[gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 24
amitabh jayaswal
amitabhjayaswal at gmail.com
Thu Jul 6 06:57:15 CEST 2017
... well, this URL under ans.2 (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm
repeatedly getting.
Please rectify/improve.
Thanks and regards!
*Amitabh Jayaswal*
*PhD Bioinformatics Scholar*
*Banaras Hindu University*
*Varanasi, U.P., India | PIN-221005*
*+*
*City Coordinator*
*United Nations*
*Rio+22 Power India Program*
M: +91 (9868 330088 and 7376 019 155)
On Thu, Jul 6, 2017 at 12:21 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: gromacs.org_gmx-users Digest, Vol 158, Issue 165
> (Davide Bonanni)
> 2. Charge Mutation (State B) for Ions (Hermann, Johannes)
> 3. Number of ions in Anionic lipid system- Charmm-GUI (Nidhin Thomas)
> 4. simulation at different temperature (Alex Mathew)
> 5. Re: simulation at different temperature (Alex)
> 6. Re: simulation at different temperature (Alex Mathew)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 5 Jul 2017 17:09:14 +0200
> From: Davide Bonanni <davide.bonanni at unito.it>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue
> 165
> Message-ID:
> <CAL99HEKY+QfSrn-cZDPL8W7azA-HAPqxkOSeRYaE+Go9dGstkQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Hannes,
>
> Thank you very much for your reply, really appreciated.
>
>
>
> > Date: Mon, 26 Jun 2017 12:09:45 +0100
> > From: Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk>
> > To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Cc: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation
> > Message-ID: <20170626120945.75215167 at stfc.ac.uk>
> > Content-Type: text/plain; charset="US-ASCII"
> >
> > On Mon, 26 Jun 2017 12:25:19 +0200
> > Davide Bonanni <davide.bonanni at unito.it> wrote:
> >
> > > 1) Can I perform the calculation in a single step with soft core
> > > potential enabled? I mean, is it correct to transform directly the
> > > hydrogen into a chlorine instead of using 2 topologys and 2
> > > complexes, where in the first step I transform the hydrogen into
> > > dummy atom, and in the second I transform the dummy atom into
> > > chlorine.
> >
> > Technically speaking you can perfectly do that but in practice it can
> > be much more efficient to directly and linearly transform one atom type
> > into another (single topology approach). There is no need for a
> > softcore potential in this case. Those would only be activated for
> > atoms that either appear or disappear i.e. atoms with zero vdW
> > parameters. The input and topology files from FEsetup should be all
> > you need.
>
>
> Can I have problems if I keep active the softcore potential whether is not
> needed?
>
>
> > > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation (
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
> > > x-tutorials/free_energy/index.html), I have to perform every step of
> > > molecular dynamics at every Lambda value, is that right?
> >
> > Yes, you will need to do a simulation for every and each lambda step.
> >
> >
> > > 3) I run a test minimization step (mdp file attached) of my complex
> > > at the last "init-lambda-state", 15 in my case. Looking at the .trr
> > > output file I can see that the bond between the carbon and the
> > > hydrogen which should be trasformed is longer than a normal C-H bond,
> > > but the atom is still recognized as hydrogen (picture
> > > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ;
> > > blue -> init-lambda-state = 15). I was wondering if this is what I am
> > > supposed to see, so if gromacs is considering the state B of my
> > > system where I have chlorine bound to carbon instead hydrogen.
> >
> > What does "recognized as hydrogen" mean? I suspect that what you are
> > referring to is the output of some visualisation program because you
> > instructed it to interpret that particular atom to be a hydrogen.
> >
> > What you need to expect to see is that a C-H bond is transformed into a
> > C-Cl bond and accordingly the bond length increases.
> >
>
> Of course, It's like you said. I see the bond length to increase as in the
> img "http://tinypic.com/r/2wp11dh/9".
> Thank you again.
>
> Cheers,
>
> Davide Bonanni
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 5 Jul 2017 18:05:08 +0200
> From: "Hermann, Johannes" <J.Hermann at lrz.tu-muenchen.de>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Charge Mutation (State B) for Ions
> Message-ID: <1a8a1886-71aa-9162-3db1-cf79b0d2df69 at lrz.tum.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear all,
>
> I am doing a FEC via alchemical transformation. In order to keep the
> charge constant I plan to mutate ions at the same time. In particular, I
> want to change the charge of MG ions. My question is did I manipulate
> the .top .itp and .gro file in the right way:
>
> In the topology.top file I added:
>
> #include "topol_MG_Hybrid.itp"
>
> in the beginning and included in the [molecules] section
>
> MG_HBRID 26
>
> at the place where my hybrid MGs begin in the .gro file. In the .tip
> file I defined the new moleculetype and the atom:
>
> [ moleculetype ]
> ; Name nrexcl
> MG_HBRID 1
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 MG 1 MGX MGHBR 1 2 24.305
> MG 2.30769 24.305
>
> In the gro file I changed the (formaly regular) MGs to:
>
> 8702MGX MGHBR55183 -1.480 0.077 2.991
>
> I.e. I changed the residue name to MGX and the atom name to MGHBR. I ran
> grompp and it compiles without errors. However, I want to make sure,
> that this is consistent with gromacs files and that I will change the
> charge in the simulation.
>
> Thank you very much for your help!
>
> All the best
> Johannes
>
>
> --
> ______________________________________
> *Technische Universit?t M?nchen*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl f?r Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.hermann at lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 5 Jul 2017 11:17:32 -0500
> From: Nidhin Thomas <nidhin.thomas0624 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Number of ions in Anionic lipid system-
> Charmm-GUI
> Message-ID: <55D343B4-B971-44FF-A428-E5799E1B40AA at gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Justin,
>
> Thanks a lot for the prompt reply.
>
> I used just 400 POPC lipids to build the lipid bilayer and when I added
> 150 mM KCl, it added 49 K+ and 49 Cl- to the system. Do you think these
> numbers are correct? Could you please tell me how I can check the correct
> number of ions?
>
> The size of the original system (300 POPC + 100 POPG) was (11.7480468
> 11.7480468 8.98 ) nm. If the size of the system is very small to
> accommodate the ions, how can I change the size of the system in charmm-gui
> ? Or should I just get the bilayer system and add ions by myself using
> gonion command in gromacs?
>
> Thanks,
>
> Nidhin Thomas
>
> >> Dear GROMACS Users,
> >>
> >> I have created a lipid bilayer system (300 POPC + 100 POPG) using
> CHARMM-GUI.
> >> I want to include 0.150 M KCl in the system. When I use the option in
> charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the
> number of ions using the size of simulation box, I am getting 98 ions.
> >>
> >> Can anyone tell me what I should do to get the exact number of ions in
> the system?
> >>
> >
> > CHARMM-GUI calculates an excluded volume due to the solute (protein,
> nucleic
> > acid, lipids, etc) so using the total box volume is incorrect when
> calculating
> > the number of ions in solution. The result you're getting tells you
> that your
> > box is too small (insufficient solvent volume) to achieve 150 mM KCl.
> >
> >> Would it be correct if I first neutralize the system using 100 K+ ions
> and then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system?
> >>
> >
> > No, because then your effective concentration is much higher than what
> you want.
> >
> > -Justin
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 5 Jul 2017 23:15:17 +0530
> From: Alex Mathew <alexmathewmd at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] simulation at different temperature
> Message-ID:
> <CAAW-8xV3xtfsPqBnczmvAvG413rmJS+Abo-LGOeYZ9GpF3BMOw at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gmx users,
>
> I would like to see the temperature dependence of an ion channel/membrane
> protein in lipid bilayer system. My plan is to run a simulation at 300 K to
> 340 K by increasing 5 K and observing the permeation of molecules, pore
> diameter, sec structure .etc. Are there any techniques available to do
> this at a time? Or I have to run the independent simulation for all these?
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 5 Jul 2017 12:31:04 -0600
> From: Alex <nedomacho at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] simulation at different temperature
> Message-ID: <7c89d0a8-6ac3-fd54-608f-ce2604a90897 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Of course: http://manual.gromacs.org/online/mdp_opt.html -- see
> 'simulated annealing'.
>
> Alex
>
>
> On 7/5/2017 11:45 AM, Alex Mathew wrote:
> > Dear gmx users,
> >
> > I would like to see the temperature dependence of an ion channel/membrane
> > protein in lipid bilayer system. My plan is to run a simulation at 300 K
> to
> > 340 K by increasing 5 K and observing the permeation of molecules, pore
> > diameter, sec structure .etc. Are there any techniques available to do
> > this at a time? Or I have to run the independent simulation for all
> these?
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 6 Jul 2017 00:21:29 +0530
> From: Alex Mathew <alexmathewmd at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] simulation at different temperature
> Message-ID:
> <CAAW-8xWpeOiyMjP5wXjd3m1Ado6huFHA4SfzAg79e_iZZk+O1w at mail.gmail.
> com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Alex,
>
> I guess this is annealing and which will give only one output.xtc, I'm
> looking for full dynamics of the system (say 100 ns for each temperature,
> 300 K,305 K....340 K ). Further, I need to compare the results with each
> other.
>
> Thank you.
>
>
> ------------------------------
>
> --
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