 16:31:18 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Difference in omega angles!!
> Message-ID: <65e7ff5c-dbb6-af55-a7e7-9be5adb6068a at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/13/17 4:30 PM, Seera Suryanarayana wrote:
> > Dear gromacs users
> >
> > First I have done simulations of peptide for 100ns. And then I have
> > generated the .pdb file after energy minimization by following commands
> > executed.
> >
> > gmx trjconv -s em.tpr -f em.trr -o em.pdb
> >
> > After generation of PDB file, I did mutation at one position in em.pdb
> file
> > and named it em_mt.pdb. Then generated topology file, created box,
> solvated
> > and added the counter ions to em_mt.pdb's simulation system to neutralize
> > the system. After this I have done energy minimization with complete
> > protein restrained. As I restrained the peptide during energy
> minimization,
> > I expected the same torsion and omega angles in em_mt.pdb after energy
> > minimization. But I got some different omega angles when I compared with
> > the omega angles of em.pdb. The maximum difference is 5. what could be
> the
> > reason in difference of omega angles between em.pdb and em_mt.pdb, even
> > though the later one is restrained?
> >
>
> A restraint is a biasing potential that disfavors movement, but does not
> prevent
> it. So it is possible that the structure changes.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
> ------------------------------
>
> --
> 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
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>
> End of gromacs.org_gmx-users Digest, Vol 160, Issue 63
> ******************************************************
>
--
*Dr. Faez Iqbal Khan (**فائز اقبال خان)*
(1) Postdoctoral Researcher (March 2017 - Present), Computational
Mechanistic Chemistry and Drug Discovery, Rhodes University, South Africa
(2) Postdoctoral Researcher (Nov 2015 - Feb 2017), Henan University of
Technology in collaboration with South China University of Technology,
China.
(3) Ph.D. (2012-2015), Durban University of Technology, South Africa.
(4) M.Sc. Bioinformatics (2009-2012), Jamia Millia Islamia, India.
(5) B.Sc. Biomedical Science (2006-2009), Delhi University, India.
*Google Scholar:* https://scholar.google.com/citations?user=viCqGO4AAAAJ&hl
*Research Gate:* https://www.researchgate.net/profile/Faez_Khan
*Scopus Author ID:* 56333298500
<http://www.scopus.com/inward/authorDetails.url?authorID=56333298500&partnerID=MN8TOARS>
*ResearcherID:* H-2830-2016 <http://www.researcherid.com/rid/H-2830-2016>
*ORCID ID: *orcid.org/0000-0001-9088-0723
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