[gmx-users] gromacs.org_gmx-users Digest, Vol 173, Issue 12
sagar bathla
sagarbathla4 at gmail.com
Thu Sep 6 08:48:02 CEST 2018
Hi Alex ,
sorry to post my problem too many times.
Coming back to your questions related to my problem
1. angles are 90,90,120 in x,y and z respectively. actually in quantum
espresso this structure is little bit easy to handle.
2. without LINCS i haven't tried the simulation, i will do it without LINCS
and get back to you.
3. I am basically interested in dynamics of water through porous graphene.
if i am not using constraint and all it is getting crumbled and shape of
graphene changes.
4. Yes, it is stable.
Regards
On Thu, Sep 6, 2018 at 5:35 AM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Orthorhombic structure and Lincs warnings (sagar bathla)
> 2. Re: Orthorhombic structure and Lincs warnings (Alex)
> 3. Re: Orthorhombic structure and Lincs warnings (Alex)
> 4. Re: Justin paper 2010 pulling (Justin Lemkul)
> 5. Re: i have a question about multiple chain simulation at the
> same box (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 6 Sep 2018 01:05:03 +0530
> From: sagar bathla <sagarbathla4 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Orthorhombic structure and Lincs warnings
> Message-ID:
> <
> CAEXVSE4C4pJpun0nsNYcSdj33gE6VLFySBbxe8w+hmAky9Qfeg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
>
> Can simulation for orthorhombic structure be done in gromacs?
> Actually I am working with 2-D graphene sheets which are like a
> parallelogram.
>
> In my system, there is a graphene sheet (restrained)and water.
> After the energy minimization, energy is coming positive (order of 10^8)
> On Visualization in vmd, the structure appears to be rectangle and there
> comes a warning with it
>
> 152 inconsistant shifts etc.
>
> When I am trying to equillibrate the system then so many lines warnings
> appears of rotation of bonds more than 90 degrees and simulation crashes
> everytime.
>
> Is there any problem with structure or y else?
> Earlier also I posted this but issue hasn't resolved yet.
>
> Please help me to find this problem.
>
> Regards
> Sagar
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 5 Sep 2018 13:45:34 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Orthorhombic structure and Lincs warnings
> Message-ID:
> <
> CAMJZ6qHX-fnmnqxgEOyPz22CQ4YRVN8EyNdDHfqPYFG1KYMyzQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> It's not the first time you're posting this message and there's a reason
> noone is replying.
>
> 1. What are the inter-axis angles of that orthorhombic box? Why not a
> rectangular box?
> 2. Why are you using LINCS with graphene, which should _not_ be simulated
> with constraints?
> 3. Why are you restraining your system on top of everything else?
> 4. Did you verify that your graphene model (without constraints or
> restraints) was stable prior to adding water?
>
> Alex
>
> On Wed, Sep 5, 2018 at 1:35 PM sagar bathla <sagarbathla4 at gmail.com>
> wrote:
>
> > Dear all,
> >
> > Can simulation for orthorhombic structure be done in gromacs?
> > Actually I am working with 2-D graphene sheets which are like a
> > parallelogram.
> >
> > In my system, there is a graphene sheet (restrained)and water.
> > After the energy minimization, energy is coming positive (order of 10^8)
> > On Visualization in vmd, the structure appears to be rectangle and there
> > comes a warning with it
> >
> > 152 inconsistant shifts etc.
> >
> > When I am trying to equillibrate the system then so many lines warnings
> > appears of rotation of bonds more than 90 degrees and simulation crashes
> > everytime.
> >
> > Is there any problem with structure or y else?
> > Earlier also I posted this but issue hasn't resolved yet.
> >
> > Please help me to find this problem.
> >
> > Regards
> > Sagar
> > --
> > 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 gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 5 Sep 2018 13:45:34 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Orthorhombic structure and Lincs warnings
> Message-ID:
> <
> CAMJZ6qHX-fnmnqxgEOyPz22CQ4YRVN8EyNdDHfqPYFG1KYMyzQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> It's not the first time you're posting this message and there's a reason
> noone is replying.
>
> 1. What are the inter-axis angles of that orthorhombic box? Why not a
> rectangular box?
> 2. Why are you using LINCS with graphene, which should _not_ be simulated
> with constraints?
> 3. Why are you restraining your system on top of everything else?
> 4. Did you verify that your graphene model (without constraints or
> restraints) was stable prior to adding water?
>
> Alex
>
> On Wed, Sep 5, 2018 at 1:35 PM sagar bathla <sagarbathla4 at gmail.com>
> wrote:
>
> > Dear all,
> >
> > Can simulation for orthorhombic structure be done in gromacs?
> > Actually I am working with 2-D graphene sheets which are like a
> > parallelogram.
> >
> > In my system, there is a graphene sheet (restrained)and water.
> > After the energy minimization, energy is coming positive (order of 10^8)
> > On Visualization in vmd, the structure appears to be rectangle and there
> > comes a warning with it
> >
> > 152 inconsistant shifts etc.
> >
> > When I am trying to equillibrate the system then so many lines warnings
> > appears of rotation of bonds more than 90 degrees and simulation crashes
> > everytime.
> >
> > Is there any problem with structure or y else?
> > Earlier also I posted this but issue hasn't resolved yet.
> >
> > Please help me to find this problem.
> >
> > Regards
> > Sagar
> > --
> > 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 gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 5 Sep 2018 20:01:06 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Justin paper 2010 pulling
> Message-ID: <44ff90db-f5dc-87d5-71fc-079650414423 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/5/18 1:50 AM, Rakesh Mishra wrote:
> > So that means
> >
> > It is may be due to the difference in the type of interaction.
> >
> > and I can not understand your this statement "you have to contend with
> > forces principally acting perpendicular to the direction of the bias"
> >
>
> Well, what interactions act along the plane perpendicular to the helix
> axis of a duplex DNA or RNA?
>
> -Justin
>
> >
> > On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 9/4/18 11:44 AM, Rakesh Mishra wrote:
> >>
> >>> Dear Justin,
> >>>
> >>> Seriously I want to remove my confusion.
> >>> I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60"
> >>> Where you have studied stability of Alzheimer. I don't want to ask
> about
> >>> umbrella sampling used for the calculation of PMF.
> >>>
> >>> But , before the calculation of PMF , you
> >>> have obtained simple dissociation using your pulling protocol of
> gromacs
> >>> with constant velocity simulation at three different velocities. I am
> >>> surprised that you have followed the obvious protocol
> >>> of minimization the nvt the npt and then 100ns md production. then you
> >>> took
> >>> final structure of 100ns and made new box for pulling and followed the
> >>> same minimisation and npt for short time. After this you did pulling
> along
> >>> only one direction (one reaction coordinate) .
> >>>
> >>> I am surprised that how such a smooth force/time data you have obtained
> >>> for
> >>> all the velocities (0.01,0.001,0.005) . I am asking because for my
> simple
> >>> 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and
> fixed
> >>> one end (say 5') of first strand and pulling opposite end (5') of
> second
> >>> strand along the helical direction of the system. Here, I am getting
> >>> force/time (in the .xvg ) data which is qualitatively similar behaviour
> >>> like yours i.e. initially increasing then reach to maximum and then
> >>> decreasing almost becomes to zero value. But , In mine case during
> initial
> >>> time of pulling force is also negative as well large fluctuation of
> force
> >>> .
> >>> But not such a smooth Variation of force/time like your in this paper.
> In
> >>> your case, force is increasing like linearly in the initial and reaches
> >>> the
> >>> maximum and then start to decrease. There is no problem to
> >>> clarify the peak of force (maximum force) in your pulling (above
> mentioned
> >>> paper). While in our case its very difficult to clarify the peak force
> due
> >>> to large fluctuation in value.
> >>> Can you please tell me something about the reason. Its smoothness is
> now
> >>> became headache for my calculation in all the case of pulling.
> >>>
> >> There is no reason to think that your outcome and mine should look
> >> anything alike. Pulling apart two proteins that interact in the way the
> >> peptides do in a protofibril is much simpler than the intertwined
> nature of
> >> a DNA or RNA duplex. If you pull along the helix axis, you have to
> contend
> >> with forces principally acting perpendicular to the direction of the
> bias,
> >> as well as the fact that the strands have to slide past one another,
> >> requiring major distortion of the helix and/or frictional forces due to
> the
> >> individual strands unwinding from one another.
> >>
> >> -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.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 gmx-users-request at gromacs.org.
> >>
> >
> >
>
> --
> ==================================================
>
> 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.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 5 Sep 2018 20:01:42 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] i have a question about multiple chain
> simulation at the same box
> Message-ID: <b7b5234d-8fdc-1489-94fb-be35d0f9aff1 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/5/18 9:25 AM, milad bagheri wrote:
> > I'm going to examine the interaction between the two proteins using
> > molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1
> > from the rcsb , which has two protein(Complex). I want to create a gap
> > between two protein, and then with the same coordinate Put these two
> > proteins in a box and run MD 100 nanoseconds, for validation this trick
> > compare rmsd x-ray pose and Md pose.
> > please help me ...
>
> Separate the coordinates of the two proteins, translate one of them with
> editconf, and concatenate the new coordinates back together.
>
> -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.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 gmx-users-request at gromacs.org.
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> End of gromacs.org_gmx-users Digest, Vol 173, Issue 12
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