[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 74

Naba nabajyoti.goswami at gmail.com
Wed Aug 16 09:38:36 CEST 2017 

Dear users,

Please let me know whether it is feasible and relevant or not if I use COM
pulling for mechanical unfolding of proteins. More specifically, whether I
can define the two group within the same molecule !!


On Wed, Aug 16, 2017 at 6:48 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: Fwd: (Justin Lemkul)
>    2. (Don't know if mail worked last time)Drift with
>       groups+tabulated potential. (sperez14 at us.es)
>    3. how to make molecular model with both ion channel and     lipid
>       bilayer? (Li, Tong)
>    4. Re: how to make molecular model with both ion channel and
>       lipid bilayer? (h.alizadeh at znu.ac.ir)
>    5. Doing restart (?farial tavakoli? ?)
>    6. npt simulation error (Mohammad Zahidul Hossain Khan)
>    7. Re: npt simulation error (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 15 Aug 2017 08:02:45 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fwd:
> Message-ID: <c2806875-ebe0-d575-e462-381c707ca501 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/15/17 1:52 AM, saranya wrote:
> > Hi,
> > I have done protein-drug simulations for 100ns. While calculating the
> hydrogen
> > bond between the protein-drug complex I am getting only 2 hydrogen bonds.
> > The number of H-bond formation is very low I have a question about is
> there
> > any influence of the drug in my protein?
> To answer that, you need to do simulations of the apo protein and
> compare whatever relevant structural metrics there are (not H-bonds, as
> these tell you about the ligand-protein interactions but nothing about
> the impact on the protein structure).
>
> -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: Tue, 15 Aug 2017 14:25:30 +0200
> From: sperez14 at us.es
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] (Don't know if mail worked last time)Drift with
>         groups+tabulated potential.
> Message-ID: <4e579ca344c855cabbbbf935a5ebc2a0 at us.es>
> Content-Type: text/plain; charset=US-ASCII
>
> Dear GROMACS Community,
>
> First of all, if someone got this email twice, I am sorry. It is my
> first post and I was not sure if it worked.
>
> I am trying to do a simulation using a tabulated potential which forces
> me to use the group cut-off. I get a drift in the conserved quantity of
> -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
> and a Na+ ion. I imagine that eventhough it will soon be deprecated the
> group cutoff scheme still works correctly. I have tryed to change the
> parameters without success and in any case the ones I use seem
> reasonable (in my experience using other programs). The rdfs of the
> system look normal so I ruled out topology problems.
>
> It seems that the problem is in the group cut-off since
> when I change the tabulated potential for a regular vdw the problem
> persists. I have followed the instructions of:
>
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>
> to implement the tabulated potentials.
>
> Is this the kind of energy drift acceptable? I have pasted a copy .mdp
>
> Thanks for your help,
>
> Sergio Perez-Conesa
>
> integrator = md
> dt = 0.001
> nsteps = 100000
> init-step = 0
> cutoff-scheme = group
> nst-list = 1
> verlet-buffer-tolerance = 0.0005
> ns-type = grid
> rlist = 1.3
> pbc = xyz
> coulombtype = PME-switch
> rcoulomb = 1.
> rcoulomb-switch = 0.95
> pme-order = 4
> fourierspacing = 0.1
> ewald-rtol = 1.e-5
> vdwtype = user
> rvdw = 1.0
> DispCorr = No
> tcoupl = v-rescale
> tc-grps = System
> ;nsttcouple = 1
> tau-t = ref-t = 300.0
> constraints = all-angles
> constraint-algorithm = LINCS
> lincs_iter = 1
> lincs_order = 4
> energygrps = NA OW
> energygrp_table = NA OW
> comm-mode = linear
>
> ------------------------------
>
> Message: 3
> Date: Tue, 15 Aug 2017 15:09:27 +0000
> From: "Li, Tong" <tongli at udel.edu>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] how to make molecular model with both ion channel
>         and     lipid bilayer?
> Message-ID: <a58e2d39d21544f2a8a14ff6e9eff077 at udel.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> I am trying to make a model of ion channel with cell membrane. Is there a
> specific software to make this? I mean just the coordination file. VMD can
> generate the membrane automatically, I can find the 'pdb' files of ion
> channels, but I have no idea how to combine them.
>
> Thanks all,
> Tong
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 15 Aug 2017 16:49:43 +0000
> From: h.alizadeh at znu.ac.ir
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] how to make molecular model with both ion
>         channel and lipid bilayer?
> Message-ID: <d39070d67bb0c37d48b5c650a2939ae3 at mail.znu.ac.ir>
> Content-Type: text/plain; charset="utf-8"
>
> Charmm-gui.org could help you.
> Bests,
> Hadi
> On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong"  wrote:
> Dear all,
>
> I am trying to make a model of ion channel with cell membrane. Is there a
> specific software to make this? I mean just the coordination file. VMD can
> generate the membrane automatically, I can find the 'pdb' files of ion
> channels, but I have no idea how to combine them.
>
> Thanks all,
> Tong
> --
> Gromacs Users mailing list
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>
> ------------------------------
>
> Message: 5
> Date: Tue, 15 Aug 2017 22:46:14 +0000 (UTC)
> From: ?farial tavakoli? ?       <farial.tavakoli at ymail.com>
> To: Discussion List for GROMACS Users <gmx-users at gromacs.org>
> Subject: [gmx-users] Doing restart
> Message-ID: <1962486576.3101166.1502837174489 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> #yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted
> {margin-left:0 !important;border-left:1px #715FFA solid
> !important;padding-left:1ex !important;background-color:white;} Dear gmx
> users
> I stoped my md simulation and now i want to restart it.
> I use gromacs 2016.3? and issued this command to perform md:Gmx grompp -f
> md.mdp -c npt.gro -t npt.cpt -p topol.tpr -n index.ndx -o md_0_1.tprGmx
> mdrun -deffnm md_0_1
> To restart simulation i issuedGmx mdrun -s md_0_1.tpr ?-cpi md_0_1.cpt
> -appendBut faced to an error:
> Fatal error:
> File appending requested, but 2 of the 3 output files are not present or
> are
> named differently. For safety reasons, GROMACS-2016 and later only allows
> file
> appending to be used when all files have the same names as they had in the
> original run. Checkpointing is merely intended for plain continuation of
> runs.
> For safety reasons you must specify all file names (e.g. with -deffnm), and
> all these files must match the names used in the run prior to checkpointing
> since we will append to them by default. If the files are not available,
> you
> can add the -noappend flag to mdrun and write separate new parts. For mere
> concatenation of files, you should use the gmx trjcat tool instead.
>
> i refered to google but i couldnt understand well what should i type
> exactly. would you please help me to restart my md simulation?
> Thanks in advanceFarial
>
>
> Sent from Yahoo Mail for iPhone
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 15 Aug 2017 18:14:49 -0700
> From: Mohammad Zahidul Hossain Khan <za.parash at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] npt simulation error
> Message-ID:
>         <CAAdBV7bGg0ZPm-R9nO8tagfPorV15h1bFp=FR30+Sf1gRW=
> z5Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Sir
>
> I am trying to simulate protein_ligand complex using epsilon = 4 and it is
> giving the below error
>
> *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x*
>
> I have no idea how to solve this problem
> --
>
>
> *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> *Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
> * Skype: parash.khan2*
> *Cell: +12085967165*
>
> ------------------------------
>
> Message: 7
> Date: Tue, 15 Aug 2017 21:18:14 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] npt simulation error
> Message-ID: <dd482641-ce0a-a873-f7f9-13b04f75292f at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
> > Dear Sir
> >
> > I am trying to simulate protein_ligand complex using epsilon = 4 and it
> is
> > giving the below error
> >
>
> What is epsilon = 4?
>
> > *2 particles communicated to PME rank 4 are more than 2/3 times the
> cut-off
> > out of the domain decomposition cell of their charge group in dimension
> x*
> >
> > I have no idea how to solve this problem
> >
>
> Have you Googled it, or gone to the GROMACS error page, where lots of
> advice
> lives? ;)
>
> -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/
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> End of gromacs.org_gmx-users Digest, Vol 160, Issue 74
> ******************************************************
>



-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India

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