Re: [gmx-users] Coulomb and vdW energies

[Shreyas Kaptan]

Hi.

I would not say that it is completely unrealistic/unphysical. Especially,
the Electrostatic part. If within two subgroups, you could show that there
is systematic repulsive or attractive potential, that could lead to some
hypothesis about how they interact (e.g. pushing/pulling). Of course, this
is only true of ratios of decomposed energies that are large proportions of
the total energy, as smaller portions might not be really
significant indicators of strong interactions.

Shreyas

On Sat, Nov 30, 2019 at 6:47 PM Justin Lemkul  wrote:

>
>
> On 11/30/19 3:14 AM, elham wrote:
> > Dear all, I want to obtain the coulomb and vdW energies between two
> atoms of separate molecules, However  the .edr output calculate coulomb
> and vdW energies of whole system. There is not any option(like -n .ndx) to
> define the the special atoms in the gmx energy command. How can I calculate
> the coulomb and vdW energies between the two atoms which are related to two
> separate molecules?Best
>
> Set energygrps in the .mdp file, generate a new .tpr, and use mdrun
> -rerun to re-evaluate the energies from an existing trajectory. Note
> that decomposition of energy in this way has no physical meaning. Total
> interaction energy may be physically realistic if the force field was
> specifically parametrized against e.g. QM target data but decomposing
> the energy in this way is not meaningful.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Non-symmetric PMF across lipid bilayer

[Shreyas Kaptan]

I am reasonably sure that if the bilayer composition is asymmetric with
respect to leaflets you should see asymmetry in the PMF. In the ideal case,
of infinite sampling, you should have zero free energy difference in the
bulk solvent for either side.

On Wed, Nov 21, 2018 at 2:52 PM Gmx QA  wrote:

> Thanks again,
>
> So then to summarize: Using -sym is appropriate in this case, even though
> the bilayer is asymmetric with respect to lipid composition.  This fact
> would show up anyway (in the limit of unlimited sampling?)
>
>
>
> Den ons 21 nov. 2018 kl 14:44 skrev Justin Lemkul :
>
> >
> >
> > On 11/21/18 8:39 AM, Per Larsson wrote:
> > > Hi,
> > >
> > > Thanks Justin, but shouldn't the PMF be (more or less) symmetric
> anyway,
> > > given the inherent bilayer symmetry?
> > > In this case I have designed the two leaflets in the bilayer to have
> > > non-identical lipid composition, so then I think using -sym would
> > > obliterate any differences between the leaflets, no?
> >
> > No, because that's completely unknown (and irrelevant) to WHAM. It sets
> > the leftmost window to a zero energy and calculates every window's
> > energy relative to that, so you'll get the steady increase you see. If
> > you tell it that the leftmost and rightmost windows are equal (which
> > -sym), then the calculation proceeds differently.
> >
> > -Justin
> >
> > >
> > >
> > >
> > > On Wed, Nov 21, 2018 at 2:24 PM Justin Lemkul  wrote:
> > >
> > >>
> > >> On 11/21/18 7:22 AM, Gmx QA wrote:
> > >>> Hi all gmx-users
> > >>>
> > >>> I am working on calculating the PMF using umbrella sampling of a
> > (rather
> > >>> large) molecule across a lipid bilayer. I have set up my umbrellas
> > with a
> > >>> 0,2 nm spacing, and run each window for 100 ns.
> > >>>
> > >>> The problem is that the resulting PMF is not symmetric with respect
> to
> > >> the
> > >>> bilayer center. Initially is looks ok, but when the molecule is
> exiting
> > >> the
> > >>> bilayer on the other side again, the PMF does not go back to
> (roughly)
> > >> the
> > >>> same value as before entering the bilayer.
> > >>>
> > >>> I have uploaded the PMF file here:
> > >>> https://files.fm/u/7ec2rshc
> > >> You didn't get a symmetric profile because you didn't ask for one. Use
> > >> the -sym option.
> > >>
> > >> -Justin
> > >>
> > >>> Any comments or suggestions are much appreciated. I understand the
> > >> problems
> > >>> and issues about calculations of a converged PMF with larger
> molecules,
> > >> but
> > >>> nevertheless I would have expected my PMF to be symmetric, albeit
> > perhaps
> > >>> not converged.
> > >>>
> > >>> Thanks
> > >>> /PK
> > >> --
> > >> ==
> > >>
> > >> 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
> > >>
> > >> jalem...@vt.edu | (540) 231-3129
> > >> http://www.thelemkullab.com
> > >>
> > >> ==
> > >>
> > >> --
> > >> Gromacs Users mailing list
> > >>
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> > >> posting!
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> > >>
> >
> > --
> > ==
> >
> > 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
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==
> >
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Re: [gmx-users] Updated tutorials and new website

[Shreyas Kaptan]

Hi Justin,

that sounds like a great plan.  Thanks for initiating something like this.

Iris,

I am up for helping with some of the tutorials, especially, the ED
simulations if you need any help. That is something I have some experience
with as well.

Shreyas

On Tue, Jul 3, 2018 at 1:13 PM Justin Lemkul  wrote:

>
> The enthusiasm for writing new tutorials is very encouraging, and
> admittedly has taken me a bit by surprise. Let me "pull back the
> curtain" on what I am thinking regarding my own site and how others
> might engage.
>
> I am about to submit an article detailing my tutorials and the
> theoretical underpinnings of them and context within the existing
> literature. Writing this article spurred me to make the move to a new
> server (which was inevitable, anyway) and update everything for version
> 2018. The paper is being submitted to LiveCoMS
> (http://www.livecomsjournal.org/), which is built upon "living" articles
> that can be revised and updated over time, with each new major version
> being a new submission and new article. If people haven't heard about
> it, please check them out. The source file and content of my article
> will be available on GitHub soon.
>
> For those interested in hosting something on my site, I'm open to
> proposals. I won't be adding anything new until after my article is out
> (it is far too late for anyone to try to contribute anything to it,
> anyway, as the article will be submitted within a few days) but for
> anything after that, please let me know what you might write. I wrote
> all of my tutorials based on things I was actively doing in my
> dissertation work, so it was natural for me to share with everyone what
> I had learned. I encourage others to do the same.
>
> The tutorial site is also a large part of a very important grant I will
> be submitting that needs to include educational components, so please
> understand and expect that I will have certain standards for inclusion,
> because as I have learned over the last 10 years of effort, it is no
> small task to write and maintain high-quality tutorial material. I
> haven't exactly formulated how all of that will work out, but anyone
> with a solid idea and the drive to write a tutorial is welcome to reach
> out to me. While I have contributed some code to GROMACS over the years,
> my biggest contribution is obviously in documentation and teaching,
> which I enjoy doing and will continue to do in support of this community
> and the important science that people are doing.
>
> If people want to continue the discussion here, that's great and I'll
> comment as needed, or feel free to send ideas to me off-list.
>
> -Justin
>
> On 7/3/18 4:28 AM, Mark Abraham wrote:
> > Hi,
> >
> > We have several new tutorials from the core/BioExcel team also (done as
> > Jupyter notebooks) that we plan to make available, though I have not
> > thought much yet about the form of delivery.
> >
> > Obviously the GROMACS website is overdue for renovation (and yes, that's
> on
> > my to-do list), but we're very happy to make a central home for content
> > people would prefer to host there.
> >
> > As Oliver notes, some basic CI testing is really nice for smoothing over
> > version differences, so I particularly encourage authors to record some
> > kind of script (bash, python, whatever suits you) that enables the
> > regeneration of any saved output from GROMACS, or other tools. Then when
> we
> > publish new versions of GROMACS it's straightforward to update the
> content
> > as needed, and that can evolve into a useful framework. There's also ways
> > to embed lightweight molecular viewers in web pages and Jupyter
> notebooks,
> > which helps avoid classes of students needing to deal also with vmd or
> > pymol in their first rodeo...
> >
> > Mark
> >
> > On Tue, Jul 3, 2018 at 7:01 AM David van der Spoel  >
> > wrote:
> >
> >> Den 2018-07-03 kl. 03:32, skrev Oliver Beckstein:
> >>> Hi,
> >>>
> >>> Justin's tutorials are really a great boon to the community (and to new
> >> students joining my group – they are part of our introductory
> “bootcamp”).
> >> It would be nice to also have a “community” repository of repositories,
> >> especially with some templates or structure that other could follow.
> >>> A while back we started a tutorial on simulating the globular enzyme
> AdK
> >> in solution https://adkgromacstutorial.readthedocs.io <
> >> https://adkgromacstutorial.readthedocs.io/> (but it’s not always been
> >> kept up-to-date (this is hard – kudos to Justin for doing it for his
> >> tutorials!). It was written in restructured text and built with sphinx
> and
> >> automatically published on ReadTheDocs, i.e., publishing the pages and
> >> hosting could be done automatically. If combined with basic continuous
> >> integration that checks that a PR builds the docs nicely then one might
> be
> >> able to turn this into a framework for community-based tutorials.
> >>> Anyone who wants to use this as a starting point: Please 

Re: [gmx-users] [EXT] Re: Updated tutorials and new website

[Shreyas Kaptan]

Dear Iris,

that sounds like a great idea. I would like to ask what topics would be
considered useful for tutorials. I can think of a few:

1. Fast thermodynamic integration for alchemical transformations with the
CGI method with hybrid topologies for more complex examples
2. Replica exchange methods
3. An Essential dynamics tutorial
4. QM/MM tutorial (is that still viable ?)
5. Computational electrophysiology setup example from scratch?

I must admit I am myself very interested in some of these (especially the
QM/MM setups) and would like to see them in an accessible manner. For other
techniques, like CompEL, Essential dynamics, I am concerned that they are
underused by the community because no concrete tutorials for them exist.

If necessary I would help in setting some of these up if there is enough
demand.

Shreyas


On Mon, Jul 2, 2018 at 8:34 PM Justin Lemkul  wrote:

>
>
> On 7/2/18 2:13 PM, Smith, Iris wrote:
> > That's a great idea Mark!
> > Should we submit these to you or Justin?
>
> Everyone has always been welcome to write and publish whatever tutorials
> they might come up with, and link them to the Tutorials page of
> gromacs.org. My new website is part of a publishing effort (coming soon,
> later this summer) and I'm not presently prepared to review submissions
> for inclusion. It's something I may think about in the future if there
> is sufficient interest, but probably not right now.
>
> -Justin
>
> > Iris
> >
> > Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
> > Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195
> | (216) 445-7885
> >
> >
> >
> > On 6/30/18, 12:11 PM, "
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark
> Abraham"  mark.j.abra...@gmail.com> wrote:
> >
> >  Hi,
> >
> >  A great contribution would be to write some for your own area of
> expertise.
> >  Or with similar content but done in a different way.
> >
> >  Mark
> >
> >  On Sat, Jun 30, 2018, 02:42 paul buscemi  wrote:
> >
> >  > Justin,
> >  >
> >  > Thank you for all the hard work !   What can we do in return ???
> >  >
> >  > Paul
> >  >
> >  > > On Jun 29, 2018, at 5:17 PM, Justin Lemkul 
> wrote:
> >  > >
> >  > >
> >  > > Hi All,
> >  > >
> >  > > I have updated all of my tutorials for use with GROMACS 2018.
> They are
> >  > now hosted on a new site:
> >  > >
> >  > > http://www.mdtutorials.com/gmx/
> >  > >
> >  > > The tutorials currently hosted on bevanlab.biochem.vt.edu will
> be
> >  > permanently taken offline by the end of the summer. I realize
> that many
> >  > other sites link to these tutorials, so please update links and
> bookmarks
> >  > if possible. In the meantime, the old tutorials will redirect to
> the new
> >  > ones.
> >  > >
> >  > > I hope the new tutorials will be helpful - there are many new
> and
> >  > improved sections, and the protein-ligand tutorial has
> essentially been
> >  > completely rewritten with a newer approach and different force
> field. I
> >  > apologize if there are any difficulties due to links that will
> now break,
> >  > but the situation is unavoidable due to the permanent
> decommissioning of
> >  > the Bevan lab server.
> >  > >
> >  > > Please let me know if there are any difficulties with the new
> tutorials
> >  > or website.
> >  > >
> >  > > -Justin
> >  > >
> >  > > --
> >  > > ==
> >  > >
> >  > > Justin A. Lemkul, Ph.D.
> >  > > Assistant Professor
> >  > > Virginia Tech Department of Biochemistry
> >  > >
> >  > > 303 Engel Hall
> >  > > 340 West Campus Dr.
> >  > > Blacksburg, VA 24061
> >  > >
> >  > > jalem...@vt.edu | (540) 231-3129
> >  > > http://www.thelemkullab.com
> >  > >
> >  > > ==
> >  > >
> >  > > --
> >  > > Gromacs Users mailing list
> >  > >
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> before
> >  > posting!
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> >  >
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Re: [gmx-users] Essential dynamics

[Shreyas Kaptan]

Thanks a lot, Carsten!!! Exactly what I needed :).

Shreyas

On Tue, Jun 26, 2018 at 3:41 PM Kutzner, Carsten  wrote:

> Hi Shreyas,
>
> > On 26. Jun 2018, at 15:21, Shreyas Kaptan 
> wrote:
> >
> > Dear All,
> >
> > I have a question regarding the make_edi tool. I used it some time back
> to
> > restrain my structures to a particular projection value of an eigen
> vector
> > with the -restrain keyword. However, I seem to have forgotten how to set
> > the value of the projection in the .edi file. Does anyone here know how
> to
> > set it correctly?
> Yes, you can put it directly in the .edi file.
> You can add the restraint center as the third value (a signed float is
> accepted)
> on the 2nd line after the "GROUP 7" heading. Group 7 is the one used for
> harmonic restraining if you use make_edi -harmonic -flood 1 -restrain
> For instance, the following potential is centered about "-7.0 nm”:
>
> # NUMBER OF EIGENVECTORS + COMPONENTS GROUP 7
>  1
>1   1 -7.0
>
> Best,
>   Carsten
>
> >
> > Thanks in advance!
> >
> > --
> > Shreyas Sanjay Kaptan
> > --
> > 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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> send a mail to gmx-users-requ...@gromacs.org.
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
> --
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[gmx-users] Essential dynamics

[Shreyas Kaptan]

Dear All,

I have a question regarding the make_edi tool. I used it some time back to
restrain my structures to a particular projection value of an eigen vector
with the -restrain keyword. However, I seem to have forgotten how to set
the value of the projection in the .edi file. Does anyone here know how to
set it correctly?

Thanks in advance!

-- 
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Re: [gmx-users] tilt angle

[Shreyas Kaptan]

If you fire the 'gmx make_ndx' you will find that there is a section there
for c-alpha atoms. By combining the c-alpha group with the index of the
protein with the "&" operator (without quotations) should work.

On Wed, Jun 20, 2018 at 8:41 AM Fa Hamedi 
wrote:

> Hi,
> I am new in this mailing list and I have a question:
> I haveve performed MD simulation of transmembrane protein using
> Gromacs. Now, I want to calculate the angle of tilt of the
> transmembrane protein against the bilayer normal. I know that I can
> use
>
> gmx helixorient but I don t know how should make index file?? My
> protein is a dimer helix and has 61 residues. I don t know how choose
> carbo alpha atoms for calculating tilt angle! can anyone help me??
>
> Thank you.
> --
> Gromacs Users mailing list
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Re: [gmx-users] membrane-protein system by using charmm36 ff

[Shreyas Kaptan]

Hi.

it is quite important that you do a pre-equilibration generally. This is
assuming that you are starting with membranes built from scratch. If you
have a patch that you obtained from charmm-gui website or other sources
that someone has previously equilibrated, then, of course, you can forgo
the pre-equilibration. The reason pre-equilibration is so important is that
membranes generated by insertion methods tend to have a lot of clashes. NVT
simulations (even short ones, approx. 1ns) ensure that given a box size you
can accommodate the lipids and relax them before you attach the pressure
coupling.

An equlibration of 200-300 ns *might* be an overkill if your protein does
not have a too large hydrophobic mismatch. but of course, more
equilibration only helps. Once again, use parameters appropriate for the
system to determine if the equilibration is enough instead of using some
default timescale.

Shreyas

On Mon, Jun 18, 2018 at 10:51 AM Olga Press  wrote:

> Thank you for your help!
> How important is it to make a good pre-equilibration before embedding a
> protein into the membrane if I'm going to perform long (200-300ns)
> equilibration of the whole system (mempare+protein) using NVT followed by
> NPT ensemble before production of MD simulation?
> Thank you all for your help.
>
>
> Olga
>
>
>
>
> 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan :
>
> > Hi.
> >
> > Maybe you already know this but you can also build the whole embedded
> > system with charmm-gui. Also, your parameters appear reasonable to me at
> > first glance.
> >
> > As for the equilibration, that is a system specific question. If you
> have a
> > "simple" uniform lipid content in the bilayer I would say from my
> > experience, that the equilibration depends on the lipid heads and tails.
> > Large heads and long tails generally imply a longer equilibration. Mixed
> > lipids can require up to "microseconds" worth of equilibratio. I would
> take
> > the saturation to a nearly fixed value of the Area per lipid and the
> > bilayer thickness as an indication that it is safe to consider the
> > "equilibration" enough.
> >
> > Do not use the 0.495 ns as some timescale. It is in fact quite short.
> >
> >
> >
> > On Sun, Jun 17, 2018 at 1:25 PM Olga Press 
> wrote:
> >
> > > Dear Gromacs users,
> > > I'm new in the field of Molecular Dynamics especially in using Gromacs.
> > > I have several questions regarding mdp file and I'll be very grateful
> if
> > > you can help me with them.
> > > I'm using a membrane-protein system with Charmm36 ff. After I have
> > > constructed bilayer membrane by using CHARMM-GUI membrane builder I
> have
> > > run the README file as it, without changing the equilibration time
> (total
> > > equilibration time of 0.475ns). Followed by embedded protein into the
> > > membrane by using g_membed and performed solvation and minimization of
> > the
> > > entire system as was described in the KALP15-DPPC  tutorial by Dr.
> Justin
> > > A.Lemkul.
> > >
> > > those are my questions:
> > > 1. Does the pre-equilibration of 0.475ns is enough before embedding
> > protein
> > > into the membrane and followed by long equilibration of the whole
> system
> > > for 200ns  by using NVT followed by NPT equilibration?
> > >
> > > 2. I've read that when using CHARMM36 ff in gromacs is better to switch
> > the
> > > following parameters
> > >  constraints = h-bonds
> > > cutoff-scheme = Verlet
> > > vdwtype = cutoff
> > > vdw-modifier = force-switch
> > > rlist = 1.2
> > > rvdw = 1.2
> > > rvdw-switch = 1.0
> > > coulombtype = PME
> > > rcoulomb = 1.2
> > > DispCorr = no
> > >
> > > I'm using the original mdout.mdp files produces by gromacs.Are those
> > > parameters optimal for a membrane-protein system or just for the
> lipids?
> > >
> > > Thank you all for your help.
> > > Olga
> > > --
> > > 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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> > >
> >
> >
> > --
> > Shreyas Sanjay Kaptan
&

Re: [gmx-users] membrane-protein system by using charmm36 ff

[Shreyas Kaptan]

Hi.

Maybe you already know this but you can also build the whole embedded
system with charmm-gui. Also, your parameters appear reasonable to me at
first glance.

As for the equilibration, that is a system specific question. If you have a
"simple" uniform lipid content in the bilayer I would say from my
experience, that the equilibration depends on the lipid heads and tails.
Large heads and long tails generally imply a longer equilibration. Mixed
lipids can require up to "microseconds" worth of equilibratio. I would take
the saturation to a nearly fixed value of the Area per lipid and the
bilayer thickness as an indication that it is safe to consider the
"equilibration" enough.

Do not use the 0.495 ns as some timescale. It is in fact quite short.



On Sun, Jun 17, 2018 at 1:25 PM Olga Press  wrote:

> Dear Gromacs users,
> I'm new in the field of Molecular Dynamics especially in using Gromacs.
> I have several questions regarding mdp file and I'll be very grateful if
> you can help me with them.
> I'm using a membrane-protein system with Charmm36 ff. After I have
> constructed bilayer membrane by using CHARMM-GUI membrane builder I have
> run the README file as it, without changing the equilibration time (total
> equilibration time of 0.475ns). Followed by embedded protein into the
> membrane by using g_membed and performed solvation and minimization of the
> entire system as was described in the KALP15-DPPC  tutorial by Dr. Justin
> A.Lemkul.
>
> those are my questions:
> 1. Does the pre-equilibration of 0.475ns is enough before embedding protein
> into the membrane and followed by long equilibration of the whole system
> for 200ns  by using NVT followed by NPT equilibration?
>
> 2. I've read that when using CHARMM36 ff in gromacs is better to switch the
> following parameters
>  constraints = h-bonds
> cutoff-scheme = Verlet
> vdwtype = cutoff
> vdw-modifier = force-switch
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 1.0
> coulombtype = PME
> rcoulomb = 1.2
> DispCorr = no
>
> I'm using the original mdout.mdp files produces by gromacs.Are those
> parameters optimal for a membrane-protein system or just for the lipids?
>
> Thank you all for your help.
> Olga
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] About the "g_contacts" program for gromacs

[Shreyas Kaptan]

In the paper it mentions that:

This paper and its associated computer program are available via the
Computer Physics Communication homepage on ScienceDirect (
http://www.sciencedirect.com/science/journal/00104655).

Hope that helps.

On Thu, Jun 14, 2018 at 5:53 PM ABEL Stephane  wrote:

> Hi there,
>
> Do you know where I can find the program g_contacts developed by Christian
> Blau & Helmut Grubmuller and described in the following paper "g_contacts:
> Fast contact search in bio-molecular ensemble data. Computer Physics
> Communications
> Volume 184, Issue 12, December 2013, Pages 2856-2859"
> https://www.sciencedirect.com/science/article/pii/S0010465513002464. I
> would like to test it. In addition, does this tool work with the  5.1.X or
> newer versions of gromacs. (It was initially developed for gromacs 4.6) .
>
> Thanks
>
> A bientôt
>
> Stéphane
>
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Re: [gmx-users] High pressure

[Shreyas Kaptan]

>Why is the pressure not relieved in the Z-direction
That can only be answered predicated on the answer to the question if it
arises from the 0 compressibility. Also, what system are you using?

>Can I ignore it?

You should not. Your expected ensembles are in the 1 bar pressure regime.

On Thu, Jun 14, 2018 at 5:40 PM Alex  wrote:

> Hi,
> The "compressibility  = 0.0 4.46e-5" means box is fixed in X-Y
> directions and free to change only in Z direction. I agree that fixing the
> box in two direction might be the reason for such huge pressure in spied
> of  setting the ref-p = 1. The question is that why the pressure does not
> ultimately get release in the Z direction?
> Also, is this pressure is an artificial pressure so that it can be ignored?
> If so, how I can find out (to be reported) the current real pressure in the
> system in such situation?
>
> Regards,
> Alex
>
> On Wed, Jun 13, 2018 at 5:30 PM, Shreyas Kaptan 
> wrote:
>
> > That is indeed strange. Could it be because of the compressibility = 0 in
> > the first coordinate direction? if your simulations start with a badly
> > adjusted (minimized) structure in the TPR then it might get stuck there
> > because the 0 compressibility might not allow any change in the box
> > dimensions along that coordinate.
> >
> > Shreyas
> >
> > On Wed, Jun 13, 2018 at 7:47 PM Alex  wrote:
> >
> > > Dear all,
> > > I have mixture of two types of short polymer in aqcuse solution on top
> > of a
> > > slab surface. After NVT equilibration, I run NPT with ref-p = 1
> > > semiisotropically, below is part of my npt.mdp file.
> > > I wonder why the pressure in the system is stable around *3* after
> > 3ns
> > > in spite of of ref-p = 1?
> > >
> > >
> > > pcoupl  = berendsen
> > > Pcoupltype   = semiisotropic
> > > tau-p = 2.0
> > > compressibility  = 0.0 4.46e-5
> > > ref-p  = 1.0 1.0
> > > refcoord-scaling = com
> > >
> > > Thanks.
> > > Regards,
> > > Alex
> > > --
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> > >
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> > > posting!
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> > >
> >
> >
> > --
> > Shreyas Sanjay Kaptan
> > --
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Re: [gmx-users] High pressure

[Shreyas Kaptan]

That is indeed strange. Could it be because of the compressibility = 0 in
the first coordinate direction? if your simulations start with a badly
adjusted (minimized) structure in the TPR then it might get stuck there
because the 0 compressibility might not allow any change in the box
dimensions along that coordinate.

Shreyas

On Wed, Jun 13, 2018 at 7:47 PM Alex  wrote:

> Dear all,
> I have mixture of two types of short polymer in aqcuse solution on top of a
> slab surface. After NVT equilibration, I run NPT with ref-p = 1
> semiisotropically, below is part of my npt.mdp file.
> I wonder why the pressure in the system is stable around *3* after 3ns
> in spite of of ref-p = 1?
>
>
> pcoupl  = berendsen
> Pcoupltype   = semiisotropic
> tau-p = 2.0
> compressibility  = 0.0 4.46e-5
> ref-p  = 1.0 1.0
> refcoord-scaling = com
>
> Thanks.
> Regards,
> Alex
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Re: [gmx-users] Cavity in the system after NVT equilibration

[Shreyas Kaptan]

The cavity, which is due to negative pressure in the system, might imply
one of the two things:

The Box is too big for the system or that the MD simulation implodes the
system somehow. I have seen issues like these when the system is not well
minimized and has some obvious artefacts like "broken" bonds or missing
atoms in the structure and in topology.

But if it is none of the above, I would try a smaller timestep if possible.
Maybe it is a bad clash that somehow generates a negative pressure in the
system (although I do not profess to know how).

On Sat, Jun 2, 2018 at 6:28 AM Alex  wrote:

> Equilibration under NVT is a very bizarre approach, I am not even going
> to ask why you're doing this.
>
> I am known for perverse use of Gromacs, but please follow EM > NPT
> equilibration (Berendsen thermostat, etc) > production.
>
> The fact that you don't see the cavity at high temperature is that you
> have overheated gas under high pressure. The fact that annealing it down
> brings back the cavity means that the physics works and everyone should
> rejoice.
>
> Alex
>
>
> On 6/1/2018 10:21 PM, Alex wrote:
> > Dear all,
> > I have a system containing 4000 water molecules+700 of molecule A + 300
> of
> > molecule B. After minimization, the system undergoes a 2ns NVT
> equalization
> > at 298.15 K which gives a big cavity in the system at the end, whereas
> the
> > cavity does not show up at 650 K equlibration. But what I need is the
> > system at 298.15 K. So, I tried to rampe down the temperature from fully
> > equilibrated system at 650 to 298.15 by the step of 35 K (in total 10 ns)
> > hoping to solve the problem by cooling down the system from the
> temperature
> > at which the system is normal to the desired temperature, but at the end
> > the cavity appears  unfortunately.
> > So, I wonder how I should equilibrate the system in order to avoid having
> > the cavity?
> > Thank you,
> > Alex
>
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Re: [gmx-users] free energy landscape

[Shreyas Kaptan]

Sounds like a problem for string methods. However, it's hard to judge
without actually looking at what you have. Cheers.

On Sun, May 13, 2018 at 3:47 PM Rezgar Pakravan 
wrote:

> ​HI there
>
> I got free energy landscape using Mathematica software to get coordinates
> with the least free energy.
>
> 3d image of the landscape shows a gap though!? would that be reliable to
> get coordinates from any point on the lowest energy coordinate
> ?
> any recommendation would be appreciated
>
> Pakravan/Rezgar
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Re: [gmx-users] replicates with different random seed

[Shreyas Kaptan]

If you use the .cpt file then the velocities will be provided as from the
checkpoint. This would effectually only lengthen the simulation. In order
to truly sample the simulation space from a "random" seed, you
should reassign velocities from scratch as in the .mdp file. In *principle*
the starting coordinates, if used from the end point of your 100ns data,
would actually bias the new trajectory. But that should not be a
substantial bias if, for example, the simulation system did not undergo
drastic conformational change during your 100ns run.  if it did, then I
would rather restart the whole simulation from the same starting
coordinates and different velocities to test the dynamics of the system
i.e. if the conformational change is reproducible or just a flue of N=1.

On Tue, May 8, 2018 at 11:13 AM Alex  wrote:

> Ideally, you should repeat your entire procedure with a new seed from the
> step that first generates velocities.
>
> Repeating hundreds of nanoseconds of simulation a few times probably would
> not be my response to your likely 85 year old reviewer, but I hope this
> helps.
>
> Alex
>
> On May 8, 2018 2:58 AM, "vijayakumar gosu" 
> wrote:
>
> Hello all,
>
> I have submitted a paper with 100ns simulations data, however reviewer
> suggested to provide replicates with different random seeds. I have used
> below lines in the mdp file of equilibration step for my first simulation.
> now i am confused  for replicates (minimum 2) whether i have to start from
> equilibration step or i can start from production step using the npt.gro
> and npt.cpt from first simulation. additionally, I assume that when we have
> ( for example 3 replicates) we have to consider the average from the 3
> simulations data. Please advise me whether my approach is reliable...
>
>
> nvt.mdp
>
> ; Velocity generation
> gen_vel = yes
> gen_temp = 300
> gen_seed = -1
>
> Thanks in advance
>
>
> Best,
>
> Vijayakumar Gosu
>
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Re: [gmx-users] Index file regarding

[Shreyas Kaptan]

You need to combine the C-alpha default group with the selected category
with the & operator.

On Mon, May 7, 2018 at 3:31 PM RAHUL SURESH <drrahulsur...@gmail.com> wrote:

> Hi, I have created the index file. Now I want to calculate the rmsd of the
> C-alpha atoms of the index group alone.. So what group should i select?
>
> On Mon, May 7, 2018 at 6:50 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> wrote:
>
> > thank you.
> >
> > On Mon, May 7, 2018 at 3:39 PM, Shreyas Kaptan <shreyaskap...@gmail.com>
> > wrote:
> >
> >> It's 'r37-70 | r 120-167 | ...'  so on and so forth.
> >>
> >> On Mon, May 7, 2018 at 12:06 PM RAHUL SURESH <drrahulsur...@gmail.com>
> >> wrote:
> >>
> >> > Dear all,
> >> >
> >> > My protein structure has 400 residues of which I want to calculate
> RMSD
> >> of
> >> > particular 200 residues (approx) and they are not continuous. For
> >> example,
> >> > from 34-70; 120-167; 180-210; For this how can I create an index
> >> file?
> >> >
> >> > Thank you
> >> >
> >> > --
> >> > *Regards,*
> >> > *Rahul Suresh*
> >> > *Research Scholar*
> >> > *Bharathiar University*
> >> > *Coimbatore*
> >> > --
> >> > Gromacs Users mailing list
> >> >
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> >> > posting!
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> >> >
> >>
> >>
> >> --
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> >> --
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> >>
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] Index file regarding

[Shreyas Kaptan]

It's 'r37-70 | r 120-167 | ...'  so on and so forth.

On Mon, May 7, 2018 at 12:06 PM RAHUL SURESH 
wrote:

> Dear all,
>
> My protein structure has 400 residues of which I want to calculate RMSD of
> particular 200 residues (approx) and they are not continuous. For example,
> from 34-70; 120-167; 180-210; For this how can I create an index file?
>
> Thank you
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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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Re: [gmx-users] gmx potential

[Shreyas Kaptan]

Hi.

Interestingly, I did exactly that compared it with the simulation without
an applied field and gmx potential does not seem to be consistent at
different times even after a 50ns early "equilibration".  I am not at work
today, but I will make the output available tomorrow.

On Mon, Apr 2, 2018 at 5:40 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Shouldn't you be comparing the distribution with and without the external
> field to verify that it has an effect that is physically consistent? Even
> if there was output from mdrun that said "the applied field was blah blah
> on step x" that still wouldn't mean anything unless the other output is
> consistent.
>
> Mark
>
> On Mon, Apr 2, 2018, 15:01 Shreyas Kaptan <shreyaskap...@gmail.com> wrote:
>
> > Hi.
> >
> > Can anyone else try to answer my query about using gmx potential? I feel
> > there must be a way to use it to check the potential as applied by
> external
> > electric field.
> >
> > Shreyas
> >
> > On Thu, Mar 22, 2018 at 5:08 PM, Alex <nedoma...@gmail.com> wrote:
> >
> > > Not sure what you mean by "correct." The "voltage" would be the field,
> > > times the box size in the direction of the field. Which is of course
> fake
> > > for a periodic boundary.
> > >
> > > If you're set on doing e.g. permeation studies that require applying a
> > > particular voltage across the box, external fields aren't really the
> way
> > to
> > > go. Gromacs has a built-in computational electrophysiology (called
> > CompEl,
> > > I think) protocol as part of the package. I've never used it, and it
> > works
> > > by artificially maintaining an ionic concentration gradient, but it
> could
> > > be useful. The issue with zero actual correspondence between external
> > > fields and actual voltage drops isn't specific to Gromacs -- it's all
> > part
> > > of Ewald sum legacy with electrostatics. I am only aware of one
> software
> > > suite that precisely solves Poisson on a real-space 3-D multigrid, but
> > it's
> > > neither free, nor available to the public in any way.
> > >
> > > Alex
> > >
> > >
> > >
> > > On 3/22/2018 4:59 AM, Shreyas Kaptan wrote:
> > >
> > >> Okay. But then how can one confirm that the correct potential is
> applied
> > >> if
> > >> not by looking at the charge distribution?
> > >>
> > >> Shreyas
> > >>
> > >> On Thu, Mar 22, 2018, 00:32 Alex <nedoma...@gmail.com> wrote:
> > >>
> > >> No, you are exactly right -- it does NOT include the external field
> > >>> explicitly. The external field acts as a magical force here and gmx
> > >>> potential would produce a potential distribution based on the
> resulting
> > >>> charge distribution. The external field itself, once again, however,
> > does
> > >>> not exist in that picture. I mean, you could add it as a linear drop
> of
> > >>> potential from one end to the other, but that is purely artificial. I
> > >>> stay
> > >>> away as much as possible from plotting charge distributions from
> > >>> simulations steered by external fields.
> > >>>
> > >>> Alex
> > >>>
> > >>> On Wed, Mar 21, 2018 at 4:29 PM, Shreyas Kaptan <
> > shreyaskap...@gmail.com
> > >>> >
> > >>> wrote:
> > >>>
> > >>> I am confused about which potential it actually calculates. As I
> > >>>> understand, the electric field (external) adds a force for each
> > charged
> > >>>> particle. This ought to change the ion distribution. If I read the
> gmx
> > >>>> potential documentation right, it uses the distribution of the
> charges
> > >>>> in
> > >>>> the box to calculate the electrostatic potential in the box. Should
> > that
> > >>>> not include the external field-induced potential? I admit, that I
> > >>>> assumed
> > >>>> that this was the dominant part of the potential.
> > >>>>
> > >>>> Was I wrong?
> > >>>>
> > >>>> Shreyas
> > >>>>
> > >>>> On Wed, Mar 21, 2018 at 11:16 PM, Alex <nedoma...@gmail.com> wrote:
> > >>>>
> > >>>> It does exactly what it s

Re: [gmx-users] gmx potential

[Shreyas Kaptan]

Hi.

Can anyone else try to answer my query about using gmx potential? I feel
there must be a way to use it to check the potential as applied by external
electric field.

Shreyas

On Thu, Mar 22, 2018 at 5:08 PM, Alex <nedoma...@gmail.com> wrote:

> Not sure what you mean by "correct." The "voltage" would be the field,
> times the box size in the direction of the field. Which is of course fake
> for a periodic boundary.
>
> If you're set on doing e.g. permeation studies that require applying a
> particular voltage across the box, external fields aren't really the way to
> go. Gromacs has a built-in computational electrophysiology (called CompEl,
> I think) protocol as part of the package. I've never used it, and it works
> by artificially maintaining an ionic concentration gradient, but it could
> be useful. The issue with zero actual correspondence between external
> fields and actual voltage drops isn't specific to Gromacs -- it's all part
> of Ewald sum legacy with electrostatics. I am only aware of one software
> suite that precisely solves Poisson on a real-space 3-D multigrid, but it's
> neither free, nor available to the public in any way.
>
> Alex
>
>
>
> On 3/22/2018 4:59 AM, Shreyas Kaptan wrote:
>
>> Okay. But then how can one confirm that the correct potential is applied
>> if
>> not by looking at the charge distribution?
>>
>> Shreyas
>>
>> On Thu, Mar 22, 2018, 00:32 Alex <nedoma...@gmail.com> wrote:
>>
>> No, you are exactly right -- it does NOT include the external field
>>> explicitly. The external field acts as a magical force here and gmx
>>> potential would produce a potential distribution based on the resulting
>>> charge distribution. The external field itself, once again, however, does
>>> not exist in that picture. I mean, you could add it as a linear drop of
>>> potential from one end to the other, but that is purely artificial. I
>>> stay
>>> away as much as possible from plotting charge distributions from
>>> simulations steered by external fields.
>>>
>>> Alex
>>>
>>> On Wed, Mar 21, 2018 at 4:29 PM, Shreyas Kaptan <shreyaskap...@gmail.com
>>> >
>>> wrote:
>>>
>>> I am confused about which potential it actually calculates. As I
>>>> understand, the electric field (external) adds a force for each charged
>>>> particle. This ought to change the ion distribution. If I read the gmx
>>>> potential documentation right, it uses the distribution of the charges
>>>> in
>>>> the box to calculate the electrostatic potential in the box. Should that
>>>> not include the external field-induced potential? I admit, that I
>>>> assumed
>>>> that this was the dominant part of the potential.
>>>>
>>>> Was I wrong?
>>>>
>>>> Shreyas
>>>>
>>>> On Wed, Mar 21, 2018 at 11:16 PM, Alex <nedoma...@gmail.com> wrote:
>>>>
>>>> It does exactly what it says it does. Which part is misunderstood?
>>>>>
>>>>> Alex
>>>>>
>>>>> On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan <
>>>>>
>>>> shreyaskap...@gmail.com
>>>
>>>> wrote:
>>>>>
>>>>> Hi.
>>>>>>
>>>>>> Thanks for the reply! Maybe I misunderstood the tool documentation.
>>>>>>
>>>>> So
>>>
>>>> what
>>>>>
>>>>>> does it *really* do?
>>>>>>
>>>>>> On Wed, Mar 21, 2018 at 8:27 PM, Alex <nedoma...@gmail.com> wrote:
>>>>>>
>>>>>> Also, here is a message for the authors of the documentation:
>>>>>>>
>>>>>>> *-[no]spherical*(no)
>>>>>>>
>>>>>>> Calculate spherical thingie
>>>>>>>
>>>>>>> Come on, guys. :)
>>>>>>>
>>>>>>> Alex
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 3/21/2018 1:24 PM, Alex wrote:
>>>>>>>
>>>>>>> Two things:
>>>>>>>>
>>>>>>>> 1. We cannot see your attachment, upload to a file share.
>>>>>>>>
>>>>>>>> 2. gmx potential does not reveal the actual potential drop due to
>>>>>>>> external electric field itself. What it 

Re: [gmx-users] gmx potential

[Shreyas Kaptan]

Okay. But then how can one confirm that the correct potential is applied if
not by looking at the charge distribution?

Shreyas

On Thu, Mar 22, 2018, 00:32 Alex <nedoma...@gmail.com> wrote:

> No, you are exactly right -- it does NOT include the external field
> explicitly. The external field acts as a magical force here and gmx
> potential would produce a potential distribution based on the resulting
> charge distribution. The external field itself, once again, however, does
> not exist in that picture. I mean, you could add it as a linear drop of
> potential from one end to the other, but that is purely artificial. I stay
> away as much as possible from plotting charge distributions from
> simulations steered by external fields.
>
> Alex
>
> On Wed, Mar 21, 2018 at 4:29 PM, Shreyas Kaptan <shreyaskap...@gmail.com>
> wrote:
>
> > I am confused about which potential it actually calculates. As I
> > understand, the electric field (external) adds a force for each charged
> > particle. This ought to change the ion distribution. If I read the gmx
> > potential documentation right, it uses the distribution of the charges in
> > the box to calculate the electrostatic potential in the box. Should that
> > not include the external field-induced potential? I admit, that I assumed
> > that this was the dominant part of the potential.
> >
> > Was I wrong?
> >
> > Shreyas
> >
> > On Wed, Mar 21, 2018 at 11:16 PM, Alex <nedoma...@gmail.com> wrote:
> >
> > > It does exactly what it says it does. Which part is misunderstood?
> > >
> > > Alex
> > >
> > > On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan <
> shreyaskap...@gmail.com
> > >
> > > wrote:
> > >
> > > > Hi.
> > > >
> > > > Thanks for the reply! Maybe I misunderstood the tool documentation.
> So
> > > what
> > > > does it *really* do?
> > > >
> > > > On Wed, Mar 21, 2018 at 8:27 PM, Alex <nedoma...@gmail.com> wrote:
> > > >
> > > > > Also, here is a message for the authors of the documentation:
> > > > >
> > > > > *-[no]spherical*(no)
> > > > >
> > > > >Calculate spherical thingie
> > > > >
> > > > > Come on, guys. :)
> > > > >
> > > > > Alex
> > > > >
> > > > >
> > > > >
> > > > > On 3/21/2018 1:24 PM, Alex wrote:
> > > > >
> > > > >>
> > > > >> Two things:
> > > > >>
> > > > >> 1. We cannot see your attachment, upload to a file share.
> > > > >>
> > > > >> 2. gmx potential does not reveal the actual potential drop due to
> > > > >> external electric field itself. What it does instead is described
> in
> > > the
> > > > >> utility documentation.
> > > > >>
> > > > >> Alex
> > > > >>
> > > > >>
> > > > >> On 3/21/2018 12:42 PM, Shreyas Kaptan wrote:
> > > > >>
> > > > >>> Dear GMX users,
> > > > >>>
> > > > >>> I am trying to use the gmx potential tool to calculate the
> > potential
> > > > >>> created by applying a constant electric field in the Z-direction.
> > > > >>>
> > > > >>> I am using the 2018 gromacs version. The electric field was
> applied
> > > > with:
> > > > >>>
> > > > >>>
> > > > >>> electric-field-z = 0.00625 0 0 0; 0.1 V voltage for 160
> > > > angstrom
> > > > >>> Z
> > > > >>> len
> > > > >>>
> > > > >>> When I use the gmx potential (from 2016.1 version) on the result
> of
> > > the
> > > > >>> simulation, I get the attached output.  I am not sure how to
> > > interpret
> > > > >>> the
> > > > >>> result. I expected a 100 V potential drop across the box, but I
> do
> > > not
> > > > s
> > > > >>> that. Is that an error on part of my interpretation or is there
> > > > something
> > > > >>> wrong with my setup?
> > > > >>>
> > > > >>> Thanks in advance!
> > > > >>>
> > > > >>> Shreyas
> > > &

Re: [gmx-users] gmx potential

[Shreyas Kaptan]

I am confused about which potential it actually calculates. As I
understand, the electric field (external) adds a force for each charged
particle. This ought to change the ion distribution. If I read the gmx
potential documentation right, it uses the distribution of the charges in
the box to calculate the electrostatic potential in the box. Should that
not include the external field-induced potential? I admit, that I assumed
that this was the dominant part of the potential.

Was I wrong?

Shreyas

On Wed, Mar 21, 2018 at 11:16 PM, Alex <nedoma...@gmail.com> wrote:

> It does exactly what it says it does. Which part is misunderstood?
>
> Alex
>
> On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan <shreyaskap...@gmail.com>
> wrote:
>
> > Hi.
> >
> > Thanks for the reply! Maybe I misunderstood the tool documentation. So
> what
> > does it *really* do?
> >
> > On Wed, Mar 21, 2018 at 8:27 PM, Alex <nedoma...@gmail.com> wrote:
> >
> > > Also, here is a message for the authors of the documentation:
> > >
> > > *-[no]spherical*(no)
> > >
> > >Calculate spherical thingie
> > >
> > > Come on, guys. :)
> > >
> > > Alex
> > >
> > >
> > >
> > > On 3/21/2018 1:24 PM, Alex wrote:
> > >
> > >>
> > >> Two things:
> > >>
> > >> 1. We cannot see your attachment, upload to a file share.
> > >>
> > >> 2. gmx potential does not reveal the actual potential drop due to
> > >> external electric field itself. What it does instead is described in
> the
> > >> utility documentation.
> > >>
> > >> Alex
> > >>
> > >>
> > >> On 3/21/2018 12:42 PM, Shreyas Kaptan wrote:
> > >>
> > >>> Dear GMX users,
> > >>>
> > >>> I am trying to use the gmx potential tool to calculate the potential
> > >>> created by applying a constant electric field in the Z-direction.
> > >>>
> > >>> I am using the 2018 gromacs version. The electric field was applied
> > with:
> > >>>
> > >>>
> > >>> electric-field-z = 0.00625 0 0 0; 0.1 V voltage for 160
> > angstrom
> > >>> Z
> > >>> len
> > >>>
> > >>> When I use the gmx potential (from 2016.1 version) on the result of
> the
> > >>> simulation, I get the attached output.  I am not sure how to
> interpret
> > >>> the
> > >>> result. I expected a 100 V potential drop across the box, but I do
> not
> > s
> > >>> that. Is that an error on part of my interpretation or is there
> > something
> > >>> wrong with my setup?
> > >>>
> > >>> Thanks in advance!
> > >>>
> > >>> Shreyas
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>
> > > --
> > > 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-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Shreyas Sanjay Kaptan
> > --
> > 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-requ...@gromacs.org.
> >
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Shreyas Sanjay Kaptan
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] gmx potential

[Shreyas Kaptan]

Hi.

Thanks for the reply! Maybe I misunderstood the tool documentation. So what
does it *really* do?

On Wed, Mar 21, 2018 at 8:27 PM, Alex <nedoma...@gmail.com> wrote:

> Also, here is a message for the authors of the documentation:
>
> *-[no]spherical*(no)
>
>Calculate spherical thingie
>
> Come on, guys. :)
>
> Alex
>
>
>
> On 3/21/2018 1:24 PM, Alex wrote:
>
>>
>> Two things:
>>
>> 1. We cannot see your attachment, upload to a file share.
>>
>> 2. gmx potential does not reveal the actual potential drop due to
>> external electric field itself. What it does instead is described in the
>> utility documentation.
>>
>> Alex
>>
>>
>> On 3/21/2018 12:42 PM, Shreyas Kaptan wrote:
>>
>>> Dear GMX users,
>>>
>>> I am trying to use the gmx potential tool to calculate the potential
>>> created by applying a constant electric field in the Z-direction.
>>>
>>> I am using the 2018 gromacs version. The electric field was applied with:
>>>
>>>
>>> electric-field-z = 0.00625 0 0 0; 0.1 V voltage for 160 angstrom
>>> Z
>>> len
>>>
>>> When I use the gmx potential (from 2016.1 version) on the result of the
>>> simulation, I get the attached output.  I am not sure how to interpret
>>> the
>>> result. I expected a 100 V potential drop across the box, but I do not s
>>> that. Is that an error on part of my interpretation or is there something
>>> wrong with my setup?
>>>
>>> Thanks in advance!
>>>
>>> Shreyas
>>>
>>>
>>>
>>>
>>>
>>>
>>
> --
> 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-requ...@gromacs.org.
>



-- 
Shreyas Sanjay Kaptan
-- 
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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] gmx potential

[Shreyas Kaptan]

Dear GMX users,

I am trying to use the gmx potential tool to calculate the potential
created by applying a constant electric field in the Z-direction.

I am using the 2018 gromacs version. The electric field was applied with:


electric-field-z = 0.00625 0 0 0; 0.1 V voltage for 160 angstrom Z
len

When I use the gmx potential (from 2016.1 version) on the result of the
simulation, I get the attached output.  I am not sure how to interpret the
result. I expected a 100 V potential drop across the box, but I do not see
that. Is that an error on part of my interpretation or is there something
wrong with my setup?

Thanks in advance!

Shreyas



-- 
Shreyas Sanjay Kaptan
-- 
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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