Re: [gmx-users] a99SB-disp forcefield

[João Henriques]

Yes. E-mail him directly.

J

On Wed, Jul 3, 2019 at 8:48 AM Timofey Tyugashev 
wrote:

> Paul as Paul Robustelli, the paper author?
>
> 02.07.2019 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
> > Message: 3
> > Date: Tue, 2 Jul 2019 09:52:04 +0200
> > From: Jo?o Henriques
> > To:gmx-us...@gromacs.org, "Greener, Joe"
> > Subject: Re: [gmx-users] a99SB-disp forcefield
> > Message-ID:
> >zu-3jypzd3tsxy...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Ask Paul, they have a Gromacs version of it and he'll most likely be
> happy
> > to share it with you.
> >
> > J
> >
> > On Mon, Jul 1, 2019 at 8:19 PM Joe Greener  wrote:
> >
> >> Dear Gromacs users,
> >>
> >> I am looking to use the a99SB-disp forcefield from Robustelli et al.
> >> PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs
> 2019.3.
> >>
> >> The details of the forcefield are in the paper supplementary material. I
> >> have carried out the following steps:
> >> - Downloaded the Amber99SB*-ILDN-Q forcefield from
> >> http://www.gromacs.org/Downloads/User_contributions/Force_fields  as
> >> ff99sb-star-ildn-q.tgz.
> >> - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz
> >> and extracted the water files.
> >> - Modified the water parameters to match a99SB-disp and created a
> >> pre-equilibrated water box.
> >> - Modified the partial charges on certain residues as required.
> >>
> >> Two steps remain that I could do with some advice on:
> >>
> >> - The torsion parameters in the paper are given as phi_0, k_1, k_2, ...,
> >> k_6. Sometimes k_2 onwards are missing, and values generally range -1.0
> >> to 1.0. I have looked at the list of dihedral types in the Gromacs
> >> manual and can't find which type these correspond to, or how to convert
> >> the values to a valid dihedral format. I guess this format is the one
> >> used by Desmond.
> >> - The a99SB-disp forcefield has a non-bonded LJ override between all
> >> backbone carbonyl oxygens and amide hydrogens. It seems I could have an
> >> entry something like this in the forcefield files:
> >>
> >> [ nonbond_params ]
> >> O H1sigma_val   epsilon_val
> >>
> >> Would this be sufficient to add this constraint?
> >>
> >> Has anyone else tried to implement the a99SB-disp forcefield in Gromacs?
> >> If not I'm happy to make it available if I get it working.
> >>
> >> Best,
> >> Joe
> >>
> >> Joe Greener
> >> Research Associate, UCL
> >> http://jgreener64.github.io/
> >>
> >> --
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> >>
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> >> posting!
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Re: [gmx-users] a99SB-disp forcefield

[João Henriques]

Ask Paul, they have a Gromacs version of it and he'll most likely be happy
to share it with you.

J

On Mon, Jul 1, 2019 at 8:19 PM Joe Greener  wrote:

> Dear Gromacs users,
>
> I am looking to use the a99SB-disp forcefield from Robustelli et al.
> PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3.
>
> The details of the forcefield are in the paper supplementary material. I
> have carried out the following steps:
> - Downloaded the Amber99SB*-ILDN-Q forcefield from
> http://www.gromacs.org/Downloads/User_contributions/Force_fields as
> ff99sb-star-ildn-q.tgz.
> - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz
> and extracted the water files.
> - Modified the water parameters to match a99SB-disp and created a
> pre-equilibrated water box.
> - Modified the partial charges on certain residues as required.
>
> Two steps remain that I could do with some advice on:
>
> - The torsion parameters in the paper are given as phi_0, k_1, k_2, ...,
> k_6. Sometimes k_2 onwards are missing, and values generally range -1.0
> to 1.0. I have looked at the list of dihedral types in the Gromacs
> manual and can't find which type these correspond to, or how to convert
> the values to a valid dihedral format. I guess this format is the one
> used by Desmond.
> - The a99SB-disp forcefield has a non-bonded LJ override between all
> backbone carbonyl oxygens and amide hydrogens. It seems I could have an
> entry something like this in the forcefield files:
>
> [ nonbond_params ]
> O H1sigma_val   epsilon_val
>
> Would this be sufficient to add this constraint?
>
> Has anyone else tried to implement the a99SB-disp forcefield in Gromacs?
> If not I'm happy to make it available if I get it working.
>
> Best,
> Joe
>
> Joe Greener
> Research Associate, UCL
> http://jgreener64.github.io/
>
> --
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> * Please search the archive at
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> posting!
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Re: [gmx-users] Coarse-grained Protein-ligand simulations

[João Henriques]

@Peter: Please don't take it the wrong way, it was just my lame attempt at
a tongue in cheek reply to your comment.

Now, to actually contribute with something of relevance to the topic at
hand, I agree with what most users/developers have mentioned before, i.e. a
ligand binding study using mixed representation with a CG active site is
not ideal for all the above stated reasons (and more). Given that resources
are scarce, I'd give metadynamics a serious try. It has been used
successfully in the past for this type of study (we have used it in our
group for GPCRs quite recently). Funnel metadynamics, in particular, seems
like a good candidate:

https://www.pnas.org/content/110/16/6358.short

We have quite decent resources at our group and we still use metadynamics
and other enhanced sampling methods all the time. Unless you're at DE Shaw
Research, brute force atomistic MD is almost never feasible for
large/complex systems.

J

On Tue, Apr 2, 2019 at 10:49 AM Peter Kroon  wrote:

> @Joao: I didn't mean to imply in any way that everyone has (or should
> have) a couple hundred nodes at their beck and call. Although it would
> be nice. I underestimated the size of the GPCR complex, as well as how
> slow atomistic simulations are :)
>
> Now that I've tried to pull my foot out of my mouth again, back on
> topic: although Martini can do (almost) anything, I am rather skeptical
> of CG docking/binding studies because of the reasons I outlined earlier.
> In addition, in Martini the error in the entropic term (due to a lack of
> conformational freedom) in the free energy equation is compensated in
> the enthalpic term. However, in a confined environment (protein pocket!)
> this compensation may have to be different --- and the ligand was
> parametrised in solution.
>
>
> Peter
>
>
> On 02-04-19 05:18, Billy Williams-Noonan wrote:
> > Have you considered accelerated MD?  Like metadynamics.  Plumed has a lot
> > of options there
> >
> > Cheers,
> > Billy
> >
> > On Tue, 2 Apr 2019 at 09:18, Mac Kevin Braza  wrote:
> >
> >> Hello Sir Benson,
> >>
> >> We are using Supermicro SYS-1028R-WC1R Server with 2 x 2.2Ghz 12-Core
> Intel
> >> Processors
> >> (4 x 8GB DDR4) with a single node only. Ideally, to reach the
> microsecond
> >> simulation of GPCR-membrane
> >> simulation in all-atom, we will be needing a computer cluster with at
> least
> >> 200 parallel nodes system.
> >> But even with a 50-100 parallel nodes, we will reach the simulation time
> >> for a month, although we know that this is
> >> challenging for us here in the Philippines.
> >>
> >> The specialized super-computer cluster Anton is an example of hardware
> that
> >> have reached more than 100 microseconds
> >> simulation of the all-atom GPCR-membrane simulation in a month of total
> CPU
> >> time. It has 512 processing nodes.
> >>
> >> Best regards,
> >> Mac Kevin E. Braza
> >>
> >> On Tue, Apr 2, 2019, 12:40 AM Benson Muite 
> >> wrote:
> >>
> >>> Hi Mac Kevin E. Braza,
> >>>
> >>> What hardware are you using? What kind of hardware would be needed to
> do
> >>> a full simulation instead of a coarse-grained one?
> >>>
> >>> Regards,
> >>>
> >>> Benson
> >>>
> >>> On 4/1/19 6:49 PM, João Henriques wrote:
> >>>> GPCR + membrane systems are notoriously big systems to work with for
> >> most
> >>>> research groups, regardless of your location on the map. Even in
> >>>> "privileged Europe" many research groups would struggle to produce
> >>>> microsecond long atomistic simulations of this system within a short
> >>> period
> >>>> of time. Moreover, "privileged Europe" is also home to significant
> >>> computer
> >>>> resource discrepancies among its member countries. This is actually
> one
> >>> of
> >>>> the main reasons why your group's CG model is so popular :)
> >>>>
> >>>> On Mon, Apr 1, 2019 at 5:09 PM P C Kroon  wrote:
> >>>>
> >>>>> Hi,
> >>>>>
> >>>>> I work in privileged Europe, so it’s good for me to get a reality
> >> check
> >>>>> once every while. Thanks.
> >>>>>
> >>>>> Coarse graining molecules for Martini is not too hard. There should
> be
> >>>>> some tutorials on cgmartini.nl that should help you get underway.
> You
> >>>>

Re: [gmx-users] Coarse-grained Protein-ligand simulations

[João Henriques]

GPCR + membrane systems are notoriously big systems to work with for most
research groups, regardless of your location on the map. Even in
"privileged Europe" many research groups would struggle to produce
microsecond long atomistic simulations of this system within a short period
of time. Moreover, "privileged Europe" is also home to significant computer
resource discrepancies among its member countries. This is actually one of
the main reasons why your group's CG model is so popular :)

On Mon, Apr 1, 2019 at 5:09 PM P C Kroon  wrote:

> Hi,
>
> I work in privileged Europe, so it’s good for me to get a reality check
> once every while. Thanks.
>
> Coarse graining molecules for Martini is not too hard. There should be
> some tutorials on cgmartini.nl that should help you get underway. You
> will, however, run into the problems I mentioned, and you will need to do
> extensive validation on the topologies of your ligands. Again, it depends
> on your exact research question: if you’re doing high-throughput like
> screening, qualitative models might be good enough. Also see T Bereau’s
> automartini.
>
> Peter
>
> From: Mac Kevin Braza
> Sent: 01 April 2019 16:06
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Coarse-grained Protein-ligand simulations
>
> Dear Sir Peter Kroon,
>
> We are currently maximizing the computer capabilities to reach microsecond,
> but to reach 1 microsecond in our lab, it would take me at least 6 months
> to finish all one microsecond.
> We do not have that high level capacities here in the Philippines to reach
> it. Membrane proteins are
> typically longer, with all the lipid bilayers, solvent, and ions present on
> top of the protein.
> We will need more powerful computers in this part.
>
> I found few works from literature on the protein-ligand representation in
> Coarse-grained.
> We found several papers but they are either have vague methodology in
> describing the ligand coarse-graining method and/or not necessarily have
> the same research problem
> as we want to explore.
>
> All in all, we will finish the simulation in all-atom as long as we can,
> and still be hopeful with
> the coarse-graining method. What we explored as in the present is the
> CHARMM-GUI Martini Maker,
> yet they do not include the drug ligands in representing them in
> coarse-grained. I still have to search for other means
> to do this. Thank you very much!
>
> Best regards,
> Mac Kevin E. Braza
>
> On Mon, Apr 1, 2019 at 5:59 PM Peter Kroon  wrote:
>
> > Hi,
> >
> > that's probably a tough cookie. My first instinct would be to just apply
> > a more hardware, and do it all atomistically. A microsecond should be
> > within reach. Whether it's enough is a separate matter. The problem is
> > that most CG representations don't get the shape of both your pocket and
> > ligand exactly right, producing unreliable answers. In addition, in most
> > CG FFs hydrogen bonds are isotropic and not specific enough for this
> > kind of problem.
> >
> > If "more hardware" is not an option you'll need to dive into literature
> > to see if people did CG protein-ligand binding/docking/unbinding
> > (depening on research question). I would also be very skeptical of any
> > (absolute) kinetics produced by CG simulations.
> >
> > As a last ditch effort you could look into multiscaling, but that's a
> > research topic in its own.
> >
> >
> > Peter
> >
> >
> > On 01-04-19 11:49, Mac Kevin Braza wrote:
> > > Thank you Prof. Lemkul,
> > >
> > > I appreciate your comment on this part.
> > >
> > > Sir Peter Kroon,
> > >
> > > We want to do the coarse-grained MD simulation to access long timescale
> > > events of the
> > > effect of the ligand binding to the GPCR, at least microsecond . For
> now,
> > > the most accessible means for us is to
> > > do the CGMD. But we are currently being cornered in choosing which
> set-up
> > > will best suit, and
> > > if it will allow us to see these events. We are looking also in the
> > > possibility of coarse-graining
> > > the ligand, and if you can share your expertise in coarse-graining also
> > the
> > > ligand that would be great.
> > > I appreciate this Sir Kroon, thank you very much!
> > >
> > > Best regards,
> > > Mac Kevin E. Braza
> > >
> > > On Mon, Apr 1, 2019 at 5:07 PM Peter Kroon  wrote:
> > >
> > >> If I may chip in: It really depends on what you're studying, and what
> > >> forcefield you're using to do it. Unfortunately there is no FF that
> > >> reproduces all behaviour accurately. The art is in picking one that
> (at
> > >> least) reproduces what you're interested in.
> > >>
> > >>
> > >> Peter
> > >>
> > >> On 29-03-19 17:26, Justin Lemkul wrote:
> > >>>
> > >>> On 3/29/19 9:17 AM, Mac Kevin Braza wrote:
> >  Thank you Professor Lemkul,
> > 
> >  But would you suggest on how can I coarse-grained the ligand I am
> >  using? I
> >  have been searching resources online but they do not work in our
> part.

Re: [gmx-users] gmx do_dssp

[João Henriques]

Hello Eduardo,

The xpm file contains all the info about axes, keys, etc. Look at this
excerpt from a random xpm file from one of my simulations:

/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title:   "Secondary structure" */
/* legend:  "" */
/* x-label: "Time (us)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"50001 69   8 1",
"~  c #FF " /* "Coil" */,
"E  c #FF " /* "B-Sheet" */,
"B  c #00 " /* "B-Bridge" */,
"S  c #008000 " /* "Bend" */,
"T  c #00 " /* "Turn" */,
"H  c #FF " /* "A-Helix" */,
"I  c #800080 " /* "5-Helix" */,
"G  c #808080 " /* "3-Helix" */,

With a bit of scripting you can turn this xpm file into anything you like.
Also, I haven't used it yet, but this exists and can perform several
operations/analyses on xpm files:
https://github.com/HITS-MBM/conan/blob/master/docs/index.md

Cheers,
João

On Mon, Mar 18, 2019 at 5:45 PM Eduardo Diniz 
wrote:

> Hello!
>
> I'm wanting to keep track of secondary structure (ss) elements in my
> protein simulation but I have some questions about the do_dssp tool of
> gromacs. The two main output files it produces is a ss.xpm file which I've
> found very difficult to interpret, mainly because I don't know what that
> colors code represent and the x and y axis are not specified (I think the x
> axis is time and the y axis is residue).
>
> The second file is the scount.xvg file which indicates the number of
> residues belonging to one of eight secondary structure elements, but for me
> this information isn't enough, because I want to know what residues belong
> to what ss element.
>
> One optinal output file that I think might be useful for me is the
> ssdump.dat file, which shows (I suppose) what residues belongs to what ss
> elements, but I don't know what those letters (E, S H etc) means.
>
> Sorry if what I ask is stupid. Hope someone can help me. Thanks in advance
> for your time.
>
> Eduardo
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Re: [gmx-users] Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

[João Henriques]

Hi Hassan,

Yes, this is something that I usually do with MDAnalysis, but from
experience I've noticed that people are often reluctant to try it.
Therefore you could try playing with gmx_select. Something like this should
output the number of water oxygen atoms within 5 Å of residue 1 as a
function of time:
gmx_mpi select -f md.xtc -s md.tpr -os -select "name OW and within 0.5 of
resnr 1"

This is just an example, play around with the selection syntax and other
options to get the desired result.

Cheers,
J

On Thu, Nov 22, 2018 at 5:57 PM Hassan Aaryapour 
wrote:

> Dear Gromacs Users
> I would like to calculate the presence of water molecules number as a
> function of time, around a ligand during binding to its pocket from a
> trj.xtc file.
> How can I do it by Gromacs or any other program?
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Re: [gmx-users] How to fix the box size during the simulation?

[João Henriques]

"Is it possible to fix dimensions of the simulation box during the
production run?" ---> Of course, simulate in the canonical ensemble (NVT).
The isothermal-isobaric ensemble (NPT) employs a barostat, which means that
the box volume will have to vary in order to keep the pressure constant.

J
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Re: [gmx-users] Population Density Plot

[João Henriques]

I'm sure there's lots of software that can perform that task, I just felt
it was important to underline that a kernel density estimation is what is
needed in this case. If you go back to your original reply, there's nothing
in there that can help the original poster solving his problem.

J

On Mon, Sep 17, 2018 at 3:43 PM Vytautas Rakeviius 
wrote:

>  Also you can use R for that task. Very easy like:density(x, ...)
>
> On Monday, September 17, 2018, 4:26:38 PM GMT+3, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
>  How does that reply the OP's question? To calculate the joint probability
> distribution you need to perform a kernel density estimation. I'd recommend
> either SciPy or Seaborn if you're not averse to coding in Python:
>
>
> https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.gaussian_kde.html
> https://seaborn.pydata.org/examples/joint_kde.html
>
> With Seaborn this is an incredibly simple task.
>
> J
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Re: [gmx-users] Population Density Plot

[João Henriques]

How does that reply the OP's question? To calculate the joint probability
distribution you need to perform a kernel density estimation. I'd recommend
either SciPy or Seaborn if you're not averse to coding in Python:

https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.gaussian_kde.html
https://seaborn.pydata.org/examples/joint_kde.html

With Seaborn this is an incredibly simple task.

J
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Re: [gmx-users] Regarding index .ndx files

[João Henriques]

What is your system composed of? It is generally a good idea to couple
solvent and solute separately (as long as solute is "big enough", see
http://www.gromacs.org/Documentation/Terminology/Thermostats), so Vytautas
reply isn't the best advice. It will solve your problem, but that's
generally not the way to proceed, and definitely not the most educative.

Regarding the part about index groups, you can group groups into a single
index entry to facilitate things. You can easily create a group with all
things solute and another with solvent + salt. This way you can couple them
separately, assuming that makes sense for your system (you didn't specify
what it is, so it's hard to help a lot more than this).

J

On Mon, Sep 17, 2018 at 1:15 PM Vytautas Rakeviius 
wrote:

>  Without going into details and setting:
> tc-grps = System
> should allow to proceed without fatal errors.
> On Monday, September 17, 2018, 1:58:50 PM GMT+3, Sebastian Muraru <
> sebastian.mur...@grabtop.upb.ro> wrote:
>
>  Hi there! I am a Masters student and this is my first email to the list.
> I would just like to ask whether someone can clarify something for me
> regarding the index .ndx files.
> I am using an nvt.mdp file in order to run an nvt equilibration step. The
> section of interest is the following (currently receiving an error):
>
> ###
> ; Temperature coupling is on
> tcoupl  = V-rescale; modified Berendsen thermostat
> tc-grps= CX ssdna; two coupling groups - more accurate
> tau_t  = 0.10.1; time constant, in ps
> ref_t  = 300300; reference temperature, one for each
> group, in K
> ###
>
> The current error says that a number of atoms are not part of any of the
> T-Coupling groups. Therefore I have the following questions:
> - Does this mean all atoms (including SOL) must be included in the groups
> specified using 'tc-grps'?
> - If my index.ndx file is very large (contains > 20 groups), do I have to
> manually write them down at 'tc-grps' in the mdp file or is there a way to
> automatically import the groups present in the index.ndx file?
>
> Best,
> Sebastian
> --
> 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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> --
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> * Please search the archive at
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Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[João Henriques]

Ok, that's not a gromacs problem, that's you not understanding what you are
doing in regard to the selections. You can't just pass all the atoms of all
water molecules and all the atoms of your surface and expect gromacs to
define the planes for you. What I meant in my simple example was that you
should try passing 3 atoms on your surface to define a reference plane and
3 atoms on a single water molecule to define its H-O-H plane. Then see if
it runs. If it does, then it's time to think about how you can do that for
all water molecules in the system. Do you follow me?

Unless you plan on defining these points in a .ndx file, I suggest you get
familiar with the selection syntax:

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

J

On Wed, Sep 12, 2018 at 8:04 PM rose rahmani  wrote:

> On Wed, Sep 12, 2018 at 9:15 PM João Henriques <
> joao.m.a.henriq...@gmail.com>
> wrote:
>
> > Did you try with gmx gangle again, after my reply?
>
> yes.
>
>  gmx gangle -f umbrella0.xtc -s umbrella0.tpr -n index.ndx -g1 plane -g2
> plane -group1 -group2 -oh -oav
>
> Available static index groups:
>  Group  0 "System" (4336 atoms)
>  Group  1 "Other" (760 atoms)
>  Group  2 "ZnS" (560 atoms)
>  Group  3 "WAL" (200 atoms)
>  Group  4 "NA" (5 atoms)
>  Group  5 "CL" (5 atoms)
>  Group  6 "Protein" (26 atoms)
>  Group  7 "Protein-H" (12 atoms)
>  Group  8 "C-alpha" (1 atoms)
>  Group  9 "Backbone" (5 atoms)
>  Group 10 "MainChain" (7 atoms)
>  Group 11 "MainChain+Cb" (8 atoms)
>  Group 12 "MainChain+H" (9 atoms)
>  Group 13 "SideChain" (17 atoms)
>  Group 14 "SideChain-H" (5 atoms)
>  Group 15 "Prot-Masses" (26 atoms)
>  Group 16 "non-Protein" (4310 atoms)
>  Group 17 "Water" (3540 atoms)
>  Group 18 "SOL" (3540 atoms)
>  Group 19 "non-Water" (796 atoms)
>  Group 20 "Ion" (10 atoms)
>  Group 21 "ZnS" (560 atoms)
>  Group 22 "WAL" (200 atoms)
>  Group 23 "NA" (5 atoms)
>  Group 24 "CL" (5 atoms)
>  Group 25 "Water_and_ions" (3550 atoms)
>  Group 26 "Protein" (26 atoms)
>  Group 27 "ZnS" (560 atoms)
>  Group 28 "ZnS" (560 atoms)
> Specify any number of selections for option 'group1'
> (First analysis/vector selection):
> (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> > 17
> Selection '17' parsed
> > 27
> Selection '27' parsed
> > Available static index groups:
>  Group  0 "System" (4336 atoms)
>  Group  1 "Other" (760 atoms)
>  Group  2 "ZnS" (560 atoms)
>  Group  3 "WAL" (200 atoms)
>  Group  4 "NA" (5 atoms)
>  Group  5 "CL" (5 atoms)
>  Group  6 "Protein" (26 atoms)
>  Group  7 "Protein-H" (12 atoms)
>  Group  8 "C-alpha" (1 atoms)
>  Group  9 "Backbone" (5 atoms)
>  Group 10 "MainChain" (7 atoms)
>  Group 11 "MainChain+Cb" (8 atoms)
>  Group 12 "MainChain+H" (9 atoms)
>  Group 13 "SideChain" (17 atoms)
>  Group 14 "SideChain-H" (5 atoms)
>  Group 15 "Prot-Masses" (26 atoms)
>  Group 16 "non-Protein" (4310 atoms)
>  Group 17 "Water" (3540 atoms)
>  Group 18 "SOL" (3540 atoms)
>  Group 19 "non-Water" (796 atoms)
>  Group 20 "Ion" (10 atoms)
>  Group 21 "ZnS" (560 atoms)
>  Group 22 "WAL" (200 atoms)
>  Group 23 "NA" (5 atoms)
>  Group 24 "CL" (5 atoms)
>  Group 25 "Water_and_ions" (3550 atoms)
>  Group 26 "Protein" (26 atoms)
>  Group 27 "ZnS" (560 atoms)
>  Group 28 "ZnS" (560 atoms)
> Specify any number of selections for option 'group2'
> (Second analysis/vector selection):
> (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> > 17
> Selection '17' parsed
> > 27
> Selection '27' parsed
> > Reading file umbrella0.tpr, VERSION 4.5.4 (single precision)
> Reading file umbrella0.tpr, VERSION 4.5.4 (single precision)
>
> ---
> Program: gmx gangle, VERSION 5.1.4
> Source file: src/gromacs/trajectoryanalysis/modules/angle.cpp (line 468)
> Function:void
> gmx::analysismodules::{anonymous}::Angle::initFromSelections(const
> SelectionList&, const SelectionList&)
>
> Inconsistency in user input:
> Number of positions in selection 2 in the first group not divisible by 3
>
> For more information and tips for troubleshoo

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[João Henriques]

Did you try with gmx gangle again, after my reply? Before writing code you
should always make sure that what is at hand can't do the job first.

Also, I've already directed you to an example in my previous email. Check
the MDAnalysis link again. If Python isn't your thing, feel free to use any
other language. Even the PLUMED driver could do the trick with some work.

J




On Wed, Sep 12, 2018 at 6:04 PM Nick Johans  wrote:

> Sorry i'm nick's friend and i couldn't access to my email so i had to send
> it by his account.
>
> Rose
>
> On Wed, 12 Sep 2018, 20:16 Nick Johans,  wrote:
>
> > Thank you so much Joao for detailed answer. You are right, i think i
> > should write my own code. But since i don't have much experience in
> > programming, would you please introduce me some useful examples?
> >  And(see below; our former conversations)
> >
> > Best
> > Rose
> > On Wed, 12 Sep 2018, 20:04 João Henriques,  >
> > wrote:
> >
> >> Ok, being that the reference is a surface gmx gangle might work. Notice
> >> that I wrote might, because I believe it will still be cumbersome for
> the
> >> many water molecules in the box. For the example of the two planes, you
> >> just basically need to set "-g1 plane", "-g2 plane" and pass the
> >> selections
> >> of the surface and water molecule H-O-H plane to "-group1" and
> "-group2",
> >> respectively. For the example of the surface and the H-O vector, you
> adapt
> >> it accordingly ("-g1 plane", "-g2 vector" and the corresponding
> >> selections). I easily can see this working for a single water molecule,
> >> but
> >> for all the water molecules in the box this might get tricky. Specially
> if
> >> you're gonna try to tackle them all under a single selection. You could
> >> aways run the command in a loop for each water molecule in the box, but
> >> that doesn't look very "smart" and/or fast.
> >>
> >> I'd still probably look into doing my own code using some third party
> >> module/package to parse and analyze trajectories.
> >>
> >> J
> >>
> >> On Wed, Sep 12, 2018 at 5:01 PM rose rahmani 
> >> wrote:
> >>
> >> > On Wed, 12 Sep 2018, 19:13 João Henriques, <
> >> joao.m.a.henriq...@gmail.com>
> >> > wrote:
> >> >
> >> > > "It gives me the histogram of angles" ---> what is "it" in this
> >> sentence?
> >> > >
> >> > It= -oh output of gmx gangle which writes the histogram of 'angleS'
> not
> >> the
> >> > angle that i have already defined.( THE beta angle= angle between HOH
> >> plane
> >> > of water molecules and surface plane , THE alpha angke= angle between
> >> OH of
> >> > water molecules and surface plane. The surface is ZnS surface(i have
> an
> >> > slab of ZnS) not protein.
> >> >
> >> > > There are 26 emails on the link I shared. What did you actually
> try? I
> >> > > mean, an histogram and a distribution function aren't that far
> >> apart...
> >> > > Also, I believe understand what you want to do, you want to
> calculate
> >> the
> >> > > ADF of the water molecules with the protein surface as the
> reference.
> >> > > Something
> >> > > like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see
> >> Figures
> >> > 3
> >> > > and 5). Well, I've played around with a similar problem and there's
> no
> >> > > simple answer. I ended up using MDAnalysis
> >> > > <
> >> > >
> >> >
> >>
> https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html
> >> > > >
> >> > > (click on the link, see 4.8.3.1.3. AngularDistribution).
> >> >
> >>
> > How can i use it in gromacs?
> >
> >> > Thank you.
> >> >
> >> > > I tried doing the
> >> > > same with the native Gromacs tools but found it too be too much of a
> >> pain
> >> > > in the a**.
> >> > >
> >> > I think gromacs can do it. But first i should define all O-H and in
> box
> >> > then calculate the angle between  for ALPHA
> >> > Maybe should define H-O-H plane then for BETA).
> >> >
> >> > I found the documentation of gmx gangle gmx angle

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[João Henriques]

"being that the reference is a surface" ---> I meant a "planar surface"

J

On Wed, Sep 12, 2018 at 5:34 PM João Henriques 
wrote:

> Ok, being that the reference is a surface gmx gangle might work. Notice
> that I wrote might, because I believe it will still be cumbersome for the
> many water molecules in the box. For the example of the two planes, you
> just basically need to set "-g1 plane", "-g2 plane" and pass the selections
> of the surface and water molecule H-O-H plane to "-group1" and "-group2",
> respectively. For the example of the surface and the H-O vector, you adapt
> it accordingly ("-g1 plane", "-g2 vector" and the corresponding
> selections). I easily can see this working for a single water molecule, but
> for all the water molecules in the box this might get tricky. Specially if
> you're gonna try to tackle them all under a single selection. You could
> aways run the command in a loop for each water molecule in the box, but
> that doesn't look very "smart" and/or fast.
>
> I'd still probably look into doing my own code using some third party
> module/package to parse and analyze trajectories.
>
> J
>
> On Wed, Sep 12, 2018 at 5:01 PM rose rahmani 
> wrote:
>
>> On Wed, 12 Sep 2018, 19:13 João Henriques, 
>> wrote:
>>
>> > "It gives me the histogram of angles" ---> what is "it" in this
>> sentence?
>> >
>> It= -oh output of gmx gangle which writes the histogram of 'angleS' not
>> the
>> angle that i have already defined.( THE beta angle= angle between HOH
>> plane
>> of water molecules and surface plane , THE alpha angke= angle between OH
>> of
>> water molecules and surface plane. The surface is ZnS surface(i have an
>> slab of ZnS) not protein.
>>
>> > There are 26 emails on the link I shared. What did you actually try? I
>> > mean, an histogram and a distribution function aren't that far apart...
>> > Also, I believe understand what you want to do, you want to calculate
>> the
>> > ADF of the water molecules with the protein surface as the reference.
>> > Something
>> > like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see
>> Figures 3
>> > and 5). Well, I've played around with a similar problem and there's no
>> > simple answer. I ended up using MDAnalysis
>> > <
>> >
>> https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html
>> > >
>> > (click on the link, see 4.8.3.1.3. AngularDistribution).
>>
>> Thank you.
>>
>> > I tried doing the
>> > same with the native Gromacs tools but found it too be too much of a
>> pain
>> > in the a**.
>> >
>> I think gromacs can do it. But first i should define all O-H and in box
>> then calculate the angle between  for ALPHA
>> Maybe should define H-O-H plane then for BETA).
>>
>> I found the documentation of gmx gangle gmx angle so complicated and
>> confusing. I don't know how can i hsethem priperly...
>>
>> Best
>>
>> >
>> > I hope this is at least somewhat useful.
>> >
>> > Cheers,
>> > João
>> >
>> >
>> >
>> > On Wed, Sep 12, 2018 at 3:41 PM rose rahmani 
>> > wrote:
>> >
>> > > Thank you Joao,
>> > >
>> > > On Wed, 12 Sep 2018, 14:04 João Henriques, <
>> joao.m.a.henriq...@gmail.com
>> > >
>> > > wrote:
>> > >
>> > > > Dear Rose,
>> > > >
>> > > > Spamming is not the answer. There have been quite a few threads
>> about
>> > > this
>> > > > subject in the recent past. Searching the mailing list before
>> posting
>> > is
>> > > > usually good practice. If then something remains unclear, please
>> feel
>> > > free
>> > > > to ask. I remember having quite long discussions with a Dilip H. N.
>> > about
>> > > > this subject (on and off the mailing list).
>> > > >
>> > > > A simple query fetched 26 results:
>> > > >
>> > > >
>> > >
>> >
>> https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0
>> > >
>> > > I search and read about but it didn't help me. It gives me the
>> histogram
>> > of
>> > > angles but what i really want is the distribituion

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[João Henriques]

Ok, being that the reference is a surface gmx gangle might work. Notice
that I wrote might, because I believe it will still be cumbersome for the
many water molecules in the box. For the example of the two planes, you
just basically need to set "-g1 plane", "-g2 plane" and pass the selections
of the surface and water molecule H-O-H plane to "-group1" and "-group2",
respectively. For the example of the surface and the H-O vector, you adapt
it accordingly ("-g1 plane", "-g2 vector" and the corresponding
selections). I easily can see this working for a single water molecule, but
for all the water molecules in the box this might get tricky. Specially if
you're gonna try to tackle them all under a single selection. You could
aways run the command in a loop for each water molecule in the box, but
that doesn't look very "smart" and/or fast.

I'd still probably look into doing my own code using some third party
module/package to parse and analyze trajectories.

J

On Wed, Sep 12, 2018 at 5:01 PM rose rahmani  wrote:

> On Wed, 12 Sep 2018, 19:13 João Henriques, 
> wrote:
>
> > "It gives me the histogram of angles" ---> what is "it" in this sentence?
> >
> It= -oh output of gmx gangle which writes the histogram of 'angleS' not the
> angle that i have already defined.( THE beta angle= angle between HOH plane
> of water molecules and surface plane , THE alpha angke= angle between OH of
> water molecules and surface plane. The surface is ZnS surface(i have an
> slab of ZnS) not protein.
>
> > There are 26 emails on the link I shared. What did you actually try? I
> > mean, an histogram and a distribution function aren't that far apart...
> > Also, I believe understand what you want to do, you want to calculate the
> > ADF of the water molecules with the protein surface as the reference.
> > Something
> > like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see Figures
> 3
> > and 5). Well, I've played around with a similar problem and there's no
> > simple answer. I ended up using MDAnalysis
> > <
> >
> https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html
> > >
> > (click on the link, see 4.8.3.1.3. AngularDistribution).
>
> Thank you.
>
> > I tried doing the
> > same with the native Gromacs tools but found it too be too much of a pain
> > in the a**.
> >
> I think gromacs can do it. But first i should define all O-H and in box
> then calculate the angle between  for ALPHA
> Maybe should define H-O-H plane then for BETA).
>
> I found the documentation of gmx gangle gmx angle so complicated and
> confusing. I don't know how can i hsethem priperly...
>
> Best
>
> >
> > I hope this is at least somewhat useful.
> >
> > Cheers,
> > João
> >
> >
> >
> > On Wed, Sep 12, 2018 at 3:41 PM rose rahmani 
> > wrote:
> >
> > > Thank you Joao,
> > >
> > > On Wed, 12 Sep 2018, 14:04 João Henriques, <
> joao.m.a.henriq...@gmail.com
> > >
> > > wrote:
> > >
> > > > Dear Rose,
> > > >
> > > > Spamming is not the answer. There have been quite a few threads about
> > > this
> > > > subject in the recent past. Searching the mailing list before posting
> > is
> > > > usually good practice. If then something remains unclear, please feel
> > > free
> > > > to ask. I remember having quite long discussions with a Dilip H. N.
> > about
> > > > this subject (on and off the mailing list).
> > > >
> > > > A simple query fetched 26 results:
> > > >
> > > >
> > >
> >
> https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0
> > >
> > > I search and read about but it didn't help me. It gives me the
> histogram
> > of
> > > angles but what i really want is the distribituion of special defined
> > > angle(between two plane) during simulation. I refer you ahain to
> > >
> > >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface?_ec=topicPostOverviewAuthoredQuestions&_sg=hV7QNgmmW-MkZF5OKfgZlaI5O0G5HeVQGSGoneQ1gDaXV_96qBhs2Re6IrsBNcXYMTf0FzIqXPyDrI9r.8ylTJZVEy00BT4mPuq0m2nGK5dREPBjukd2plNMaXf5ocFCOJCRriPhzJum_Vt2KLoZVmTZVBDoQZQOcBKAP8EU
> > >
> > >
> > >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface
> > >
>

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[João Henriques]

"It gives me the histogram of angles" ---> what is "it" in this sentence?
There are 26 emails on the link I shared. What did you actually try? I
mean, an histogram and a distribution function aren't that far apart...
Also, I believe understand what you want to do, you want to calculate the
ADF of the water molecules with the protein surface as the reference. Something
like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see Figures 3
and 5). Well, I've played around with a similar problem and there's no
simple answer. I ended up using MDAnalysis
<https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html>
(click on the link, see 4.8.3.1.3. AngularDistribution). I tried doing the
same with the native Gromacs tools but found it too be too much of a pain
in the a**.

I hope this is at least somewhat useful.

Cheers,
João



On Wed, Sep 12, 2018 at 3:41 PM rose rahmani  wrote:

> Thank you Joao,
>
> On Wed, 12 Sep 2018, 14:04 João Henriques, 
> wrote:
>
> > Dear Rose,
> >
> > Spamming is not the answer. There have been quite a few threads about
> this
> > subject in the recent past. Searching the mailing list before posting is
> > usually good practice. If then something remains unclear, please feel
> free
> > to ask. I remember having quite long discussions with a Dilip H. N. about
> > this subject (on and off the mailing list).
> >
> > A simple query fetched 26 results:
> >
> >
> https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0
>
> I search and read about but it didn't help me. It gives me the histogram of
> angles but what i really want is the distribituion of special defined
> angle(between two plane) during simulation. I refer you ahain to
>
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface?_ec=topicPostOverviewAuthoredQuestions&_sg=hV7QNgmmW-MkZF5OKfgZlaI5O0G5HeVQGSGoneQ1gDaXV_96qBhs2Re6IrsBNcXYMTf0FzIqXPyDrI9r.8ylTJZVEy00BT4mPuq0m2nGK5dREPBjukd2plNMaXf5ocFCOJCRriPhzJum_Vt2KLoZVmTZVBDoQZQOcBKAP8EU
>
>
> https://www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface
>
>  I asked different questions several times last 2 days and i thought my
> email doesn't recieve and share in mailing-list.
>
> I'm really confused about what people suggest. I'm a student and i think, i
> clearly explained what i want after huge searches, it's not because of
> indolence and i would be appreciated if any one could answer me.
>
> Regards
>
>
>
> > Play with the query a bit and it should get you a lot of info on your
> > problem.
> >
> > Best regards,
> > João
> >
> >
> >
> >
> >
> > On Mon, Sep 10, 2018 at 10:29 AM rose rahmani 
> > wrote:
> >
> > > Hi,
> > > How can i calculate the angular distribution of the angles between
> water
> > > molecule water and surface? surface during molecular dynamics
> simulation?
> > >  is it possible by GROMACS? gmx gangle?
> > >
> > > would you please help me?
> > >
> > > To be clear; i refer you to these plots
> > >
> > >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface
> > >
> > >
> > > Best regards
> > >
> > > Rose
> > > --
> > > 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
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Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[João Henriques]

Dear Rose,

Spamming is not the answer. There have been quite a few threads about this
subject in the recent past. Searching the mailing list before posting is
usually good practice. If then something remains unclear, please feel free
to ask. I remember having quite long discussions with a Dilip H. N. about
this subject (on and off the mailing list).

A simple query fetched 26 results:
https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0

Play with the query a bit and it should get you a lot of info on your
problem.

Best regards,
João





On Mon, Sep 10, 2018 at 10:29 AM rose rahmani  wrote:

> Hi,
> How can i calculate the angular distribution of the angles between water
> molecule water and surface? surface during molecular dynamics simulation?
>  is it possible by GROMACS? gmx gangle?
>
> would you please help me?
>
> To be clear; i refer you to these plots
>
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface
>
>
> Best regards
>
> Rose
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Re: [gmx-users] Regarding rigidity of water models

[João Henriques]

Hi,

[1] CHARMM36 is to be used with the CHARMM-modified TIP3P water model
(TIP3P with LJ parameters on the water molecule hydrogen atoms).

[2] By default it's rigid, but check "define =" under your mdout.mdp file.
If there's no -DFLEXIBLE, then it's rigid.

[3] No idea of what that is, sorry.

Cheers,
J
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Re: [gmx-users] gmx mindist error

[João Henriques]

Yes, I understand what you and Justin refer to. Until your first email I
completely forgot to consider that certain simulations require variations
to the normal 3D periodicity, and thus my ramble about the box vectors. It
makes perfect sense now.

Also, thank you suggesting the alternative using the PDB, really
appreciated. It can certainly make things easier in this particular case.

Best regards,
J

On Tue, Mar 27, 2018 at 9:48 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Looking at the code, if your PDB file had suitable CRYST1 fields then you
> would not have needed a .tpr. I improved the docs a bit at
> https://gerrit.gromacs.org/#/c/7729/
>
> Mark
>
> On Tue, Mar 27, 2018 at 8:58 PM Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I have no idea how ACEMD works, but one can certainly imagine an MD
> > package that hard codes the assumption of a cubic box with normal 3D
> > periodicity. But there's nothing intrinsic to the file format that
> implies
> > any periodicity to a box. That's either a convention, or given by other
> > information from the user.
> >
> > Mark
> >
> > On Tue, Mar 27, 2018, 18:26 João Henriques <joao.m.a.henriq...@gmail.com
> >
> > wrote:
> >
> >> I see, I didn't consider that. I was strictly thinking about the
> geometry
> >> of the box.
> >>
> >> Anyway, with some tricks I managed to build a tpr and am now able to
> >> calculate the mindist to the periodic image.
> >>
> >> Thanks!
> >> J
> >>
> >> On 18:19, Tue, Mar 27, 2018 Mark Abraham <mark.j.abra...@gmail.com>
> >> wrote:
> >>
> >> > Hi,
> >> >
> >> > The box sizes say nothing about whether the boundary is fully or
> >> partially
> >> > periodic, or screw, or not.
> >> >
> >> > Mark
> >> >
> >> > On Tue, Mar 27, 2018, 16:13 João Henriques <
> >> joao.m.a.henriq...@gmail.com>
> >> > wrote:
> >> >
> >> > > Thanks Justin, I was really trying to avoid making a tpr file,
> >> because my
> >> > > ACEMD uses the Amber format. I sort of hoped gmx mindist could
> figure
> >> it
> >> > > out from the box components present in the xtc file. In principle,
> >> > couldn't
> >> > > it be done by using that info alone? Just curious.
> >> > >
> >> > > J
> >> > >
> >> > > On Tue, Mar 27, 2018 at 4:04 PM, Justin Lemkul <jalem...@vt.edu>
> >> wrote:
> >> > >
> >> > > >
> >> > > >
> >> > > > On 3/27/18 9:59 AM, João Henriques wrote:
> >> > > >
> >> > > >> Dear users and developers,
> >> > > >>
> >> > > >> I am trying to use gmx mindist to calculate the minimum distance
> >> > between
> >> > > >> periodic images but I get the following error:
> >> > > >>
> >> > > >> Fatal error:
> >> > > >> pbc = no is not supported by g_mindist
> >> > > >>
> >> > > >> This is the command I am running:
> >> > > >>
> >> > > >> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc
> >> > > >>
> >> > > >> Now, I have to admit that the .xtc file I'm using is generated by
> >> > ACEMD
> >> > > >> and
> >> > > >> not mdrun, but I used gmx dump to check it and everything looks
> >> sane.
> >> > > The
> >> > > >> cuboid box sizes are clearly specified and I don't understand
> what
> >> the
> >> > > >> problem is...
> >> > > >>
> >> > > >> box (3x3):
> >> > > >> box[0]={ 8.16756e+00,  0.0e+00,  0.0e+00}
> >> > > >> box[1]={ 0.0e+00,  8.25175e+00,  0.0e+00}
> >> > > >> box[2]={ 0.0e+00,  0.0e+00,  9.73586e+00}
> >> > > >>
> >> > > >> Is gmx mindist reading the box vector lengths from the structure
> >> file
> >> > > >> instead?
> >> > > >>
> >> > > >
> >> > > > When you don't provide a .tpr file, the program does not know what
> >> type
> >> > > of
> >> &g

Re: [gmx-users] gmx mindist error

[João Henriques]

I see, I didn't consider that. I was strictly thinking about the geometry
of the box.

Anyway, with some tricks I managed to build a tpr and am now able to
calculate the mindist to the periodic image.

Thanks!
J

On 18:19, Tue, Mar 27, 2018 Mark Abraham <mark.j.abra...@gmail.com> wrote:

> Hi,
>
> The box sizes say nothing about whether the boundary is fully or partially
> periodic, or screw, or not.
>
> Mark
>
> On Tue, Mar 27, 2018, 16:13 João Henriques <joao.m.a.henriq...@gmail.com>
> wrote:
>
> > Thanks Justin, I was really trying to avoid making a tpr file, because my
> > ACEMD uses the Amber format. I sort of hoped gmx mindist could figure it
> > out from the box components present in the xtc file. In principle,
> couldn't
> > it be done by using that info alone? Just curious.
> >
> > J
> >
> > On Tue, Mar 27, 2018 at 4:04 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 3/27/18 9:59 AM, João Henriques wrote:
> > >
> > >> Dear users and developers,
> > >>
> > >> I am trying to use gmx mindist to calculate the minimum distance
> between
> > >> periodic images but I get the following error:
> > >>
> > >> Fatal error:
> > >> pbc = no is not supported by g_mindist
> > >>
> > >> This is the command I am running:
> > >>
> > >> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc
> > >>
> > >> Now, I have to admit that the .xtc file I'm using is generated by
> ACEMD
> > >> and
> > >> not mdrun, but I used gmx dump to check it and everything looks sane.
> > The
> > >> cuboid box sizes are clearly specified and I don't understand what the
> > >> problem is...
> > >>
> > >> box (3x3):
> > >> box[0]={ 8.16756e+00,  0.0e+00,  0.0e+00}
> > >> box[1]={ 0.0e+00,  8.25175e+00,  0.0e+00}
> > >> box[2]={ 0.0e+00,  0.0e+00,  9.73586e+00}
> > >>
> > >> Is gmx mindist reading the box vector lengths from the structure file
> > >> instead?
> > >>
> > >
> > > When you don't provide a .tpr file, the program does not know what type
> > of
> > > periodicity the simulation used, so it cannot do the requested
> > calculation
> > > because the shifts cannot be calculated.
> > >
> > > -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
> > >
> > > * 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.
> > --
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Re: [gmx-users] gmx mindist error

[João Henriques]

Thanks Justin, I was really trying to avoid making a tpr file, because my
ACEMD uses the Amber format. I sort of hoped gmx mindist could figure it
out from the box components present in the xtc file. In principle, couldn't
it be done by using that info alone? Just curious.

J

On Tue, Mar 27, 2018 at 4:04 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 3/27/18 9:59 AM, João Henriques wrote:
>
>> Dear users and developers,
>>
>> I am trying to use gmx mindist to calculate the minimum distance between
>> periodic images but I get the following error:
>>
>> Fatal error:
>> pbc = no is not supported by g_mindist
>>
>> This is the command I am running:
>>
>> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc
>>
>> Now, I have to admit that the .xtc file I'm using is generated by ACEMD
>> and
>> not mdrun, but I used gmx dump to check it and everything looks sane. The
>> cuboid box sizes are clearly specified and I don't understand what the
>> problem is...
>>
>> box (3x3):
>> box[0]={ 8.16756e+00,  0.0e+00,  0.0e+00}
>> box[1]={ 0.0e+00,  8.25175e+00,  0.0e+00}
>> box[2]={ 0.0e+00,  0.0e+00,  9.73586e+00}
>>
>> Is gmx mindist reading the box vector lengths from the structure file
>> instead?
>>
>
> When you don't provide a .tpr file, the program does not know what type of
> periodicity the simulation used, so it cannot do the requested calculation
> because the shifts cannot be calculated.
>
> -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
>
> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] gmx mindist error

[João Henriques]

"Is gmx mindist reading the box vector lengths from the structure file
instead?" ---> That would make no sense, since NPT simulations have varying
box sizes. Silly question, sorry. Still, I would really appreciate if
anyone could help me solving this issue.

J

On Tue, Mar 27, 2018 at 3:59 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Dear users and developers,
>
> I am trying to use gmx mindist to calculate the minimum distance between
> periodic images but I get the following error:
>
> Fatal error:
> pbc = no is not supported by g_mindist
>
> This is the command I am running:
>
> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc
>
> Now, I have to admit that the .xtc file I'm using is generated by ACEMD
> and not mdrun, but I used gmx dump to check it and everything looks sane.
> The cuboid box sizes are clearly specified and I don't understand what the
> problem is...
>
> box (3x3):
>box[0]={ 8.16756e+00,  0.0e+00,  0.0e+00}
>box[1]={ 0.0e+00,  8.25175e+00,  0.0e+00}
>box[2]={ 0.0e+00,  0.0e+00,  9.73586e+00}
>
> Is gmx mindist reading the box vector lengths from the structure file
> instead?
>
> Thank you for your attention,
> Best regards,
> J
>
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[gmx-users] gmx mindist error

[João Henriques]

Dear users and developers,

I am trying to use gmx mindist to calculate the minimum distance between
periodic images but I get the following error:

Fatal error:
pbc = no is not supported by g_mindist

This is the command I am running:

gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc

Now, I have to admit that the .xtc file I'm using is generated by ACEMD and
not mdrun, but I used gmx dump to check it and everything looks sane. The
cuboid box sizes are clearly specified and I don't understand what the
problem is...

box (3x3):
   box[0]={ 8.16756e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  8.25175e+00,  0.0e+00}
   box[2]={ 0.0e+00,  0.0e+00,  9.73586e+00}

Is gmx mindist reading the box vector lengths from the structure file
instead?

Thank you for your attention,
Best regards,
J
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

Ok, there's quite a lot going on here. The mkdssp the OP talks about is the
default name for the executable you get upon compilation from source.
Naming it dssp makes more sense, so that's why I suggested making a link
called dssp. Either way, it shouldn't matter because if you give the right
path to mkdssp or dssp or whatever name you give it, it should work.

If the standalone execution of dssp works, the problem must be with the
export.

Please confirm that you have exported the DSSP environment variable
correctly. Type "$DSSP -h" for example. If that works, then there's no
reason for gmx do_dssp to not work.

P.S.: dssp is notoriously tricky to compile, e.g. the static flag issue. I
also recently noticed that with boost >= 1.65.1, the code gets seriously
broken and needs some major modifications (see https://pastebin.com/NiQJkjuC
).

J





On Tue, Mar 13, 2018 at 10:30 AM, Simon Kit Sang Chu <simoncks1...@gmail.com
> wrote:

> Thank you, Joe. I re-ensure that dssp works in my case. I tried:
>
> dssp prod-protein.pdb -o test.dssp
>
> The result looks fine without error text.
>
> Simon
>
> 2018-03-13 17:24 GMT+08:00 Joe Jordan <e.jjorda...@gmail.com>:
>
> > You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/
> > It is also in the ubuntu repo.
> > You should to get mkdssp and/or dssp to work on their own and if you
> can't
> > then your problem is not with gmx.
> >
> > On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu <
> > simoncks1...@gmail.com
> > > wrote:
> >
> > > Hi everyone,
> > >
> > > I linked dssp as mkdssp and it still does not work. I try to run dssp
> in
> > > terminal. This is the result.
> > >
> > > mkdssp 2.2.1 options:
> > >   -h [ --help ] Display help message
> > >   -i [ --input ] argInput file
> > >   -o [ --output ] arg   Output file, use 'stdout' to output to screen
> > >   -v [ --verbose ]  Verbose output
> > >   --version Print version
> > >   -d [ --debug ] argDebug level (for even more verbose output)
> > >
> > >
> > > Examples:
> > >
> > > To calculate the secondary structure for the file 1crn.pdb and
> > > write the result to a file called 1crn.dssp, you type:
> > >
> > >   dssp -i 1crn.pdb -o 1crn.dssp
> > >
> > > Hope it behaves normally.
> > >
> > > Simon
> > >
> > > 2018-03-13 17:07 GMT+08:00 Mark Abraham <mark.j.abra...@gmail.com>:
> > >
> > > > Hi,
> > > >
> > > > gmx do_dssp -h
> > > >
> > > > says everything there is to say about how to get this to work. I've
> no
> > > idea
> > > > what mkdssp is, but unless it does the same things as dssp, it won't
> > > work.
> > > >
> > > > Mark
> > > >
> > > > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu <
> > > simoncks1...@gmail.com
> > > > >
> > > > wrote:
> > > >
> > > > > Hi João,
> > > > >
> > > > > Thanks for your suggestion. Unfortunately, the error persists. I
> > > thought
> > > > > -ver 2 was the default value.
> > > > >
> > > > > Regards,
> > > > > Simon
> > > > >
> > > > > 2018-03-13 15:58 GMT+08:00 João Henriques <
> > > joao.m.a.henriq...@gmail.com>
> > > > :
> > > > >
> > > > > > "Fatal error: Failed to execute command: Try specifying your dssp
> > > > version
> > > > > > with the -ver option."
> > > > > >
> > > > > > Did you follow the error message suggestion? With DSSP 2.2.1 you
> > need
> > > > to
> > > > > > set "-ver 2" on your gmx do_dssp command.
> > > > > >
> > > > > > J
> > > > > >
> > > > > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > > > > > simoncks1...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi everyone.
> > > > > > >
> > > > > > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1.
> It
> > > > > returned
> > > > > > > an error:
> > > > > > >
> > > > > > >
> > > > > > > Fatal error:
> > > > > > > Failed to execute co

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

Is the export consistent with the executable name?

J

On Tue, Mar 13, 2018 at 9:55 AM, Simon Kit Sang Chu <simoncks1...@gmail.com>
wrote:

> Hi João,
>
> Thanks for your suggestion. Unfortunately, the error persists. I thought
> -ver 2 was the default value.
>
> Regards,
> Simon
>
> 2018-03-13 15:58 GMT+08:00 João Henriques <joao.m.a.henriq...@gmail.com>:
>
> > "Fatal error: Failed to execute command: Try specifying your dssp version
> > with the -ver option."
> >
> > Did you follow the error message suggestion? With DSSP 2.2.1 you need to
> > set "-ver 2" on your gmx do_dssp command.
> >
> > J
> >
> > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > simoncks1...@gmail.com>
> > wrote:
> >
> > > Hi everyone.
> > >
> > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It
> returned
> > > an error:
> > >
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option.
> > >
> > >
> > > I can run mkdssp and it is placed in bin. Is it a compatibility problem
> > > here?
> > >
> > > Thanks in advance.
> > >
> > > Regards.
> > > Simon
> > > --
> > > 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.
> > >
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

Also, if you're exporting DSSP="/.../dssp" and your bin contains mkdssp and
not dssp, then that's going to fail for obvious reasons. Either export
DSSP="/.../mkdssp"
or create a link to mkdssp within the same directory with the name "dssp"
(ln -s mkdssp dssp). Export and executable name must match.

J

On Tue, Mar 13, 2018 at 8:58 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> "Fatal error: Failed to execute command: Try specifying your dssp version
> with the -ver option."
>
> Did you follow the error message suggestion? With DSSP 2.2.1 you need to
> set "-ver 2" on your gmx do_dssp command.
>
> J
>
> On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> simoncks1...@gmail.com> wrote:
>
>> Hi everyone.
>>
>> I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned
>> an error:
>>
>>
>> Fatal error:
>> Failed to execute command: Try specifying your dssp version with the -ver
>> option.
>>
>>
>> I can run mkdssp and it is placed in bin. Is it a compatibility problem
>> here?
>>
>> Thanks in advance.
>>
>> Regards.
>> Simon
>> --
>> 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.
>>
>
>
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

"Fatal error: Failed to execute command: Try specifying your dssp version
with the -ver option."

Did you follow the error message suggestion? With DSSP 2.2.1 you need to
set "-ver 2" on your gmx do_dssp command.

J

On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu 
wrote:

> Hi everyone.
>
> I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned
> an error:
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option.
>
>
> I can run mkdssp and it is placed in bin. Is it a compatibility problem
> here?
>
> Thanks in advance.
>
> Regards.
> Simon
> --
> Gromacs Users mailing list
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Re: [gmx-users] g_sans calculation

[João Henriques]

I understand your pain, and the same could be said about gmx saxs as well.
As Micholas said, CRYSON might be a good choice as far as implicit solvent
methods go. Please notice that CRYSON is closed source, but it is well
documented in the literature (it is basically a reimplementation of
CRYSOL*).

*Svergun, D., Barberato, C., & Koch, M. H. (1995). J. Appl. Crystallogr.,
28(6), 768-773

J


On Fri, Feb 23, 2018 at 9:14 PM, Udaya Dahal  wrote:

>  Dear Gromacs Users,
>
> I am calculating the g_sans in the simulation but I am not able to find how
> it is calculated. The help content is minimal. I am just wondering if
> anyone has looked into how it is calculated (any reference to algorithm?).
>
> Regards,
> --
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Re: [gmx-users] Calculate RDF within a certain distance from atom

[João Henriques]

Justin already properly addressed the original post, so I'll just add a few
comments about the last message:

> I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
around 0.47nm.

So you've managed to calculate it then as Justin suggested? FYI the RDF
minimum occurs at a larger distance for C atoms (~5 Å) than for O and N
atoms (3.3-3.5 Å), so the peak you see at 4.7 Å seems about right.

> So, i am further interested in studying how water molecules are oriented
towards it closely...what is happening around within 0.7nm distance of
Calpha w.r.t Ow...

Maybe I'm just not seeing the full picture, but how does this have anything
to do with the RDF? The RDF shows how density varies as a function of
distance from a reference particle. There certainly is some correlation
with particle orientation, but extracting this information from the RDF
profile alone seems unfeasible.

J



On Wed, Feb 21, 2018 at 5:00 AM, Dilip H N 
wrote:

> I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
> around 0.47nm. So, i am further interested in studying how water molecules
> are oriented towards it closely...what is happening around within 0.7nm
> distance of Calpha w.r.t Ow...
>
> Any suggestions...??
>
> Thank you.
>
>
>
>
> ‌
>  Sent with Mailtrack
>  ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> medium=signature_campaign=signaturevirality>
>
> On Tue, Feb 20, 2018 at 10:58 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 2/20/18 11:53 AM, Dilip H N wrote:
> >
> >> Hello,
> >> How to get RDF within a certain distance..??
> >>
> >> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen
> water
> >> atoms within 0.7nm of C-alpha (Calpha-Ow).
> >>
> >> how can i get it from in-house gmx rdf command...??
> >>
> >
> > What do you hope to achieve from such a metric? RDF has to be normalized
> > against bulk occupancy, which will of course not be achieved at a 0.7-nm
> > distance. If you are interested in certain properties within given
> > solvation shells, distances, etc. compute the normal RDF so that it is
> > properly normalized and interpret the outcome of that calculation.
> >
> > -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.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
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> > * Please search the archive at http://www.gromacs.org/Support
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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Re: [gmx-users] simulation time vs side chain flexibility

[João Henriques]

To be honest, I don't see how an increased side chain flexibility is proof
that the protein is more flexible. They're not necessarily correlated.
Protein flexibility involves larger movements concerning the protein
backbone. These would probably be better captured by the RMSF, radius or
gyration, end-to-end distance, etc.

J

On Tue, Feb 20, 2018 at 6:16 PM, MD <refm...@gmail.com> wrote:

> Thanks J. I agree. I should have added that the RMSD plateaued. And I am
> more looking at side chain flexibility instead of secondary structure
> changes.
> Ming
>
> On Tue, Feb 20, 2018 at 12:09 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > This is not strictly a gromacs related question, but long answer short:
> it
> > depends, but most likely not. You must be able to convince people that
> the
> > property you're interested in is properly converged within the simulation
> > time you're considering. Multiple, reversible events need to be clearly
> > visible.
> >
> > In general, significant protein conformational changes occur at a much
> > larger time scale (and I'm talking orders of magnitude larger). 10 ns is
> a
> > very, very short time for most purposes in protein simulation.
> >
> > I could go on and on, this is a complex topic that can easily be written
> > about at length.
> >
> > J
> >
> > On Tue, Feb 20, 2018 at 5:48 PM, MD <refm...@gmail.com> wrote:
> >
> > > Hi Gromacs folks,
> > >
> > > I am trying to tell if a mutation can cause some part of the protein
> > > becoming more flexible. I started with the apo protein. I did two
> > > simulations in parallel, with one wild type and one with a silico
> > mutation.
> > >
> > > After a 10 ns simulation I was able to tell some region of the protein
> is
> > > more flexible based on the RMS chart. Since side chain flexibility is
> in
> > > the range of 1 ns, I wonder if 10 ns simulation is convincing enough?
> > >
> > > Thanks,
> > >
> > > Ming
> > > --
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Re: [gmx-users] simulation time vs side chain flexibility

[João Henriques]

This is not strictly a gromacs related question, but long answer short: it
depends, but most likely not. You must be able to convince people that the
property you're interested in is properly converged within the simulation
time you're considering. Multiple, reversible events need to be clearly
visible.

In general, significant protein conformational changes occur at a much
larger time scale (and I'm talking orders of magnitude larger). 10 ns is a
very, very short time for most purposes in protein simulation.

I could go on and on, this is a complex topic that can easily be written
about at length.

J

On Tue, Feb 20, 2018 at 5:48 PM, MD  wrote:

> Hi Gromacs folks,
>
> I am trying to tell if a mutation can cause some part of the protein
> becoming more flexible. I started with the apo protein. I did two
> simulations in parallel, with one wild type and one with a silico mutation.
>
> After a 10 ns simulation I was able to tell some region of the protein is
> more flexible based on the RMS chart. Since side chain flexibility is in
> the range of 1 ns, I wonder if 10 ns simulation is convincing enough?
>
> Thanks,
>
> Ming
> --
> Gromacs Users mailing list
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Re: [gmx-users] How to obtain TIP4P/ε water model topology file

[João Henriques]

I'm not very familiar with the TIP4P/ε water model, but if my memory serves
me correctly, isn't it meant for pure water simulations? I'm not sure it's
a good idea to mix it up with a protein force field without proper testing.
Also, CHARMM36 was parametrized to be used with the CHARMM-modified TIP3P
water model, so that makes it even more risky. In any case, I doubt
CHARMM36 comes packaged with it, you'll probably have to create it yourself.

J

On Tue, Feb 20, 2018 at 5:30 PM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi All,
> I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone let
> me know where can I get the corresponding .itp file.
>
> Thanks a lot.
>
> "A society with free knowledge is better than a society with free food"
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
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Re: [gmx-users] installation problem

[João Henriques]

This is completely vague. Please report what the actual error is and then
people might be able to help.

J

On Mon, Feb 19, 2018 at 9:43 AM, banijamali_fs 
wrote:

> Hi there,
>
> unfortunately I uninstall the gromacs program from my PC and I couldn't
> install it again with so many ways that I tested, I want to ask you that
> in which step I made mistake that I can't install it.
>
> these are the steps that I've done but I didn't get the suitable result.
>
> tar xfz gromacs-5.0.7.tar.gz
> cd gromacs-5.0.7
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> make
> make check
> sudo make install
> source /usr/local/gromacs/bin/GMXRC
>
> I would be vary thankful if anybody help me.
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Re: [gmx-users] Calculation of shape change of a protein during simulation

[João Henriques]

You can calculate the asphericity, for example. You just need the
components of the gyration tensor which are given by gmx polystat, if my
memory serves me right.

There are several papers about this. A quick search on Google scholar will
surely produce results.

I would link the papers or the formula, but I'm on the phone. Let me know
if you don't manage to find it yourself.

J

On Feb 13, 2018 7:52 PM, "Sudip Das"  wrote:

> Dear All,
>
> Is there any way to calculate the change in shape of a protein with respect
> to simulation time using GROMACS or VMD? By the use of the word 'shape', I
> mean to say 'spherical' or 'elliptical'; or more specifically the value of
> eccentricity of the protein wrt simulation time.
>
> My guess is that it can be calculated from the x, y and z components of the
> radius of gyration of the protein wrt simulation time. Am I correct?
>
> Thanks in advance.
>
> Best regards,
> Sudip
>
>
> Sudip Das
>
> PhD Student
> C/o. Prof. S. Balasubramanian
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit (CPMU)
> Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> Bangalore, India
>
>
>
> ‌
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Re: [gmx-users] Possibility of adding external forces to simulating molecules

[João Henriques]

That sounds like what metadynamics. Is that what you want to do? Can you
elaborate a bit more about the your objective?

J

On Tue, Jan 30, 2018 at 4:40 PM, Lovuit CHEN  wrote:

> Hi,
>
>
> When doing MD simulation of certain molecule, is it possible to add some
> external forces (besides already generated standard force field) (e.g. add
> some constant to the forces, or to some orders of the position change, etc)
> to one or more atoms in the molecule, to change the equation of motion of
> that particular atom during simulation while keeping everything else
> intact?  Can this be done by changing of parameters of input topology file,
> or maybe other ways around (e.g. small changes of the source code)?
>
>
>
> Thank you very much!
>
>
> Lovuit
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Re: [gmx-users] (no subject)

[João Henriques]

> You need some ions to neutralise the system for long range electrostatics
to work.

This mostly applies to PME. However, because PME is basically *de
facto* nowadays,
it will most likely apply in most situations. However, I recently learned
that PME can also be run with a non-neutral system, as PME will introduce a
neutralizing background charge (and dipole corrections). Here is the
thread:
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg29536.html

> We usually add more to make the simulation more like the real system
(solution or cell).

Just to be the devil's advocate, I'd say that based on anecdotal evidence
adding salt in a MD simulation of a protein changes make little to no
difference. It doesn't behave as expected, most likely due to poor ion
parametrization and integer charges.

J


On Sun, Jan 21, 2018 at 7:16 AM,  wrote:

> You need some ions to neutralise the system for long range electrostatics
> to work. We usually add more to make the simulation more like the real
> system (solution or cell).
>
> > On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013...@sastra.ac.in>
> wrote:
> >
> > Dear all,
> >
> >I am a beginer. I would like to know the purpose of adding
> ions
> > during the simulation process.
> > --
> > Gromacs Users mailing list
> >
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Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit

[João Henriques]

I see what you mean. I've also worked with methods that required
modification/wrapping of specific (older) versions of gromacs. The amount
of people that do this is however much lower than those running vanilla
gromacs, so you should probably conserve your time and effort, unless
there's a big demand for it and you feel like providing.

Regarding the versions, if you'd like to just provide a quick way for
people to install gromacs, then sticking to the latest version of the
current and former series would probably suffice. For people wanting to
build on top of gromacs it's more difficult to guess their needs are.

J

On Fri, Jan 19, 2018 at 10:10 AM, 蕭毅  wrote:

> Hi James, Joao:
>
> Thanks for your reply. I know the 4.5.5 is a old version, but I found some
> useful paper used this version, and some of my work in graduate school is
> based on the method developed on this version. At the same time, my work is
> a stand-alone software application. I had a hard time trying to simplify
> the procedure to building the enviroment needed by my software application,
> so I initially developed this to solve some of the headache and thought
> that it might be helpful to other people who also want to build
> applications based on gromacs. I can also try to provide packages for newer
> version of gromacs, but I left the gromacs for a while. What are the most
> few important versions that you think I should support first ?
>
> Best regards,
> Leo (Yi Hsiao)
>
> Date: Fri, 19 Jan 2018 09:19:17 +0100
> From: Jo?o Henriques 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] An conda package for installing gromacs 4.5.5
> on 64-bit linux system
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Exactly, that version is 7 years old or so. It's a good initiative
> nonetheless, just wished it offered a more recent version.
>
> J
>
> On Fri, Jan 19, 2018 at 6:08 AM, James Krieger 
> wrote:
>
> > Why 4.5.5?
> >
> > On Thu, Jan 18, 2018 at 11:26 PM, ??  wrote:
> >
> > > Hi gromacs users:
> > >
> > > I just wrote this to share that I write a conda package let you to
> > install
> > > gromacs 4.5.5 on 64-bit linux system:
> > > https://anaconda.org/hsiaoyi0504/gromacs
> > >
> > > The objective of this package is to let people build applications based
> > on
> > > gromacs more easier, such as prediction system based on result produced
> > by
> > > gromacs. Some similar work for gromas 4.6.5 is in bioconda:
> > > https://anaconda.org/bioconda/gromacs. If you have any question or
> > > suggestion, you can email me or leave message on issue system of repo
> for
> > > the source code to build the conda package.
> > > https://github.com/hsiaoyi0504/conda_gromacs_4.5.5.
> > >
> > > Best regards,
> > > Leo (Yi Hsiao)
> --
> Gromacs Users mailing list
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Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit linux system

[João Henriques]

Exactly, that version is 7 years old or so. It's a good initiative
nonetheless, just wished it offered a more recent version.

J

On Fri, Jan 19, 2018 at 6:08 AM, James Krieger 
wrote:

> Why 4.5.5?
>
> On Thu, Jan 18, 2018 at 11:26 PM, 蕭毅  wrote:
>
> > Hi gromacs users:
> >
> > I just wrote this to share that I write a conda package let you to
> install
> > gromacs 4.5.5 on 64-bit linux system:
> > https://anaconda.org/hsiaoyi0504/gromacs
> >
> > The objective of this package is to let people build applications based
> on
> > gromacs more easier, such as prediction system based on result produced
> by
> > gromacs. Some similar work for gromas 4.6.5 is in bioconda:
> > https://anaconda.org/bioconda/gromacs. If you have any question or
> > suggestion, you can email me or leave message on issue system of repo for
> > the source code to build the conda package.
> > https://github.com/hsiaoyi0504/conda_gromacs_4.5.5.
> >
> > Best regards,
> > Leo (Yi Hsiao)
> > --
> > 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.
> >
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Re: [gmx-users] -inter command

[João Henriques]

A lot of OPs have the tendency to follow-up with private emails and I feel
it should stay public so other people might benefit from the information as
well. Here is the rest of the conversation regarding this thread.

"""
Dear Zaved,

I'm not aware of any tutorials for Gromacs, and Gromacs does not support
constant-pH MD simulations straight out of the box. It must be (heavily)
modified. Amber comes pre-packaged with constant-pH functionality, I
believe. Still, you probably don't want to get involved in any of this. My
comment about it was merely to make you aware that changing the protonation
states by hand doesn't make mean you're really simulating at a given pH.
Still, 99.9% of the people in this field do what you were wanting to do,
i.e., change the protonation states during pdb2gmx to whatever they feel is
more representative of that residue at a given pH and then hit run. I also
do it, unless I'm studying something where charge regulation playes a major
role, so by all means go ahead and try the simpler solution first.

P.S.: Please avoid sending private messages about these subjects. It
started in gmx-users and should stay there for several reasons. The main
one is that other people might have the same problem and this information
might be useful for them as well.

Best regards,
J

On Tue, Jan 16, 2018 at 6:54 AM, <za...@tezu.ernet.in> wrote:

> Dear Sir
>
> Thank you for your kind response regarding the -inter command.
>
> Sir can you guide / provide any tutorial for constant-pH MD simulation in
> gromacs (eg., to perform simulation at pH 9)?
>
> I shall be grateful to you for the same.
>
> Thank You
>
> Regards
> Zaved Hazarika
> Research Scholar
> C/O Dr. A.N. Jha
> Dept. Of Molecular Biology and Biotechnology,
> Tezpur University,
> Napam, 784028,
> Assam,
> India
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.

"""

J

On Mon, Jan 15, 2018 at 11:51 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> -inter sets the interactive mode for a bunch of other flags. Most are used
> for selecting the protonation states of the termini and other residues. It
> can also be used for interactive SS bridge selection.
>
> > "for setting the protonation state of charged amino acids in order to
> perform simulation at different pH?"
>
> Please note that changing the protonation states of the residues does not
> mean you're performing the simulation at a "different pH". A proper
> constant-pH MD simulation allows the residues to titrate in respect to the
> solution pH as well as the their "molecular environment". In this case,
> your residues will be "stuck" in a user defined protonation state that may
> or may not reflect the most populated protonation states of those residues
> at a given pH, irrespectively of their surroundings.
>
> Cheers,
> J
>
> On Mon, Jan 15, 2018 at 11:00 AM, <za...@tezu.ernet.in> wrote:
>
>> Dear Gromacs Users
>>
>> I have an query regarding gmx pdb2gmx -inter command.
>>
>> Do we use -inter command only for setting the protonation state of charged
>> amino acids in order to perform simulation at different pH?
>>
>>
>> Thank You
>>
>> Regards
>> Zaved Hazarika
>> Research Scholar
>> Dept. Of Molecular Biology and Biotechnology,
>> Tezpur University,
>> India
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely for
>> the individual named. If you are not the named addressee you should not
>> disseminate, distribute or copy this e-mail. Please notify the sender
>> immediately by e-mail if you have received this e-mail in error and destroy
>> it from your system. Though considerable effort has been made to deliver
>> error free e-mail messages but it can not be guaranteed to be secure or
>> error-free as information could be intercepted, corrupted, lost, destroyed,
>> delayed, or may contain viruses. The recipient must verify the integrity of
>> this e-mail message.
>> --
>> Gromacs Users ma

Re: [gmx-users] -inter command

[João Henriques]

-inter sets the interactive mode for a bunch of other flags. Most are used
for selecting the protonation states of the termini and other residues. It
can also be used for interactive SS bridge selection.

> "for setting the protonation state of charged amino acids in order to
perform simulation at different pH?"

Please note that changing the protonation states of the residues does not
mean you're performing the simulation at a "different pH". A proper
constant-pH MD simulation allows the residues to titrate in respect to the
solution pH as well as the their "molecular environment". In this case,
your residues will be "stuck" in a user defined protonation state that may
or may not reflect the most populated protonation states of those residues
at a given pH, irrespectively of their surroundings.

Cheers,
J

On Mon, Jan 15, 2018 at 11:00 AM,  wrote:

> Dear Gromacs Users
>
> I have an query regarding gmx pdb2gmx -inter command.
>
> Do we use -inter command only for setting the protonation state of charged
> amino acids in order to perform simulation at different pH?
>
>
> Thank You
>
> Regards
> Zaved Hazarika
> Research Scholar
> Dept. Of Molecular Biology and Biotechnology,
> Tezpur University,
> India
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Umbrella sampling-gmx distance

[João Henriques]

The output is very explicitly telling you what the problem is. You didn't
provide a topology. Pass one the the -s flag.  How do you want the COM to
be computed when you're not providing any masses?

J

On Jan 13, 2018 9:19 AM, "rose rahmani"  wrote:

> I'm relly sorry for asking you again and again but...
>
> GROMACS:  gmx distance, VERSION 5.1.4
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>   gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
> of group 6'
>
>
> ---
> Program: gmx distance, VERSION 5.1.4
> Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
> Function:void
> gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::
> SelectionCollection*)
>
> Inconsistency in user input:
> No topology provided, but one is required for analysis
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> Whai is the problem?;(
>
> On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 1/11/18 11:38 AM, rose rahmani wrote:
> >
> >>   [ ZnS ]
> >> 123456789   10   11   12   13   14
> >>  15
> >>16   17   18   19   20   21   22   23   24   25   26   27   28   29
> >>  30
> >>31   32   33   34   35   36   37   38   39   40   41   42   43   44
> >>   45..
> >>
> >> [ Protein ]
> >>   761  762  763  764  765  766  767  768  769  770  771  772  773  774
> >> 775
> >>   776  777  778  779  780  781  782  783  784  785  786
> >>
> >> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group
> >> "ZnS"
> >> plus com of group "Protein"' -oxyz -oall
> >> i exactly select index groups!!!
> >> ---
> >> Program: gmx distance, VERSION 5.1.4
> >> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
> >> Function:void gmx::SelectionCollection::setI
> >> ndexGroups(gmx_ana_indexgrps_t*)
> >>
> >> Inconsistency in user input:
> >> Invalid index group reference(s)
> >>Cannot match 'group "ZnS"', because no such index group can be found.
> >>Cannot match 'group "Protein"', because no such index group can be
> >> found.
> >>
> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >> 
> >> -
> >> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
> >> -select -oxyz
> >> GROMACS:  gmx distance, VERSION 5.1.4
> >> Executable:   /usr/local/gromacs/bin/gmx
> >> Data prefix:  /usr/local/gromacs
> >> Command line:
> >>gmx distance -n index.ndx -f conf0.gro -select -oxyz
> >>
> >> Available static index groups:
> >>   Group  0 "System" (4336 atoms)
> >>   Group  1 "Other" (760 atoms)
> >>   Group  2 "ZnS" (560 atoms)
> >>   Group  3 "WAL" (200 atoms)
> >>   Group  4 "NA" (5 atoms)
> >>   Group  5 "CL" (5 atoms)
> >>   Group  6 "Protein" (26 atoms)
> >>   Group  7 "Protein-H" (12 atoms)
> >> .
> >> .
> >> (one per line,  for status/groups, 'help' for help, Ctrl-D to
> end)
> >>
> >>> 2
> >>>
> >> Selection '2' parsed
> >>
> >>> 6
> >>>
> >> Selection '6' parsed
> >>
> >
> > You should be selecting 'com of group 2' etc. here to get what you want.
> I
> > don't know why the command-line version of this didn't work, but to get a
> > COM distance, you need to tell gmx distance to do it, otherwise it's just
> > going to produce pairwise distances, which is what you're asking for
> here.
> >
> > -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.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] phi/psi

[João Henriques]

Hello,

Don't know if there's a native gromacs tool to do so, but I'd use PLUMED
for this sort of thing:
https://plumed.github.io/doc-v2.3/user-doc/html/_t_o_r_s_i_o_n.html

The last example on that page shows something similar to what you want to
do. It's that simple.

P.S.: I am not affiliated with PLUMED in any way, I just find it simple and
useful for many types of analyses.

Best regards,
J

On Fri, Jan 12, 2018 at 3:43 PM, Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:

>
> Hi,
>
> How to get phi/psi angles from gromacs trajectory file? I used v.4.5.5.
>
> best
>
> Urszula
>
>
> 
> Urszula Uciechowska PhD
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Abrahama 58
> 80-307 Gdańsk
> Poland
>
>
> -
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
> --
> Gromacs Users mailing list
>
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Re: [gmx-users] Simulation of aggregated proteins

[João Henriques]

If the PDB has each protein with separate chain entries (A, B, etc) then
this shouldn't be a problem. pdb2gmx will produce separate topologies for
each chain and an overall topology that reads from each of the individual
topologies and contains the other directives about FF, water model, posre,
etc.

J

On Fri, Dec 22, 2017 at 9:29 AM, RAHUL SURESH 
wrote:

> Dear all
>
> I have a PDB entry having 10 models(Aggregated structure). Here I want to
> carry out the molecular dynamic simulation as such in aggregated form. But
> gromacs is considering only one model in the PDB structure. How can I
> simulate it as a whole.?
>
> Thank you
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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Re: [gmx-users] PROTEIN FOLDING

[João Henriques]

Depends. If you're interested in local folding and there are SS motifs in
the region you're interested, then yes. If not, no. In terms of overall
folding of the entire protein, yes it surely can be an important analysis.

J

On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta <nehaphysic...@gmail.com> wrote:

> Thank you Joao and Aman.
>
> I have noted the points you have suggested.
>
> Do you think analyzing DSSP would help?
>
> Thanks,
> Neha
>
> On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > "You can use various supporting tools from R language to debug your
> > trajectory but most third party software support NAMD and charmm format.
> > You can use VMD to convert the trajectory to dcd and use R language based
> > packages to read your trajectory"
> >
> > What? How is this useful or helpful? At most it confuses the OP even
> more.
> >
> > Also, the clustering analysis is unlikely to be what you want or need at
> > this stage. Why overcomplicate? One of the simplest ways to check that
> > there are conformational changes on a given set of atoms is by doing a
> RMSD
> > analysis using the folded structure as the reference. The RMSD is
> somewhat
> > degenerate, but should suffice for this purpose. You can use an index
> file
> > to restrict the RMSD analysis to a particular subset of your system (the
> > docking site, for example).
> >
> > You could look at the radius of gyration as well, Rg, as Aman Deep also
> > suggests. This can either be calculated on a subset of atoms or on the
> > entire protein. The latter could potentially be used to compare with the
> > experimental reference obtained by SAXS, for example. Or you could
> > calculate the SAXS curve and get a better understanding of size and shape
> > differences between your protein and the reference, but that's more
> > advanced stuff.
> >
> > J
> >
> > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <drrahulsur...@gmail.com>
> > wrote:
> >
> > > Also you must know, a lot analysis are available over the entire manual
> > of
> > > Gromacs where all cannot be performed. Gromacs always provide you all
> > > necessary analysis but to choose which one is always your choice that
> > suits
> > > your simulation purpose.
> > >
> > >
> > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <nehaphysic...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > >
> > > > Thank you for your prompt reply.
> > > >
> > > > By clustering analysis, are you talking about gmx cluster command?
> > > >
> > > > "over particular PC sub space"
> > > >
> > > > Could you please elaborate a bit?
> > > >
> > > > Thanks a lot once again.
> > > >
> > > > Thanks,
> > > > Neha
> > > >
> > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <
> drrahulsur...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <
> nehaphysic...@gmail.com
> > >
> > > > > wrote:
> > > > >
> > > > > > Hi gromacs users,
> > > > > >
> > > > > > After MD simulation of protein-ligand complex for 5ns, can we
> view
> > > > > protein
> > > > > > folding?
> > > > > >
> > > > > > How to do it?
> > > > > >
> > > > > > I want to ascertain if there is any conformation change in
> protein
> > > > where
> > > > > > the ligand binds. Is it possible?
> > > > > >
> > > > > > We observe hydrogen bonds through molecular docking. Hence, I
> want
> > to
> > > > > make
> > > > > > observation through MD simulation which is not obtained through
> > > > docking.
> > > > >
> > > > >
> > > > > You can perform Clustering analysis over particular PC sub space to
> > > > measure
> > > > > the structural changes.
> > > > >
> > > > > >
> > > > > >
> > > > > > Can someone help me regarding this?
> > > > > >
> > > > > > Thank you very much in advance.
> > > > > >
> > > > > > Thanks,
> > > > > > Neha
> >

Re: [gmx-users] PROTEIN FOLDING

[João Henriques]

"You can use various supporting tools from R language to debug your
trajectory but most third party software support NAMD and charmm format.
You can use VMD to convert the trajectory to dcd and use R language based
packages to read your trajectory"

What? How is this useful or helpful? At most it confuses the OP even more.

Also, the clustering analysis is unlikely to be what you want or need at
this stage. Why overcomplicate? One of the simplest ways to check that
there are conformational changes on a given set of atoms is by doing a RMSD
analysis using the folded structure as the reference. The RMSD is somewhat
degenerate, but should suffice for this purpose. You can use an index file
to restrict the RMSD analysis to a particular subset of your system (the
docking site, for example).

You could look at the radius of gyration as well, Rg, as Aman Deep also
suggests. This can either be calculated on a subset of atoms or on the
entire protein. The latter could potentially be used to compare with the
experimental reference obtained by SAXS, for example. Or you could
calculate the SAXS curve and get a better understanding of size and shape
differences between your protein and the reference, but that's more
advanced stuff.

J

On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH 
wrote:

> Also you must know, a lot analysis are available over the entire manual of
> Gromacs where all cannot be performed. Gromacs always provide you all
> necessary analysis but to choose which one is always your choice that suits
> your simulation purpose.
>
>
> On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta 
> wrote:
>
> > Hi,
> >
> >
> > Thank you for your prompt reply.
> >
> > By clustering analysis, are you talking about gmx cluster command?
> >
> > "over particular PC sub space"
> >
> > Could you please elaborate a bit?
> >
> > Thanks a lot once again.
> >
> > Thanks,
> > Neha
> >
> > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH 
> > wrote:
> >
> > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta 
> > > wrote:
> > >
> > > > Hi gromacs users,
> > > >
> > > > After MD simulation of protein-ligand complex for 5ns, can we view
> > > protein
> > > > folding?
> > > >
> > > > How to do it?
> > > >
> > > > I want to ascertain if there is any conformation change in protein
> > where
> > > > the ligand binds. Is it possible?
> > > >
> > > > We observe hydrogen bonds through molecular docking. Hence, I want to
> > > make
> > > > observation through MD simulation which is not obtained through
> > docking.
> > >
> > >
> > > You can perform Clustering analysis over particular PC sub space to
> > measure
> > > the structural changes.
> > >
> > > >
> > > >
> > > > Can someone help me regarding this?
> > > >
> > > > Thank you very much in advance.
> > > >
> > > > Thanks,
> > > > Neha
> > > > --
> > > > 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.
> > > >
> > > --
> > > *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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> > > 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!
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> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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Re: [gmx-users] Dynamic selection of a shell in a trajectory

[João Henriques]

Very unlikely and/or impractical. The water selections/analyses you can do
with gromacs' native tools are unfortunately rather limited. From personal
experience I'd suggest trying MDAnalysis or something similar, because it
gives you the freedom to code your our analysis routine with minimal effort
in terms of programming. Plus it allows dynamic selections, which I never
found truly possible with gromacs' native tools.

J




On Wed, Dec 20, 2017 at 9:43 AM, Matteo Busato 
wrote:

> Dear all,
>
>
> I'm performing a dynamic of a metal ion in a box consisting of a solvent,
> where the metal is coordinated by six solvent molecules.
>
> I'm writing here because I want to reduce the trajectory including the
> intire box to a trajectory containing only the first coordination shell of
> the metal, e.g. say to the system "consider a sphere of 8 Angstroms radius
> from the metal and pick up any residue which has a least one atom inside
> this sphere". In addition, it would be nice to perform a sort of "dynamic
> selection", e.g. if one residue exits and another one enters the sphere I
> want the selection to keep the first one and then the second.
>
>
> Is this possible with Gromacs or do I need to use other tools? I've tryed
> to understand if this was possible with trjconv or gmx select, but I think
> they're not the right utilities and I couldn't find anyone with this
> problem in a web research.
>
> I would be gratefull if you can help me.
>
>
> Thank you in advance for your answer.
>
>
> Kind regards,
>
> Matteo Busato
> --
> Gromacs Users mailing list
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Re: [gmx-users] WHAM

[João Henriques]

This has nothing to do with your initial question, but I there are a few
misconceptions in your last email that you should be aware of.

First, you don't need "special computers" to run or compile gromacs. It
helps to have multiple compute nodes at your disposal, but it isn't a
requirement *per se*. Also, you don't need to be root to compile your own
gromacs installation. You can indeed install your own gromacs version on
the cluster you use to run your simulations.

Finally, version 2018 is still a beta testing version, so it's probably not
a good idea to use it until it's released as a stable version.

P.S.: Justin does a lot more than the average mortal, specially when it
comes to MD simulations and Gromacs. However, no one ever knows everything.

Cheers,

J

On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani  wrote:

> Dear Justin,I don't have special computers to be compatible with these
> softwares and run complex calculations.So i have to connect to some
> computers which is not mine and the old version is installed there.i can't
> update them because i'm just a normal user and not a root one! So there are
> two choices; not using GROMACS at all OR be convinced with the old
> versions. i choose latter!
> WHO don't like an upgraded software sir?! you are not talking with a
> headstrong person ;) i like to use V.2018 but it's not possible for me, i
> hope you understand me.Just this!
> You are talking with 3 months experienced student without any experience in
> any similar simulation software before!
>
> I agree with you Alex he is a modest person ;)
> I understand sometimes it's not possible to say what the problem exactly
> is, but i ask to know if you had these problems before how did you solve it
> in your system, yes maybe it couldn't be the right answer for another's
> system but maybe a clue for someone!
>
> You have helped me many times and i really appreciate you for your
> attentions and kindness
>
> Thank you again dear Justin and Alex
> Best regards
>
> -Rose
>
> On Mon, Dec 18, 2017 at 12:52 AM, Alex  wrote:
>
> > Rose,
> >
> > Although in my opinion Justin does know everything, the problem is with
> > your question. You've posted the same thing over and over (and over), and
> > noone replied -- this could be an indicator that people simply have
> nothing
> > to say. We don't know anything about your system, we don't know whether
> it
> > is stable, what is its dynamics, etc, etc. On top of this, you are using
> a
> > very outdated Gromacs version.
> >
> > From my own experience with all versions above 5.0.x, pull in Gromacs
> does
> > work well, as long as your system behaves as expected without pulling,
> and,
> > once that has been confirmed, you use a properly selected set of pull
> > parameters. There are basic procedures for checking your system _prior
> to_
> > production simulations involving external stimuli (fields, pulling, etc)
> --
> > please follow them. And please, Please be mindful of what this message
> > board is, and especially of what it is not.
> >
> > Good luck!
> >
> > Alex
> >
> >
> >
> > On 12/17/2017 1:44 PM, Justin Lemkul wrote:
> >
> >>
> >>
> >> On 12/17/17 3:39 PM, Rose wrote:
> >>
> >>> Why you don't answer me?is there anything wrong in my question?
> >>>
> >>
> >> Contrary to popular opinion, I don't know everything :) If I don't reply
> >> to a question, it is because I have nothing useful to contribute.
> >>
> >> But since you asked, diagnosing what appears to be buggy behavior in
> >> wildly outdated (and unsupported, as I warned you) versions of the code
> is
> >> not a wise use of time. Upgrade to the latest version and try again.
> >>
> >> -Justin
> >>
> >> Thank you
> >>>
> >>> Sent from my iPhone
> >>>
> >>> On Dec 17, 2017, at 17:36, rose rahmani  wrote:
> 
>  Hi,
> 
>  I try to use umbrella sampling for calculating PMF. i change distance
>  between protein and ZNS nanosheet. I use gomacsV4.5.4
> 
>  after minimization and equilibration. i use:
> 
>  grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
>  this is md_pull.mdp:
>  integrator   = md
>  dt   = 0.002
>  nsteps   = 100
>  nstxout  = 5000
>  nstvout  = 5000
>  nstfout  = 500
>  nstlog   = 500
>  nstenergy= 1000
>  nstxtcout= 1000
>  nstlist  = 10
>  rlist= 1.5
>  coulombtype  = pme
>  rcoulomb = 1.5
>  vdwtype  = Switch
>  rvdw_switch  = 1.0
>  rvdw = 1.2
>  pcoupl   = no
>  gen_vel  = no
>  constraints  = h-bonds
>  ns_type  = grid
>  pbc  = xy
>  

Re: [gmx-users] SPC model hydrogen bonding

[João Henriques]

"Is my simulation wrong or SPC give similar values. Please give a
suggestion."

My suggestion is that you look at the extensive literature on bulk water
simulations using the SPC water model (and other more recent and accurate
water models for bulk water studies). There have been studies on the SPC
water model since the 80's. Also, the specific way you calculate the mean
no. of H-bonds influences the results. You'll see that the reported numbers
vary from paper to paper, depending on their definition of H-bond.

J

On Thu, Dec 14, 2017 at 6:53 AM, atb files  wrote:

>
>
>
>
> Hello Experts,I did a simulation for bulk SPC water. I got
> water hydrogen bonding of ~1.7 per water molecule, for hydrogen bonding
> radius of 0.35 nm and 60 degrees, at 310K and 1 bar. Experimental data
> shows observed hydrogen bonding of 3.5-4.0 at 310K. Is my simulation wrong
> or SPC give similar values. Please give a suggestion. ThanksSent using Zoho
> Mail
>
>
>
>
>
>
>
>
> --
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> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] DSSP installation

[João Henriques]

I already told you, use a DSSP executable that is compatible (versions 1 or
2) and pass the right version number to the -ver flag of do_dssp.

J

On Sat, Dec 9, 2017 at 1:06 PM, <sp...@iacs.res.in> wrote:

>  - Message from João Henriques <joao.m.a.henriq...@gmail.com>
> -
> Date: Sat, 9 Dec 2017 11:29:41 +0100
> From: João Henriques <joao.m.a.henriq...@gmail.com>
> Reply-To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] DSSP installation
>   To: gmx-us...@gromacs.org
>
> The output is telling you what is wrong. Gromacs doesn't support version
>> 3.
>> Install either version 1 or 2. In fact, I didn't even know there was a
>> version 3 of DSSP, where did you get it? It certainly isn't on the
>> official
>> website (http://swift.cmbi.ru.nl/gv/dssp/).
>>
>> J
>>
>> When I try version 2 there is no warning but only this fatal error comes
>>
>
>
> Program: gmx do_dssp, version 2016.3
>  Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>
>  Fatal error:
>  Failed to execute command: Try specifying your dssp version with the -ver
>  option.
>
> I have have exported the path in bashrc file though this error comes.
> Please give any suggestion.
>
> Sunipa
>
>
>
>>
>> On Fri, Dec 8, 2017 at 4:04 PM, <sp...@iacs.res.in> wrote:
>>
>> Hii all
>>> I want to calculate the number of helical contain of protein. For that I
>>> tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
>>> tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
>>> and exported the path to ./bashrc file
>>> export DSSP=/usr/local/bin/dssp
>>>
>>> Then when I was trying to use gmx do_dssp and select protein then the
>>> following error comes
>>>
>>> WARNING: You use DSSP version 3, which is not explicitly
>>> supported by do_dssp. Assuming version 2 syntax.
>>>
>>> dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
>>> /dev/null'
>>> trr version: GMX_trn_file (single precision)
>>> Reading frame   0 time0.000
>>> Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#
>>>
>>> ---
>>> Program: gmx do_dssp, version 2016.3
>>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>>>
>>> Fatal error:
>>> Failed to execute command: Try specifying your dssp version with the
>>>
>> -ver
>
>> option
>>>
>>> Then I tried using the version -ver 3
>>> But still the error comes.
>>> Please help me to fix this problem.
>>> Thanks
>>>
>>> Sunipa Sarkar
>>>
>>> --
>>> 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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>>>
>>> * 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
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>> posting!
>>
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>>
>
> - End message from João Henriques <joao.m.a.henriq...@gmail.com> -
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Re: [gmx-users] DSSP installation

[João Henriques]

The output is telling you what is wrong. Gromacs doesn't support version 3.
Install either version 1 or 2. In fact, I didn't even know there was a
version 3 of DSSP, where did you get it? It certainly isn't on the official
website (http://swift.cmbi.ru.nl/gv/dssp/).

J



On Fri, Dec 8, 2017 at 4:04 PM,  wrote:

>
> Hii all
> I want to calculate the number of helical contain of protein. For that I
> tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
> tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
> and exported the path to ./bashrc file
> export DSSP=/usr/local/bin/dssp
>
> Then when I was trying to use gmx do_dssp and select protein then the
> following error comes
>
> WARNING: You use DSSP version 3, which is not explicitly
> supported by do_dssp. Assuming version 2 syntax.
>
> dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
> /dev/null'
> trr version: GMX_trn_file (single precision)
> Reading frame   0 time0.000
> Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#
>
> ---
> Program: gmx do_dssp, version 2016.3
> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option
>
> Then I tried using the version -ver 3
> But still the error comes.
> Please help me to fix this problem.
> Thanks
>
> Sunipa Sarkar
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] DSSP

[João Henriques]

There's no DSSP version 3 that I know of. That can't be right.

J

On Tue, Dec 5, 2017 at 5:52 PM, Vidya R <vidyadevi2...@gmail.com> wrote:

> Hi,
>
> I have installed dssp version
>
>
> *3.0.0-win32*
>
> *What should be the command now?*
>
> On Tue, Dec 5, 2017 at 10:08 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > Did you specify the DSSP version as the error message suggests? DSSP
> > version 2 has different syntax from the previous one. On the gromacs
> 5.1.4
> > do_dssp assumes that you're using version 2, but maybe yours is version
> 1.
> >
> > P.S.: I am assuming you have done everything else correctly, i.e., you
> have
> > a working DSSP executable and you have exported that executable path as
> > $DSSP.
> >
> > J
> >
> > On Tue, Dec 5, 2017 at 3:41 PM, Vidya R <vidyadevi2...@gmail.com> wrote:
> >
> > > I got the error
> > >
> > > dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2>
> > /dev/null'
> > > Reading frame   0 time0.000
> > > Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#
> > >
> > > ---
> > > Program gmx do_dssp, VERSION 5.1.4
> > > Source code file:
> > > /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/
> > >
> > > gmx_do_dssp.c, line: 663
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option  .
> > >
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > >
> > > On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <
> > > joao.m.a.henriq...@gmail.com
> > > > wrote:
> > >
> > > > Hi!
> > > >
> > > > This is not so much for you as it is for the other users and
> > developers.
> > > I
> > > > think I found a problem with the DSSP code when compiling using the
> > > latest
> > > > boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> > > > "include" directory of this new boost, and the compilation fails. The
> > > error
> > > > is reproducible if you instead use homebrew to install DSSP.
> > > >
> > > > I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure
> this
> > > > email is active anymore. Hopefully it is, otherwise please let me
> know.
> > > >
> > > > Best regards,
> > > > J
> > > >
> > > > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R <vidyadevi2...@gmail.com>
> > wrote:
> > > >
> > > > > Hi gromacs users,
> > > > >
> > > > > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> > > > >
> > > > > I want to download and install dssp tool.
> > > > >
> > > > > How to proceed?
> > > > >
> > > > >
> > > > > Thanks,
> > > > > Vidya.R
> > > > > --
> > > > > 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
> > > >
> > > > * 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/
> > &g

Re: [gmx-users] DSSP

[João Henriques]

Did you specify the DSSP version as the error message suggests? DSSP
version 2 has different syntax from the previous one. On the gromacs 5.1.4
do_dssp assumes that you're using version 2, but maybe yours is version 1.

P.S.: I am assuming you have done everything else correctly, i.e., you have
a working DSSP executable and you have exported that executable path as
$DSSP.

J

On Tue, Dec 5, 2017 at 3:41 PM, Vidya R <vidyadevi2...@gmail.com> wrote:

> I got the error
>
> dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> /dev/null'
> Reading frame   0 time0.000
> Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#
>
> ---
> Program gmx do_dssp, VERSION 5.1.4
> Source code file:
> /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/
>
> gmx_do_dssp.c, line: 663
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option  .
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <
> joao.m.a.henriq...@gmail.com
> > wrote:
>
> > Hi!
> >
> > This is not so much for you as it is for the other users and developers.
> I
> > think I found a problem with the DSSP code when compiling using the
> latest
> > boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> > "include" directory of this new boost, and the compilation fails. The
> error
> > is reproducible if you instead use homebrew to install DSSP.
> >
> > I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
> > email is active anymore. Hopefully it is, otherwise please let me know.
> >
> > Best regards,
> > J
> >
> > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R <vidyadevi2...@gmail.com> wrote:
> >
> > > Hi gromacs users,
> > >
> > > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> > >
> > > I want to download and install dssp tool.
> > >
> > > How to proceed?
> > >
> > >
> > > Thanks,
> > > Vidya.R
> > > --
> > > 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!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] DSSP

[João Henriques]

Hi!

This is not so much for you as it is for the other users and developers. I
think I found a problem with the DSSP code when compiling using the latest
boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
"include" directory of this new boost, and the compilation fails. The error
is reproducible if you instead use homebrew to install DSSP.

I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
email is active anymore. Hopefully it is, otherwise please let me know.

Best regards,
J

On Tue, Dec 5, 2017 at 6:38 AM, Vidya R  wrote:

> Hi gromacs users,
>
> I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
>
> I want to download and install dssp tool.
>
> How to proceed?
>
>
> Thanks,
> Vidya.R
> --
> 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.
>
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Re: [gmx-users] Regarding calculating the water orientation profile

[João Henriques]

Orientation has nothing to do with proximity. You can have orientation as a
function of proximity, but orientation *per se* does not necessarily
involve a distance, it just tells you about a preferential orientation of
the water molecules towards a reference. We've already been through this in
detail when I suggested looking at the angular probability function,
defining the vectors you want to compute the angle from, etc. I really
don't understand what is hindering you from performing such analysis, which
seems to be exactly what you want/need.

J



On Fri, Nov 24, 2017 at 9:08 AM, Dilip H N 
wrote:

> So what exactly does this Orientation Profile means.??
> I am really confused with the exact approach towards it...
>
>
>  Sent with Mailtrack
>  ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> medium=signature_campaign=signaturevirality>
>
> On Fri, Nov 24, 2017 at 12:47 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > "Coming closer" implies you care about distance, but your original
> question
> > was about orientation. So it's unclear what you want.
> >
> > Mark
> >
> > On Thu, 23 Nov 2017 16:50 Dilip H N  wrote:
> >
> > > I want to calculate whether the water molecules are coming closer
> towards
> > > the N-terminal or towards the C-terminal of the amino-acid throughout
> > the
> > > simualtion.
> > > And hence it can shed some light on the Hydrogen bond
> > > dynamicshopefully...
> > >
> > > Thank you
> > >
> > >
> > >
> > >  Sent with Mailtrack
> > > <
> > > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> > medium=signature_campaign=signaturevirality
> > > >
> > >
> > > On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > It sounds like to need to be more clear about what you want to
> > calculate
> > > > before you can sensibly find a tool to do it. You should be able to
> > write
> > > > down the equation for what you want to compute as your observation
> long
> > > > before you run a simulation, or how will you know what data to
> collect?
> > > >
> > > > Mark
> > > >
> > > > On Thu, 23 Nov 2017 07:26 Dilip H N 
> wrote:
> > > >
> > > > > Hello Sir,
> > > > > I have run a simulation of amino-acid (glycine) with water
> molecules
> > > for
> > > > 10
> > > > > ns. Now i need to find out/analyze that whether the water molecules
> > are
> > > > > getting/more oriented towards N-terminal of glycine or towards the
> > > > > C-terminal of glycine. (i hope this is what water orientation
> profile
> > > > means
> > > > > ie., the preferential orientation of water towards particular
> > > > > moeity/group...).
> > > > > So, which is the exact module/command to find this..?? wether gmx
> > > sorient
> > > > > or gmx gangle or gmx angle ..??
> > > > >
> > > > > How to resolve this issue...
> > > > >
> > > > > Thank you
> > > > >
> > > > >
> > > > > --
> > > > > With Best Regards,
> > > > >
> > > > > DILIP.H.N
> > > > > Ph.D Student
> > > > >
> > > > >
> > > > >
> > > > > ‌
> > > > >  Sent with Mailtrack
> > > > > <
> > > > > https://chrome.google.com/webstore/detail/mailtrack-for-
> gmail-inbox/
> > > > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> > > > medium=signature_campaign=signaturevirality
> > > > > >
> > > > > --
> > > > > 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!
> > > >
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> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > >
> > >
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > > --
> > > 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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> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to 

Re: [gmx-users] THE max number of atoms in gromacs?

[João Henriques]

Hi,

The PDB format is fixed, so it's not really a gromacs problem *per se*.
Take a look at this

:

"A model cannot have more than 99,999 atoms. Where the entry does not
contain an ensemble of models, then the entry cannot have more than 99,999
atoms. Entries that go beyond this atom limit must be split into multiple
entries, each containing no more than the limits specified above."

You could go around this by writing your model in the gro format instead,
which allows you to go over 99.999 atoms by simply restarting the atom
numbering from 0 once you hit 100.000.

J



On Thu, Nov 23, 2017 at 10:01 PM, Jerry Binder 
wrote:

> Hello gmx-users:
>
> I build a large system with more than 10,000 atoms, however I cannot
> write info to pdb file correctly. The pdb file format in gromacs
> specify 5 positions for atom-id, and it will cause problem if not.
> Since I have to use rtp file and "pdb2gmx" command to generate
> conf.gro and topol.top file, a pdb file with >10 atoms is needed.
>
> How can I do with it?
> --
> Gromacs Users mailing list
>
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Re: [gmx-users] Regarding calculating the water orientation profile

[João Henriques]

Wait, now I remember, you even approached me in a private message and we
exchanged quite a few emails. Did you try any of my suggestions? No success?

J

On Thu, Nov 23, 2017 at 7:36 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Hi,
>
> I clearly remember replying to something similar sometime ago, and I'm
> almost sure the post was yours. It may be a good idea to rummage through
> the mailing list, because I'm pretty sure this type of analysis has been
> discussed here more than once.
>
> Cheers,
> J
>
> On Thu, Nov 23, 2017 at 4:41 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
>> I want to calculate whether the water molecules are coming closer towards
>> the N-terminal or towards the C-terminal of the amino-acid throughout  the
>> simualtion.
>> And hence it can shed some light on the Hydrogen bond
>> dynamicshopefully...
>>
>> Thank you
>>
>>
>>
>> <https://mailtrack.io/> Sent with Mailtrack
>> <https://chrome.google.com/webstore/detail/mailtrack-for-gma
>> il-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&
>> utm_medium=signature_campaign=signaturevirality>
>>
>> On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <mark.j.abra...@gmail.com>
>> wrote:
>>
>> > Hi,
>> >
>> > It sounds like to need to be more clear about what you want to calculate
>> > before you can sensibly find a tool to do it. You should be able to
>> write
>> > down the equation for what you want to compute as your observation long
>> > before you run a simulation, or how will you know what data to collect?
>> >
>> > Mark
>> >
>> > On Thu, 23 Nov 2017 07:26 Dilip H N <cy16f01.di...@nitk.edu.in> wrote:
>> >
>> > > Hello Sir,
>> > > I have run a simulation of amino-acid (glycine) with water molecules
>> for
>> > 10
>> > > ns. Now i need to find out/analyze that whether the water molecules
>> are
>> > > getting/more oriented towards N-terminal of glycine or towards the
>> > > C-terminal of glycine. (i hope this is what water orientation profile
>> > means
>> > > ie., the preferential orientation of water towards particular
>> > > moeity/group...).
>> > > So, which is the exact module/command to find this..?? wether gmx
>> sorient
>> > > or gmx gangle or gmx angle ..??
>> > >
>> > > How to resolve this issue...
>> > >
>> > > Thank you
>> > >
>> > >
>> > > --
>> > > With Best Regards,
>> > >
>> > > DILIP.H.N
>> > > Ph.D Student
>> > >
>> > >
>> > >
>> > > ‌
>> > > <https://mailtrack.io/> Sent with Mailtrack
>> > > <
>> > > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
>> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
>> > medium=signature_campaign=signaturevirality
>> > > >
>> > > --
>> > > 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!
>> >
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>> >
>> > * 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.
>>
>>
>>
>>
>> --
>> With Best Regards,
>>
>> DILIP.H.N
>> Ph.D Student
>> --
>> 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.
>>
>
>
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Re: [gmx-users] Regarding calculating the water orientation profile

[João Henriques]

Hi,

I clearly remember replying to something similar sometime ago, and I'm
almost sure the post was yours. It may be a good idea to rummage through
the mailing list, because I'm pretty sure this type of analysis has been
discussed here more than once.

Cheers,
J

On Thu, Nov 23, 2017 at 4:41 PM, Dilip H N 
wrote:

> I want to calculate whether the water molecules are coming closer towards
> the N-terminal or towards the C-terminal of the amino-acid throughout  the
> simualtion.
> And hence it can shed some light on the Hydrogen bond
> dynamicshopefully...
>
> Thank you
>
>
>
>  Sent with Mailtrack
>  ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> medium=signature_campaign=signaturevirality>
>
> On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > It sounds like to need to be more clear about what you want to calculate
> > before you can sensibly find a tool to do it. You should be able to write
> > down the equation for what you want to compute as your observation long
> > before you run a simulation, or how will you know what data to collect?
> >
> > Mark
> >
> > On Thu, 23 Nov 2017 07:26 Dilip H N  wrote:
> >
> > > Hello Sir,
> > > I have run a simulation of amino-acid (glycine) with water molecules
> for
> > 10
> > > ns. Now i need to find out/analyze that whether the water molecules are
> > > getting/more oriented towards N-terminal of glycine or towards the
> > > C-terminal of glycine. (i hope this is what water orientation profile
> > means
> > > ie., the preferential orientation of water towards particular
> > > moeity/group...).
> > > So, which is the exact module/command to find this..?? wether gmx
> sorient
> > > or gmx gangle or gmx angle ..??
> > >
> > > How to resolve this issue...
> > >
> > > Thank you
> > >
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
> > > ‌
> > >  Sent with Mailtrack
> > > <
> > > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> > medium=signature_campaign=signaturevirality
> > > >
> > > --
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> > > posting!
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>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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Re: [gmx-users] Typo for atom in charmm36-jul2017 ff for residue NAI

[João Henriques]

Good to know, thanks.

J

On Wed, Nov 8, 2017 at 12:54 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/8/17 5:52 AM, João Henriques wrote:
>
>> Hi Johannes,
>>
>> I'd suggest contacting someone at the MacKerell Lab instead. I believe
>> they
>> are responsible for the FF and for its maintenance. Otherwise this issue
>> might get lost here and never make it to the people that absolutely need
>> to
>> know about it.
>>
>
> I'm responsible for the GROMACS port of the CHARMM force field, so for
> issues like these this mailing list or my personal email work fine.
> Probably best to post here so people know if there are problems.
>
> Look at the original paper and send an email to the corresponding authors:
>> http://www.nature.com/nmeth/journal/v14/n1/full/nmeth.4067.html
>>
>
> Nothing to do with NAD, but people can always contact Alex with force
> field questions. But if he sees the word "GROMACS" anywhere in it, all he
> does is forward it to me :)
>
> -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
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Re: [gmx-users] Writing pdb snapshot with charge from gro trajectory

[João Henriques]

Hi,

The PDB format is strict by definition (
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html).
Every single character (and column) within a line has a specific purpose
and charges are not included there. I doubt trjconv or other gromacs tools
will allow you to tamper with it in such way. You can however make a simple
script to (i) parse the topology, (ii) match it with the PDB file, and
(iii) add an extra column at the end of the PDB with the respective
charges. This should be relatively simple to do with your favorite
scripting language.

Cheers,
J

On Wed, Nov 8, 2017 at 11:12 AM, Dawid das  wrote:

> Dear Gromacs Users,
>
> I have a trajectory of my MD simulation in *.gro format. Is it possible to
> write the pdb snapshot
> from the trajectory so that the pdb file contains the atomic charge from
> top file?
> The charge should be put at the end of my pdb file.
>
> Best wishes,
> Dawid Grabarek
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Re: [gmx-users] Typo for atom in charmm36-jul2017 ff for residue NAI

[João Henriques]

Hi Johannes,

I'd suggest contacting someone at the MacKerell Lab instead. I believe they
are responsible for the FF and for its maintenance. Otherwise this issue
might get lost here and never make it to the people that absolutely need to
know about it.

Look at the original paper and send an email to the corresponding authors:
http://www.nature.com/nmeth/journal/v14/n1/full/nmeth.4067.html

Cheers,
J

On Wed, Nov 8, 2017 at 11:32 AM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Dear all,
>
> I do not know if this is right place to put this, please feel free to
> redirect my comment.
>
> I think I found a small typo in charmm36-jul2017 ff in the merged.rtp file
> for residue NAI:
>
> In the [ atoms ] section line
>
> N71N   HN10.260 69
>
> should read
>
> H71N   HN10.260 69
>
> and consequently "N71N" should be replaced by "H71N" in the [ bonds ] and
> [ impropers ] sections. When you look at the structure, the H71N/N71N atom
> should clearly by an hydrogen atom. This can also be seen in the
> CHARMM-formatted topology and parameter files (in top_all36_cgenff.rtf,
> RESI NADH, the respective atom it is called NH71). If you leave N71N as it
> is, and rename H71N in your .gro/.pdb file, Gromacs will not treat the bond
> as hydrogen-bond (e.g. in constraints = h-bonds).
>
> I hope this helps and can be adapted in the next version of charmm ff.
>
> All the best
>
> Johannes
>
> --
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
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> 
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
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Re: [gmx-users] non-neutral system

[João Henriques]

Understood. Thank you Justin.

J

On Mon, Nov 6, 2017 at 1:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/6/17 7:06 AM, João Henriques wrote:
>
>> Hi Johannes,
>>
>> I just meant that from a purely theoretical point of view, it needs to be
>> neutral. This has to do with the convergence of the outer infinite series,
>> as the paper Micholas linked clearly states. I sincerely hope I'm not
>> botching this up, but this is the conclusion I've withdrawn from reading
>> the literature. Now, if the software implementation contains some tricks
>> to
>> account for this, that I'm not familiar with and will therefore leave that
>> discussion for someone else more acquainted with it.
>>
>
> For your reference, it's explained in dx.doi.org/10.1021/ct400626b
>
> All MD codes can do this when using PME, so it's not really a trick, just
> part of PME. It's not intuitive to most users, and not appropriate in many
> cases, hence the standard advice of "add counterions."
>
> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] non-neutral system

[João Henriques]

Hi Johannes,

I just meant that from a purely theoretical point of view, it needs to be
neutral. This has to do with the convergence of the outer infinite series,
as the paper Micholas linked clearly states. I sincerely hope I'm not
botching this up, but this is the conclusion I've withdrawn from reading
the literature. Now, if the software implementation contains some tricks to
account for this, that I'm not familiar with and will therefore leave that
discussion for someone else more acquainted with it.

Cheers,
J



On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Hey Joao,
>
> are you sure? I think PME will introduce a neutralizing background charge?
>
> All the best
>
> Johannes
>
>
>
> On 06.11.2017 11:57, João Henriques wrote:
>
>> ​Hi,
>>
>> You shouldn't use PME without neutralizing the system's charge. ​It's a
>> limitation of the Ewald summation. Take a look at the literature for
>> further details.
>>
>> I don't know much about viscosity, so I'll leave that for someone else.
>>
>> Cheers,
>> J
>>
>> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> I  have a system containing similar charged atoms. So the total charge is
>>> not zero.
>>>
>>> Simulation results with cut-off coulomb seems reasonable,  but using PME
>>> they are wrong (total columb potential is negative value which must be
>>> positive). Any idea why?
>>>
>>> If I use counter-ions to neutralize the system, I am afraid the
>>> properties
>>> I am looking for (viscosity) will be influenced.
>>>
>>> Best regards
>>> --
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>>>
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> Fax: +49 8928915714
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Re: [gmx-users] non-neutral system

[João Henriques]

​Hi,

You shouldn't use PME without neutralizing the system's charge. ​It's a
limitation of the Ewald summation. Take a look at the literature for
further details.

I don't know much about viscosity, so I'll leave that for someone else.

Cheers,
J

On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
wrote:

> Hi,
>
> I  have a system containing similar charged atoms. So the total charge is
> not zero.
>
> Simulation results with cut-off coulomb seems reasonable,  but using PME
> they are wrong (total columb potential is negative value which must be
> positive). Any idea why?
>
> If I use counter-ions to neutralize the system, I am afraid the properties
> I am looking for (viscosity) will be influenced.
>
> Best regards
> --
> Gromacs Users mailing list
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Re: [gmx-users] how to do neutralization?

[João Henriques]

​That can't be right, AMBER03 does not contain amino acid residues with
partial charges. Each residue's charge is parametrized for a final integer
net charge. Are you using any custom/modified residue blocks? If not, when
you pass the PDB of a protein to pdb2gmx, and that protein containing aa.
residues that are defined in the force field​ rtp file, pdb2gmx will
produce a topology with integer net charge. It is generally a good idea to
tell pdb2gmx to ignore the hydrogen atoms present in the PDB file and set
the protonation states on the fly (using the -ignh and -inter flags).

Now, if you're tampering with the rtp and itp files and/or parametrizing it
yourself, that's a completely different story. AMBER03 and GROMACS are not
to blame, it must be whatever the user is doing. From experience, I can
tell you that a properly performed parametrization will yield no such
issues. But it's difficult to evaluate the problem you're trying to
describe without further detail.

J


On Thu, Nov 2, 2017 at 11:31 AM, rose rahmani <rose.rhm...@gmail.com> wrote:

> HI,
> I have the same problem,i use AMBER03 force field,the structure has Zn and
> S atoms and amino acids with net charge less than 1, idont know what should
> i do,i optimized the structure in Gaussian and put H atom for make it more
> stable but its not included in itp file.
>
> On Thu, Nov 2, 2017 at 1:23 PM, João Henriques <
> joao.m.a.henriq...@gmail.com
> > wrote:
>
> > Hi,
> >
> > What system is that and what force field are you using? Building blocks
> > usually have integer net charges, this is rather unusual.
> >
> > Cheers,
> > J
> >
> > On Thu, Nov 2, 2017 at 10:02 AM, Seera Suryanarayana <
> paluso...@gmail.com>
> > wrote:
> >
> > > Dear gromacs users
> > >
> > > I got the system non-zero total charge: -0.226000. When I add one NA
> ion
> > to
> > > the system I got non-zero total charge: +0.77. What is the way to
> > > neutralize the system?
> > >
> > > Thanks in advance
> > > Surya
> > > Graduate student
> > > India.
> > > --
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Re: [gmx-users] how to do neutralization?

[João Henriques]

Hi,

What system is that and what force field are you using? Building blocks
usually have integer net charges, this is rather unusual.

Cheers,
J

On Thu, Nov 2, 2017 at 10:02 AM, Seera Suryanarayana 
wrote:

> Dear gromacs users
>
> I got the system non-zero total charge: -0.226000. When I add one NA ion to
> the system I got non-zero total charge: +0.77. What is the way to
> neutralize the system?
>
> Thanks in advance
> Surya
> Graduate student
> India.
> --
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Re: [gmx-users] Regarding water orientation profile

[João Henriques]

​Hi,

I've had similar issues in the past with the calculation of angular
distribution functions of water in respect to a given point or amino acid
residue and it wasn't easy/possible to solve with standard gromacs tools.
I'd suggest using MDAnalysis or some other equivalent tool. It definitely
gives you more freedom at the cost of having to code it yourself, plus it
can potentially be slow unless your Python skills are up to the challenge.
Here are a few examples you can use for "inspiration":

https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/waterdynamics.html

In any case, this is probably the least painful solution, since others
would revolve around wrapping one or more gromacs tools with some nasty
scripts, or coding a proper tool in C++ either from scratch or by building
on top of functions already available in gromacs source code.

Hope this helps,
Cheers,
J​

On Tue, Oct 31, 2017 at 8:55 AM, Dilip H N 
wrote:

> Hello,
> I want to do the water orientation profile for the amino-acid which is
> surrounded by water molecules as in my case amino-acid+water mixture.
> ie., i want to find out whether the water is orientation is more towards
> the N-terminal or towards the C-terminal of the amino acid and hence the
> orientation profile. I want to know throught the simulation around which
> terminal water molecules are more oriented as a function of time or etc.,
>
> I have a simulation done in GROMACS with one amino-acid in presence
> of cosolvents which is solvated with water for 10 ns. So I want to have the
> water orientation profile.But i tried with gmx sorient command, but i am
> unable to understand it.. and also through gmx h2order which
> calculates the orientation
> of water molecules with respect to the normal of the box, but i need to
> calculate with respect to N-terminal or through C-terminal.
> What is the best way to solve this..??
>
> Any suggestions are highly appreciated.
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
> ‌
>  Sent with Mailtrack
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Re: [gmx-users] How good to use triclinic box for gormacs simulations?

[João Henriques]

Hi,

How does the link to "editconf" help in answering the original question?

Anyway, no, there is no specific recipe to select a box type. You generally
have to make an educated guess by using your scientific intuition and
knowledge about the shape (and conformational plasticity) of your system.
Then as the simulation runs, you keep checking the system's integrity to
see if it holds (is it interacting with its image?, etc). No box is
inherently inferior to another, it all depends on your system and how much
computational effort a particular box shape will save you (without
compromising the simulation).

Cheers,
J

On Tue, Oct 31, 2017 at 7:39 AM, Kunal Dutta <
kunal_lif...@mail.vidyasagar.ac.in> wrote:

> Hi,
> Please check the link.
> http://manual.gromacs.org/programs/gmx-editconf.html
> Best, Kunal
>
>
> On Tue, Oct 31, 2017 at 3:22 AM, vijayakumar gosu <
> vijayakumarg...@gmail.com
> > wrote:
>
> > Hello all,
> >
> >
> > I have performed simulations for Protein RNA complex around 1500
> residues.
> > I have used triclinic box with 1.4 nm distance from the edge of the box
> to
> > protein as triclinic box takes less number of water molecules (~10)
> > compared to other boxes . The simulation results looks fine and i am able
> > to answer the biological question. however i have not seen many
> > publications using triclinic box. Hence i am bit skeptical and like to
> > know  there is any criteria to choose the simulation box.
> >
> >
> > Thanks
> > --
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> -
> Regards.
> Kunal Dutta
> Senior Research Scholar
> Microbiology and Immunology Laboratory
> Department of Human Physiology with Community Health
> Vidyasagar University, Medinipur-721102
> West Bengal, India.
> Cell: 9126181933
> 
> ORCID ID: -0002-0818-8787
> RG: https://www.researchgate.net/profile/Kunal_Dutta2
> GS: https://scholar.google.co.in/citations?user=ULby284J=en
>
> --
>
>
>
> 
> 
>
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Re: [gmx-users] CHARMM36 older version (GROMACS)

[João Henriques]

Hi Simon,

Aren't they the same force field though? As far as I've noticed they're
identical if you use them for proteins (without any fancy residues). The
latest one just includes more atom types, etc. From my understanding the
latest one is more "complete", but both are essentially the same thing.

I could be wrong though...

P.S.: I do have both versions, so email me privately if you absolutely must
have the earlier version.

Cheers,
J

On Wed, Oct 25, 2017 at 9:59 AM, Simon Kit Sang Chu 
wrote:

> Hi everyone,
>
> I plan to use CHARMM36-nov2016.ff for my simulation. However, MacKerell Lab
>  webpage does not seem to
> provide CHARMM36-nov2016. Only CHARMM36-jul2017 is provided.
>
> I tried to google "CHARMM36-nov2016" but failed to see any official
> download page. Perhaps it is a dumb question - is there any place I can
> download older versions of CHARMM forcefield?
>
> Please pardon my abruptness.
>
> Simon
> --
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Re: [gmx-users] RMSD in Angstrom

[João Henriques]

​Hi,

This is more of a xmgrace related issue. Gromacs' length units have always
been nm and there's no way to "ask" for different units. Now you either
modify the file yourself (manually or with a simple awk one-liner) or ask
the plotting program to convert the units. I don't know about xmgrace, but
in gnuplot this is trivial to do. For example, "plot ... u 1:($2*10)".

Cheers,
J

On Mon, Oct 23, 2017 at 9:56 AM, Roshan Shrestha 
wrote:

> Hi,
>  The default unit for RMSD in gromacs is in nanometer (nm). Are there
> any options available in gromacs so that I can have rmsd values in Angstrom
> while plotting it in xmgrace.
> Thanks
>
> --
> Roshan Shrestha
> M.Sc (Physics)
> Central Department of Physics, Tribhuvan University
> Kathmandu, Nepal
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Re: [gmx-users] CHARMM ff cutoffs

[João Henriques]

Dear Justin and Micholas,

First of all, I'd like thank both of you for the input. Greatly appreciated.

@Justin - I do agree with you and I understand why they might have done so
(performance-wise). Furthermore, until Davide's paper, and in light of
Stefano and Kresten's paper on the whole cutoff issue, it was more or less
assumed that something like 0.95 nm would be fine. The problem is that this
paper is special, since it is the official publication of the modification
to the C36 FF. Coherence should have been preserved, at least in my
personal opinion. In any case, I will do like you said and hand out your
name and url to the referee :) Just kidding, this isn't something I've been
asked (yet), but from experience, I have a feeling it will be a topic of
discussion. Plus, even if it isn't asked of me, I still want to have it
well justified in the paper.

@Micholas - Your argument would apply in most circumstances, but the
situation here is a bit more hairy for several reasons... which I am not at
liberty to discuss in public. I hope you understand.

Once again thank you for your input,
Best regards,
J


On Thu, Oct 19, 2017 at 4:54 PM, Smith, Micholas D. <smit...@ornl.gov>
wrote:

> Fair enough.
>
> Consider this then: of the systems tested in the CHARMM36m publication;
> which one is closest to yours (sequence similarity, structure)? That would
> be one way to decide which cut-off would be appropriate.
>
> Alternatively, you could just run the simulation multiple times with
> multiple cut-offs and see which one corresponds closest with experimental
> knowledge (though this would be challenge for IDPs, unless there is a known
> set of metastable structures that get sampled).
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João
> Henriques <joao.m.a.henriq...@gmail.com>
> Sent: Thursday, October 19, 2017 10:46 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] CHARMM ff cutoffs
>
> Dear Micholas,
>
> First of all, thank you for your input. I understand the whole cutoff
> problematic and it is my desire to stick to the standard. However (and
> maybe I didn't explain this part properly), the CHARMM36m publication
> reports different cutoffs (if you check the SI) depending on which protein
> is simulated. This publication *IS* the standard, right? I am well aware
> that other CHARMM implementations use 1.2 nm, but if you go further back in
> time, the cutoffs have taken other values. But I digress, the main question
> here is, how can I justify my choice when the official publication reports
> these two values and does not provide an explanation for it? I am well
> aware that the 1.2 nm value is the *de facto* value, but that is not an
> acceptable justification in the eyes of a journal referee, as we all can
> understand.
>
> Thanks!
> J
>
>
>
> On Thu, Oct 19, 2017 at 4:33 PM, Smith, Micholas D. <smit...@ornl.gov>
> wrote:
>
> > João,
> >
> > If you use the CHARMM-GUI (charmm-gui.org) to build your systems, they
> > set their "standard" cut-offs to be 1.2nm, unless there is a membrane,
> then
> > they set it to 1.4nm (at least that's what it use to do).
> >
> > Changing cut-offs is kind of a mess. A lot of people will argue that the
> > cut-offs are explicitly part of the force-field, and so whatever cut-offs
> > were used for the parameterization are what you absolutely must use. But
> > then you'll find papers (lake you did) that uses 0.95nm cut-offs and get
> > reasonable results.
> >
> > I would stick to the standard unless you have a really good reason (not
> > performance) for toying with the cut-offs.
> >
> > -Micholas
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João
> > Henriques <joao.m.a.henriq...@gmail.com>
> > Sent: Thursday, October 19, 2017 10:03 AM
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] CHARMM ff cutoffs
> >
> > Dear all,
> >
> > Is there any piece of literature that explicitly states what is the *de
> > facto* cutoff for CHARMM 

Re: [gmx-users] CHARMM ff cutoffs

[João Henriques]

Dear Micholas,

First of all, thank you for your input. I understand the whole cutoff
problematic and it is my desire to stick to the standard. However (and
maybe I didn't explain this part properly), the CHARMM36m publication
reports different cutoffs (if you check the SI) depending on which protein
is simulated. This publication *IS* the standard, right? I am well aware
that other CHARMM implementations use 1.2 nm, but if you go further back in
time, the cutoffs have taken other values. But I digress, the main question
here is, how can I justify my choice when the official publication reports
these two values and does not provide an explanation for it? I am well
aware that the 1.2 nm value is the *de facto* value, but that is not an
acceptable justification in the eyes of a journal referee, as we all can
understand.

Thanks!
J



On Thu, Oct 19, 2017 at 4:33 PM, Smith, Micholas D. <smit...@ornl.gov>
wrote:

> João,
>
> If you use the CHARMM-GUI (charmm-gui.org) to build your systems, they
> set their "standard" cut-offs to be 1.2nm, unless there is a membrane, then
> they set it to 1.4nm (at least that's what it use to do).
>
> Changing cut-offs is kind of a mess. A lot of people will argue that the
> cut-offs are explicitly part of the force-field, and so whatever cut-offs
> were used for the parameterization are what you absolutely must use. But
> then you'll find papers (lake you did) that uses 0.95nm cut-offs and get
> reasonable results.
>
> I would stick to the standard unless you have a really good reason (not
> performance) for toying with the cut-offs.
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João
> Henriques <joao.m.a.henriq...@gmail.com>
> Sent: Thursday, October 19, 2017 10:03 AM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] CHARMM ff cutoffs
>
> Dear all,
>
> Is there any piece of literature that explicitly states what is the *de
> facto* cutoff for CHARMM FFs, i.e., for the LJ and electrostatic
> interactions? The old gromacs site states it's 1.2 nm:
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> However, I've read Robert Best's C36 and Huang's C36m papers, along with
> older CHARMM ff publications by MacKerell and Co., and I'm rather confused
> at this point. E.g., on the C36m paper, the RS peptide is simulated with
> 0.95 nm cutoffs and other proteins with 1.2 nm. Robert is consistent and
> uses 1.2 nm all the way. Older publications use even shorter cutoffs.
>
> I know the cutoffs can probably be toyed with to a certain extent (Stefano
> Piana and Kresten Lindorff-Larsen showed that on their 2012 paper), but a
> recent paper by Davide Mercadante on JCTC seems to show that it is not so
> simple for IDPs, and shortening the cutoffs is a no-no (even though he did
> it for his KBFF and AMBER FFs, not CHARMM).
>
> In my work I use CHARMM36m with 1.2 nm, but, looking at the literature,
> there's no way I can justify my choice when the original C36m does not
> stick to a single cutoff selection...
>
> I know Justin is/was affiliated with the MacKerell lab, so maybe he can
> shed some light on this subject. Anyone else is encouraged to give their
> input as well.
>
> Thank you in advance,
> Best regards,
> João
> --
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[gmx-users] CHARMM ff cutoffs

[João Henriques]

Dear all,

Is there any piece of literature that explicitly states what is the *de
facto* cutoff for CHARMM FFs, i.e., for the LJ and electrostatic
interactions? The old gromacs site states it's 1.2 nm:

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

However, I've read Robert Best's C36 and Huang's C36m papers, along with
older CHARMM ff publications by MacKerell and Co., and I'm rather confused
at this point. E.g., on the C36m paper, the RS peptide is simulated with
0.95 nm cutoffs and other proteins with 1.2 nm. Robert is consistent and
uses 1.2 nm all the way. Older publications use even shorter cutoffs.

I know the cutoffs can probably be toyed with to a certain extent (Stefano
Piana and Kresten Lindorff-Larsen showed that on their 2012 paper), but a
recent paper by Davide Mercadante on JCTC seems to show that it is not so
simple for IDPs, and shortening the cutoffs is a no-no (even though he did
it for his KBFF and AMBER FFs, not CHARMM).

In my work I use CHARMM36m with 1.2 nm, but, looking at the literature,
there's no way I can justify my choice when the original C36m does not
stick to a single cutoff selection...

I know Justin is/was affiliated with the MacKerell lab, so maybe he can
shed some light on this subject. Anyone else is encouraged to give their
input as well.

Thank you in advance,
Best regards,
João
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Re: [gmx-users] Fwd: Related to PCA

[João Henriques]

Hello!

From your email it's difficult to understand whether you're familiar with
the analysis and just seek specialized help on a particular interpretation,
or whether you're completely new to PCA and want an overall explanation of
it. In case of the latter, I suggest literature research. To understand
PCA, you need to have an idea of what eigenvector-based multivariate
analyses are and what each eigenvector or principal component of your
system is. This is often non-trivial and I strongly suggest to study the
topic a bit before attempting the analysis for the sake of having a free
energy landscape that you then don't know how to interpret.

However, if you're familiar with the subject and merely want help
visualizing how the projection of the first 2 PCs roughly describes the
(majority of the) variance on your system, here is an old email by Tsjerk
Wassenaar. This has to be one of the best/funniest explanations about
eigenvectors and PCA in the history of gmx-users:

"""
Hi Brett,

Let's say you're sitting at your _desk_ writing that paper with a deadline
yesterday and you put a quick _meal_ next to you, wondering why on _earth_
you keep up with this. Your hands are moving between the meal and the
keyboard. You notice that the average position of your hands is somewhere
between the two and mark the mean position on your desk. Then you draw a
line through it that corresponds to the major extent of the motion of your
hands, and write 'eigenvector 1' along it. You add a line through the
average position, perfectly perpendicular to the first, and write
'eigenvector 2' along it. Now you can project every position of your hands
onto your desk, giving it an 'eigenvector 1' coordinate (or score) and an
'eigenvector 2' coordinate (or score). You notice that it's only part of
the total motion, as you neglect the height, which will be a third line,
perpendicular to the desk.

You can look at it a bit differently and say that your desk is the subspace
of your real space, spanned by the two perpendicular vectors, which
together describe most of your hand's motion.

I hope this makes some sense :)

Cheers,

Tsjerk
"""

Here is the source. Check the original post and the subsequent answers by
Tsjerk and António Baptista.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-March/095916.html

Cheers,
João



On Sat, Oct 7, 2017 at 6:02 PM, Nikhil Maroli  wrote:

> Hi,
>
> By getting the coordinates you can find the corresponding structure. I can
> send some articles or materials to understand and analyse PCA and FEL,
> Kindly drop a mail to me.
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Re: [gmx-users] Charges and Antechamber

[João Henriques]

Or this... :) I've never used it, but I'm sure it works like a charm. I
personally prefer to be more involved in all stages of the process, but I'm
a bit old school and I like to avoid "black boxes" for my own learning
benefit. That being said, I'm sure it does the job and it's faster &
simpler. It's probably the best way to go for someone with less experience
with this sort of task.

Cheers,

J

On Oct 3, 2017 5:10 PM, "ABEL Stephane"  wrote:

HI

It is quite easy to derive RESP charges and use them with GROMACS. You
could follow the steps

1) Build a pdb file of your molecule/modified residue
2)  Use the web server pyRED (http://upjv.q4md-
forcefieldtools.org/REDServer-Development/) and derive the RESP charges.
The webserver will also give you all the necessary parameters of the ff
(mol2 file, atom types, (non)bonded parameters)
3) Use these parameters to construct a rtp file for GROMACS for a given
force field
4) and finally use pdb2gmx with the pdb file to obtain the itp file.

That's all

Good luck
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Re: [gmx-users] Charges and Antechamber

[João Henriques]

This can potetially involve minimal editting or a lot of work. If you will
be using atom types already in place, you mainly need to edit the rtp file.
The charges, bonds and impropers go there. Other files need minimal work
like the residuetypes.dat and possibly the hdb, r2b, etc.

Avoid touching the original FF under share/gromacs/top. Make a copy of it
on your work directory and edit that one. Also, please don't take this task
lightly. Modifying a FF requires a good understanding of the task at hand.
Mistakes might become costly and may even go unnoticed while produce
wrong/false results.

João

On Oct 3, 2017 4:36 PM, "Sergio Manzetti" <sergio.manze...@fjordforsk.no>
wrote:
>
> Thanks, in which file do you add your residue, do you have an example?
>
> Thanks!
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
|   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/
| FAP ]
>
>
>
> From: "João Henriques" <joao.m.a.henriq...@gmail.com>
> To: "gmx-users" <gmx-us...@gromacs.org>
> Sent: Tuesday, October 3, 2017 4:33:55 PM
> Subject: Re: [gmx-users] Charges and Antechamber
>
> I just left work and I'm terrible with typing on the phone, so please bear
> with me.
>
> Since I mostly work with proteins and modified residues it was always
worth
> it for me to edit the actual FF instead of making an itp by hand. This way
> I let pdb2gmx do the tedious work of building the topology for myself. I
> simply give it a structure and it does its magic. Is it less work?
Probably
> not, since editing a FF is not exactly the simplest of tasks and requires
a
> lot of attention and knowledge about what is where in the many files that
> come in a FF folder. Still, I find it to have more pros than cons.
>
> To summarize, I don't build the topology. I add my custom residue to the
FF
> and let pdb2gmx figure the rest out.
>
> Hope it made sense,
> Cheers,
> João
>
> On Oct 3, 2017 3:53 PM, "Sergio Manzetti" <sergio.manze...@fjordforsk.no>
> wrote:
>
> Thanks Joao, I am on the way with the QM part, but making the topology for
> GMX is a little bit more complicated. I thought of generating one with
> ANTECHAMBER Of a neutral species, then edit the topology itp file
manually,
> but the propers are quite complex to re-edit.
>
> How did you get around this part?
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> | ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/
> | FAP ]
>
>
>
> From: "João Henriques" <joao.m.a.henriq...@gmail.com>
> To: "gmx-users" <gmx-us...@gromacs.org>
> Sent: Tuesday, October 3, 2017 3:50:55 PM
> Subject: Re: [gmx-users] Charges and Antechamber
>
> Hi!
>
> If your goal is to generate the atomic partial charges for a new
> residue/molecule (not existing in the FF you are interested in using),
then
> doing the QM calculations is a must in most cases. For example, AMBER FFs
> have a well documented and specific recipe you can easily follow, which
> involves deriving the electrostatic potential from QM calculations at a
> specific level of theory + basis sets and then using the RESP fit
procedure.
>
> Cornell, Wendy D., et al. "A second generation force field for the
> simulation of proteins, nucleic acids, and organic molecules." Journal of
> the American Chemical Society 117.19 (1995): 5179-5197.
>
> I've done this a couple of times and it was relatively simple. I never
> needed to use antechamber for anything else, all modelling and assignment
> of atom types were done manually. Exotic species might make things more
> complicated.
>
> P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For
> example, GROMOS FFs don't have a fixed recipe for obtaining the charges
> (you can even set them by hand according to your own whim), but the
> calculations must reproduce solvation enthalpies, etc. In sum, check the
> original literature on the FF you plan on using to understand how to
> calculate your own charges in a way that respects that specific FF's
> "philosophy".
>
> Hope it helps,
> João
>
>
>
> On Tue, Oct 3, 2017 at 3:16 PM, Se

Re: [gmx-users] Charges and Antechamber

[João Henriques]

I just left work and I'm terrible with typing on the phone, so please bear
with me.

Since I mostly work with proteins and modified residues it was always worth
it for me to edit the actual FF instead of making an itp by hand. This way
I let pdb2gmx do the tedious work of building the topology for myself. I
simply give it a structure and it does its magic. Is it less work? Probably
not, since editing a FF is not exactly the simplest of tasks and requires a
lot of attention and knowledge about what is where in the many files that
come in a FF folder. Still, I find it to have more pros than cons.

To summarize, I don't build the topology. I add my custom residue to the FF
and let pdb2gmx figure the rest out.

Hope it made sense,
Cheers,
João

On Oct 3, 2017 3:53 PM, "Sergio Manzetti" <sergio.manze...@fjordforsk.no>
wrote:

Thanks Joao, I am on the way with the QM part, but making the topology for
GMX is a little bit more complicated. I thought of generating one with
ANTECHAMBER Of a neutral species, then edit the topology itp file manually,
but the propers are quite complex to re-edit.

How did you get around this part?


Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
|   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/
| FAP ]



From: "João Henriques" <joao.m.a.henriq...@gmail.com>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Tuesday, October 3, 2017 3:50:55 PM
Subject: Re: [gmx-users] Charges and Antechamber

Hi!

If your goal is to generate the atomic partial charges for a new
residue/molecule (not existing in the FF you are interested in using), then
doing the QM calculations is a must in most cases. For example, AMBER FFs
have a well documented and specific recipe you can easily follow, which
involves deriving the electrostatic potential from QM calculations at a
specific level of theory + basis sets and then using the RESP fit procedure.

Cornell, Wendy D., et al. "A second generation force field for the
simulation of proteins, nucleic acids, and organic molecules." Journal of
the American Chemical Society 117.19 (1995): 5179-5197.

I've done this a couple of times and it was relatively simple. I never
needed to use antechamber for anything else, all modelling and assignment
of atom types were done manually. Exotic species might make things more
complicated.

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For
example, GROMOS FFs don't have a fixed recipe for obtaining the charges
(you can even set them by hand according to your own whim), but the
calculations must reproduce solvation enthalpies, etc. In sum, check the
original literature on the FF you plan on using to understand how to
calculate your own charges in a way that respects that specific FF's
"philosophy".

Hope it helps,
João



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti <
sergio.manze...@fjordforsk.no> wrote:

> Hi, I was wondering what the best approach is to simulate a negatively
> charged topology imported from ANTECHAMBER (which can't do integral
> charges):
>
> 1. Do QM calculations on the molecule, then edit the output from
> Antechamber
>
> or
>
> 2. Do something else.
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> | ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [
> http://www.phap.no/ | FAP ]
>
> --
> 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.
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a ma

Re: [gmx-users] Charges and Antechamber

[João Henriques]

Hi!

If your goal is to generate the atomic partial charges for a new
residue/molecule (not existing in the FF you are interested in using), then
doing the QM calculations is a must in most cases. For example, AMBER FFs
have a well documented and specific recipe you can easily follow, which
involves deriving the electrostatic potential from QM calculations at a
specific level of theory + basis sets and then using the RESP fit procedure.

Cornell, Wendy D., et al. "A second generation force field for the
simulation of proteins, nucleic acids, and organic molecules." Journal of
the American Chemical Society 117.19 (1995): 5179-5197.

I've done this a couple of times and it was relatively simple. I never
needed to use antechamber for anything else, all modelling and assignment
of atom types were done manually. Exotic species might make things more
complicated.

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For
example, GROMOS FFs don't have a fixed recipe for obtaining the charges
(you can even set them by hand according to your own whim), but the
calculations must reproduce solvation enthalpies, etc. In sum, check the
original literature on the FF you plan on using to understand how to
calculate your own charges in a way that respects that specific FF's
"philosophy".

Hope it helps,
João



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti <
sergio.manze...@fjordforsk.no> wrote:

> Hi, I was wondering what the best approach is to simulate a negatively
> charged topology imported from ANTECHAMBER (which can't do integral
> charges):
>
> 1. Do QM calculations on the molecule, then edit the output from
> Antechamber
>
> or
>
> 2. Do something else.
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
> --
> 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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Re: [gmx-users] Torsion analysis

[João Henriques]

gmx chi?

http://manual.gromacs.org/documentation/2016.3/onlinehelp/gmx-chi.html

I never used it though. I personally like to use PLUMED for this:

https://plumed.github.io/doc-v2.3/user-doc/html/_t_o_r_s_i_o_n.html

João

On Thu, Aug 24, 2017 at 1:43 PM, RAHUL SURESH 
wrote:

> Dear All,
>
> To deduce the the stability of ligand and protein binding, I would like to
> carry out torsion analysis. How is it possible using Gromacs?
>
> Thanks in advance
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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[gmx-users] Compiling DSSP-2.2.1 from source

[João Henriques]

Dear users and developers,

I have compiled DSSP from source a bunch of times in the past, but I
stopped being able to do it recently.

I've set the make.config file appropriately, since my boost (version
1.59.0_3) was installed through MacPorts:

BOOST_LIB_SUFFIX = -mt
BOOST_LIB_DIR= /opt/local/lib
BOOST_INC_DIR= /opt/local/include

However, upon hitting "make" I get a lot of boost related warnings, which
culminate in the following error:

linking mkdssp
clang: warning: argument unused during compilation: '-pthread'
[-Wunused-command-line-argument]
ld: library not found for -lcrt0.o
clang: error: linker command failed with exit code 1 (use -v to see
invocation)
make: *** [mkdssp] Error 1

I googled a bit and found nothing particularly useful. Has anyone seen this
before and/or have any idea of what's going on?

I'm trying to install this on a Mac laptop with all software up to date, be
it Xcode, MacPorts, etc. My g++ version is: Apple LLVM version 8.1.0
(clang-802.0.42)

Thank you for your attention,
Best regards,
João
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Re: [gmx-users] 4-letter residues

[João Henriques]

Absolutely spot on Justin! I just discovered it by myself 30 seconds ago.

Thanks!
João

On Thu, Jul 13, 2017 at 4:17 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/13/17 10:16 AM, João Henriques wrote:
>
>> Dear all,
>>
>> I have a protein with a phosphorylated threonine and the corresponding
>> residue name in my FF of interest is THP1. 4-letter residues and PDB files
>> are a recipe for disaster, but somehow pdb2gmx detects the residue's name
>> and number perfectly. What happens next is somewhat odd (at least to me).
>> It now ends in a fatal error regarding OXT atoms. This should not occur
>> and, in fact, the problem disappears as soon as I use the same exact PDB
>> but with a regular non-phosphorylated threonine residue instead. The OXT
>> atoms are still there. Anyone has any idea of what's going on? Should I
>> edit the FF to use a three letter name instead of THP1?
>>
>>
> You probably forgot to add THP1 as a Protein residue in residuetypes.dat,
> so pdb2gmx is inserting an incorrect chain termination before it.
>
> -Justin
>
>
> I'm using gmx 5.1.4.
>>
>> This is the THP1 residue in my PDB:
>>
>> ATOM   1171  N   THP1A 160  14.798   3.634  55.810  1.00 28.16
>>N
>> ATOM   1172  CA  THP1A 160  13.457   3.397  56.297  1.00 32.05
>>C
>> ATOM   1173  CB  THP1A 160  13.440   2.416  57.453  1.00 31.31
>>C
>> ATOM   1174  CG2 THP1A 160  12.002   2.135  57.857  1.00 28.13
>>C
>> ATOM   1175  OG1 THP1A 160  14.038   1.189  57.027  1.00 35.99
>>O
>> ATOM   1176  P   THP1A 160  15.501   0.748  57.510  1.00 37.49
>>P
>> ATOM   1177  O1P THP1A 160  15.810  -0.350  56.582  1.00 38.61
>>O
>> ATOM   1178  O2P THP1A 160  16.325   1.972  57.300  1.00 35.09
>>O
>> ATOM   1179  OT  THP1A 160  15.173   0.306  58.890  1.00 40.70
>>O
>> ATOM   1180  C   THP1A 160  12.747   4.659  56.712  1.00 39.18
>>C
>> ATOM   1181  O   THP1A 160  13.202   5.412  57.567  1.00 38.80
>>O
>>
>> This is the error:
>>
>> Fatal error:
>> Atom OXT in residue LEU 298 was not found in rtp entry LEU with 19 atoms
>> while sorting atoms.
>>
>> Thank you in advance,
>> Best regards,
>> João
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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[gmx-users] 4-letter residues

[João Henriques]

Dear all,

I have a protein with a phosphorylated threonine and the corresponding
residue name in my FF of interest is THP1. 4-letter residues and PDB files
are a recipe for disaster, but somehow pdb2gmx detects the residue's name
and number perfectly. What happens next is somewhat odd (at least to me).
It now ends in a fatal error regarding OXT atoms. This should not occur
and, in fact, the problem disappears as soon as I use the same exact PDB
but with a regular non-phosphorylated threonine residue instead. The OXT
atoms are still there. Anyone has any idea of what's going on? Should I
edit the FF to use a three letter name instead of THP1?

I'm using gmx 5.1.4.

This is the THP1 residue in my PDB:

ATOM   1171  N   THP1A 160  14.798   3.634  55.810  1.00 28.16
  N
ATOM   1172  CA  THP1A 160  13.457   3.397  56.297  1.00 32.05
  C
ATOM   1173  CB  THP1A 160  13.440   2.416  57.453  1.00 31.31
  C
ATOM   1174  CG2 THP1A 160  12.002   2.135  57.857  1.00 28.13
  C
ATOM   1175  OG1 THP1A 160  14.038   1.189  57.027  1.00 35.99
  O
ATOM   1176  P   THP1A 160  15.501   0.748  57.510  1.00 37.49
  P
ATOM   1177  O1P THP1A 160  15.810  -0.350  56.582  1.00 38.61
  O
ATOM   1178  O2P THP1A 160  16.325   1.972  57.300  1.00 35.09
  O
ATOM   1179  OT  THP1A 160  15.173   0.306  58.890  1.00 40.70
  O
ATOM   1180  C   THP1A 160  12.747   4.659  56.712  1.00 39.18
  C
ATOM   1181  O   THP1A 160  13.202   5.412  57.567  1.00 38.80
  O

This is the error:

Fatal error:
Atom OXT in residue LEU 298 was not found in rtp entry LEU with 19 atoms
while sorting atoms.

Thank you in advance,
Best regards,
João
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Re: [gmx-users] Issue with the PDB generated after topology

[João Henriques]

To renumber a gro file:

gmx editconf -resnr

OR

Script it, I'm sure there's a one liner for that in awk (even in Python
that shouldn't take more than 10 lines of code).

/J

On Mon, Jul 3, 2017 at 11:37 AM, Khadija Amine  wrote:

> Hi,
>
> I have already converted the .gro file to .pdb file and I'm not able
> to see the two separated chains.
>
>
> Khadija
>
>
>
>
> *Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
> Phone: 9584
> --
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Re: [gmx-users] use INTERFACE Force Field

[João Henriques]

Ok, I did a bit of reading and it may be usable in GROMACS as is. However
that doesn't mean that it will be easy to build the topology, as pdb2gmx
may not know how to read/work with it. At least the potential energy
function is compatible with GROMACS, so that's good news.

/J

On Wed, Jun 28, 2017 at 4:13 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> If only it was that straightforward. I am not familiar with this INTERFACE
> ff, but this is not just about format and layout. There's much more at
> stake. However, the team behind it appears to be planning to port it soon:
>
> "Developments in progress include a graphical user interface to construct
> realistic surface models (composition, facet, protonation state) per
> mouse-click and to generate automatically simulation input for
> inorganic-(bio)organic systems that is compatible with major molecular
> dynamics programs (LAMMPS, GROMACS, NAMD, others). Extensions of the force
> field and surface models for graphitic structures, bcc/hcp metals, alloys,
> organic semiconductors, and other compounds are under way."
>
> João
>
> On Wed, Jun 28, 2017 at 3:56 PM, Vytautas Rakeviius <
> vytautas1...@yahoo.com> wrote:
>
>> Hello,
>> Possible bot not easy.Look into Gromacs folder share/top/ all force
>> fields sit there as text files your will have to make ITERFACE text files
>> in same format and layout.What you download as ITERFACE force field are
>> also text files with parameters, but layout is for different programs.
>>
>>
>> On Wednesday, June 28, 2017 4:05 PM, Мижээ Батсайхан <
>> b.mijidd...@gmail.com> wrote:
>>
>>
>>  Dear gmx users,
>>
>> I would like to use gromacs 5.1v with INTERFACE force field. Please, any
>> advice and suggestions, thank you.
>>
>> Best regards,
>> Miji
>> --
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Re: [gmx-users] use INTERFACE Force Field

[João Henriques]

If only it was that straightforward. I am not familiar with this INTERFACE
ff, but this is not just about format and layout. There's much more at
stake. However, the team behind it appears to be planning to port it soon:

"Developments in progress include a graphical user interface to construct
realistic surface models (composition, facet, protonation state) per
mouse-click and to generate automatically simulation input for
inorganic-(bio)organic systems that is compatible with major molecular
dynamics programs (LAMMPS, GROMACS, NAMD, others). Extensions of the force
field and surface models for graphitic structures, bcc/hcp metals, alloys,
organic semiconductors, and other compounds are under way."

João

On Wed, Jun 28, 2017 at 3:56 PM, Vytautas Rakeviius 
wrote:

> Hello,
> Possible bot not easy.Look into Gromacs folder share/top/ all force fields
> sit there as text files your will have to make ITERFACE text files in same
> format and layout.What you download as ITERFACE force field are also text
> files with parameters, but layout is for different programs.
>
>
> On Wednesday, June 28, 2017 4:05 PM, Мижээ Батсайхан <
> b.mijidd...@gmail.com> wrote:
>
>
>  Dear gmx users,
>
> I would like to use gromacs 5.1v with INTERFACE force field. Please, any
> advice and suggestions, thank you.
>
> Best regards,
> Miji
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Re: [gmx-users] DNA splitting in simulations

[João Henriques]

Hi!

Your mdp file doesn't tell the engine to apply the restraints during the
simulation... You need to specify:
define = -DPOSRES

Also, didn't Justin already warn you about using separate temperature
couplings for every component of your system?

Please check the "What Not To Do" section under:
http://www.gromacs.org/Documentation/Terminology/Thermostats

Best regards,
João

On Tue, Jun 27, 2017 at 11:22 AM, Sergio Manzetti <
sergio.manze...@fjordforsk.no> wrote:

> Hi, I Have run a DNA piece in a box of 7 7 7 , with NaCl ions
> neutralizing, as discussed earlier. The simulation went fine without any
> errors, however it turns out the DNA strands separate. The position
> restraints made by pdb2gmx using the AMBERDB ISTN ff are not working ?
>
> This is the posres file:
> In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
>
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000 1000 1000
> 3 1 1000 1000 1000
> 6 1 1000 1000 1000
> 8 1 1000 1000 1000
> 9 1 1000 1000 1000
> 11 1 1000 1000 1000
> 12 1 1000 1000 1000
> 14 1 1000 1000 1000
> 15 1 1000 1.
>
>
> and here is the simulation mdp.
>
>
>
>
> itle = DNA in water stabilization
> cpp = /lib/cpp
> include = -I../top
> define =
> integrator = md
> dt = 0.002
> nsteps = 500
> nstxout = 5000
> nstvout = 5000
> nstlog = 5000
> nstenergy = 300
> nstxout-compressed = 300
> compressed-x-grps = DNA SOL NA CL
> energygrps = DNA SOL NA CL
> nstlist = 20
> ns-type = grid
> rlist = 0.8
> coulombtype = PME
> rcoulomb = 0.8
> rvdw = 0.8
> tcoupl = V-Rescale
> tc-grps = SOL DNA NA CL
> tau-t = 0.1 0.1 0.1 0.1
>
>
>
> Note that GMX gromp wanted 4 groups at tc_grps and tau_t, otherwise it
> wouldn't proceed.
>
>
> Thanks!
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
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> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
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Re: [gmx-users] MD simulation at different pH

[João Henriques]

Hi!

You technically can't perform constant-pH simulations with a regular,
straight out of the box GROMACS distribution. You can change the residue
protonation states to mimic the "pH" you're interested in simulating, but
keep in mind that these will be fixed during the entire simulation, i.e.
there are no (de)protonation events.

For actual constant-pH methods start by reading:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

There are other MD simulation packages natively distributed with the
ability to perform constant-pH simulations (e.g. AMBER).

Best regards,
João


On Mon, Jun 26, 2017 at 3:14 AM, Anand Balupuri <
anandbalupuri.ni...@gmail.com> wrote:

> Dear Gromacs users,
>
> I want to perform MD simulations at different pH using Gromacs 5.0. How can
> I carry out such simulations? Any suggestions?
>
> Many thanks,
> Anand
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Re: [gmx-users] Difference between Err. Est. And RMSD

[João Henriques]

​Hi,

It is stated in the program's description (gmx energy -h):

"An error estimate of the average is given based on a block averages over 5
blocks using the full-precision averages. The error estimate can be
performed over multiple block lengths with the options -nbmin and -nbmax.
Note that in most cases the energy files contains averages over all MD
steps, or over many more points
than the number of frames in energy file. This makes the gmx energy
statistics output more accurate than the .xvg output."​

Which one you should use? That can lead to a long discussion, so I'll leave
it to the "real" experts :)

Best regards,
João


On Tue, Jun 20, 2017 at 1:44 PM, jay patil  wrote:

> Hi all,
> When we get averages from energy file using gmx energy -f *.edr
> Output shows Average Err.Est RMSD Tot-Drift.
> Which one among Err.Est or RMSD should I use to show error bars in the
> plot.
> By definition I know RMSD, what is formula for Err.Est.
> Please help.
>
> Thanks
>
> Yogesh
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Re: [gmx-users] hydrogen bond analysis

[João Henriques]

Dear Imrul,

I believe the information you seek is right there in your xvg file header:

@xaxis  label "Time (ns)"
@yaxis  label "Number"

...

@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"

First column is always time (x-axis). All other columns are y-axes for
different properties (in this case you two, s0 and s1). s0 is clearly
stated as being hydrogen bonds and s1 as pairs within 0.35 nm.

Best regards,
João

On Mon, Jun 19, 2017 at 6:25 AM, Md. Imrul Reza Shishir <
imrul.reza.shis...@gmail.com> wrote:

> Dear all
> For hydrogen bond analysis, we generate *.xvg file for -num tag in gmx
> hbond command.  My inquiry is in the xvg file there are three column
> output. First column is time. Which one is hydrogen bond number?
> If number 2 column is hydrogen bond number in every frame than what is
> number 3 column.
> ""
> @title "Hydrogen Bonds"
> @xaxis  label "Time (ns)"
> @yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>  0   7  11
>  0.001   8  10
>  0.002   7  11
>  0.003   6  12
>  0.004   7  11
> ​""
> Thank you very much in advanced.
> ​
> ​Best Regards.​
>
> --
> *Md Imrul Reza Shishir*
> Master Student
> *Inha University*
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Re: [gmx-users] Remove all but N closest water molecules from protein

[João Henriques]

Thanks for the clarification.

João

On Thu, Jun 8, 2017 at 11:58 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> No. gmx select will write index groups that could implement a dynamic
> selection, but trjconv can't do anything sensible with it. You'd have to
> split the trajectory into a file per frame and match the index group to the
> file to get the selection into a new file. Even if trjconv was smart
> enough, you'd also need to use a trajectory format and downstream tools
> that were about to be flexible about the number of atoms (which is
> typically not the case)... In principle, our TNG format is able to be
> flexible, but there's a lot of infrastructure work if people would actually
> write such files and expect to read them and have everything work well.
> Better to work on tools that can use the dynamic selection without needing
> to serialize and de-serialize files (and the new GROMACS analysis framework
> has such support, but we don't have much funding for implementing / porting
> tools to it).
>
> Mark
>
> On Thu, Jun 8, 2017 at 10:48 AM João Henriques <
> joao.m.a.henriq...@gmail.com>
> wrote:
>
> > Hi Mark,
> >
> > Does your solution output variable numbers of water molecules per frame?
> > That is exactly what I've been wanting to do for a while, but with my
> > solution it becomes very difficult to do so and I usually end up using a
> > fixed number of closest waters for all frames.
> >
> > João
> >
> >
> >
> > On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Or gmx select to make an index group for the nearest waters, and gmx
> > > trjconv to make the subset with the index group.
> > >
> > > Mark
> > >
> > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques <
> > > joao.m.a.henriq...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > trjorder can reorder the water molecules in each frame according to
> > their
> > > > distance to the protein. Then you either manually prune the gro
> file(s)
> > > or
> > > > use an index file to get rid of the extra stuff. I don't know of any
> > > native
> > > > tool that does all of this in one step but I may be outdated
> regarding
> > > new
> > > > stuff on gmx 2016.
> > > >
> > > > Cheers,
> > > > João
> > > >
> > > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" <borregu...@gmail.com>
> > wrote:
> > > >
> > > > Dear Gromacs users,
> > > >
> > > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will
> > allow
> > > > me to create a new *.gro file containing the protein and the N
> closest
> > > > water molecules to the protein
> > > > ​, starting from a system of a solvated protein​
> > > > ?
> > > >
> > > > Best,
> > > > Jose Borreguero
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> or
> > > send
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Re: [gmx-users] Remove all but N closest water molecules from protein

[João Henriques]

Hi Mark,

Does your solution output variable numbers of water molecules per frame?
That is exactly what I've been wanting to do for a while, but with my
solution it becomes very difficult to do so and I usually end up using a
fixed number of closest waters for all frames.

João



On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Or gmx select to make an index group for the nearest waters, and gmx
> trjconv to make the subset with the index group.
>
> Mark
>
> On Thu, Jun 8, 2017 at 9:05 AM João Henriques <
> joao.m.a.henriq...@gmail.com>
> wrote:
>
> > Hi,
> >
> > trjorder can reorder the water molecules in each frame according to their
> > distance to the protein. Then you either manually prune the gro file(s)
> or
> > use an index file to get rid of the extra stuff. I don't know of any
> native
> > tool that does all of this in one step but I may be outdated regarding
> new
> > stuff on gmx 2016.
> >
> > Cheers,
> > João
> >
> > On Jun 8, 2017 2:49 AM, "Jose Borreguero" <borregu...@gmail.com> wrote:
> >
> > Dear Gromacs users,
> >
> > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
> > me to create a new *.gro file containing the protein and the N closest
> > water molecules to the protein
> > ​, starting from a system of a solvated protein​
> > ?
> >
> > Best,
> > Jose Borreguero
> > --
> > 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.
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Re: [gmx-users] Remove all but N closest water molecules from protein

[João Henriques]

Hi,

trjorder can reorder the water molecules in each frame according to their
distance to the protein. Then you either manually prune the gro file(s) or
use an index file to get rid of the extra stuff. I don't know of any native
tool that does all of this in one step but I may be outdated regarding new
stuff on gmx 2016.

Cheers,
João

On Jun 8, 2017 2:49 AM, "Jose Borreguero"  wrote:

Dear Gromacs users,

I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
me to create a new *.gro file containing the protein and the N closest
water molecules to the protein
​, starting from a system of a solvated protein​
?

Best,
Jose Borreguero
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

[João Henriques]

Just one more thing. If you're following Justin's tutorial, I guess you're
using lysozyme. This protein will not deviate very much from it's crystal
structure at 27ºC, let alone at -40ºC (*in the context of a molecular
dynamics simulation**). I understand that it may be possible to
experimentally unfold this protein reversibly using low temperature and
high pressure, but this may be unfeasible to perform using a regular
protein force field and water model. It will not behave as you expect.

* I should add that this is a very stable protein and the disulfide bonds
(which cannot be broken during the simulation) make it almost impossible to
unfold it completely at any temperature using molecular dynamics.

/J



On Wed, Jun 7, 2017 at 7:15 PM, João Henriques <joao.m.a.henriq...@gmail.com
> wrote:

> ​Higher complexity water models such as TIP5P and so on are able to better
> reproduce bulk water properties (please check the paper I linked in my
> earlier email). However, these models require more computational effort
> (due to the increased number of interactions) and may not work well in
> conjunction with a protein (many protein force fields were developed to be
> used with specific water models)​. As Justin said, none of them gets
> everything right.
>
> /J
>
> On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote:
>
>> Dear Justin,
>> Thank you very much. I will try the possible water models.
>>
>>
>> Do you know if there are water models to resemble frozen state?
>>
>>
>> Yours sincerely
>> Cheng
>>
>>
>>
>>
>> -- Original --
>> From:  "ZHANG Cheng";<272699...@qq.com>;
>> Date:  Thu, Jun 8, 2017 00:50 AM
>> To:  "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"> s.org_gmx-us...@maillist.sys.kth.se>;
>>
>> Subject:  Re: Simulate protein at subzero condition in aqueous buffer
>>
>>
>>
>> Dear Joao,
>> Thank you for your help and the paper link.
>>
>>
>> I was following Justin's tutorial
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/lysozyme/03_solvate.html
>> On that page, it says "spc216.gro as the solvent configuration for SPC,
>> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water)
>> after the solvation step. So I assume "spc216.gro" refer to all the
>> three-point water models?
>>
>>
>> I am trying to see if my protein will be denatured in cold condition.
>>
>>
>> Yours sincerely
>> Cheng
>>
>>
>> -- Original --
>> From:  "ZHANG Cheng";<272699...@qq.com>;
>> Date:  Wed, Jun 7, 2017 10:01 PM
>> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
>> Cc:  "ZHANG Cheng"<272699...@qq.com>;
>> Subject:  Simulate protein at subzero condition in aqueous buffer
>>
>>
>>
>> Dear Gromacs,
>> I would like to simulate the protein at subzero condition in aqueous
>> buffer, to see if it becomes more stable than the elevated temperature
>> (e.g. 65 C). Can I ask what is the valid temperature range for water
>> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
>> system as liquid state instead of frozen state? Thank you.
>>
>>
>> Yours sincerely
>> Cheng
>> --
>> 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.
>>
>
>
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

[João Henriques]

​Higher complexity water models such as TIP5P and so on are able to better
reproduce bulk water properties (please check the paper I linked in my
earlier email). However, these models require more computational effort
(due to the increased number of interactions) and may not work well in
conjunction with a protein (many protein force fields were developed to be
used with specific water models)​. As Justin said, none of them gets
everything right.

/J

On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear Justin,
> Thank you very much. I will try the possible water models.
>
>
> Do you know if there are water models to resemble frozen state?
>
>
> Yours sincerely
> Cheng
>
>
>
>
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Thu, Jun 8, 2017 00:50 AM
> To:  "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users" s.org_gmx-us...@maillist.sys.kth.se>;
>
> Subject:  Re: Simulate protein at subzero condition in aqueous buffer
>
>
>
> Dear Joao,
> Thank you for your help and the paper link.
>
>
> I was following Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/lysozyme/03_solvate.html
> On that page, it says "spc216.gro as the solvent configuration for SPC,
> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water)
> after the solvation step. So I assume "spc216.gro" refer to all the
> three-point water models?
>
>
> I am trying to see if my protein will be denatured in cold condition.
>
>
> Yours sincerely
> Cheng
>
>
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Wed, Jun 7, 2017 10:01 PM
> To:  "gromacs.org_gmx-users";
> Cc:  "ZHANG Cheng"<272699...@qq.com>;
> Subject:  Simulate protein at subzero condition in aqueous buffer
>
>
>
> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous
> buffer, to see if it becomes more stable than the elevated temperature
> (e.g. 65 C). Can I ask what is the valid temperature range for water
> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
> system as liquid state instead of frozen state? Thank you.
>
>
> Yours sincerely
> Cheng
> --
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

[João Henriques]

Hello,

"spc216.gro" is not a water model, it's just a pre-equilibrated simulation
box (300 K and 1 bar) with the coordinates of 216 3-site water molecules.
SPC and TIP3P are two examples of 3-site water models. Water model
properties are well studied and tabled (e.g.
http://aip.scitation.org/doi/10.1063/1.1862245).

I am no expert in pure water simulations, but I doubt 3-site water models
can reproduce ice in a realistic way. Will the force field even hold at
that temperature? I really don't understand why you'd want to try something
like this. However, and to finish, there's one thing I can tell you for
sure: your system will be much more "stable" at -40ºC. Why, because it will
barely move from it's initial conformation, due to the very low thermal
energy. In sum, you'll spend computational time sampling almost nothing.

Best regards,
João

On Wed, Jun 7, 2017 at 4:01 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous
> buffer, to see if it becomes more stable than the elevated temperature
> (e.g. 65 C). Can I ask what is the valid temperature range for water
> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
> system as liquid state instead of frozen state? Thank you.
>
>
> Yours sincerely
> Cheng
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] mdp options in GROMACS 4.5.5

[João Henriques]

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
mean, not the integration).

/J

On Tue, Jun 6, 2017 at 5:45 PM, João Henriques <joao.m.a.henriq...@gmail.com
> wrote:

> Hi!
>
> I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> manual for that version (or the closest one).
>
> Cheers,
>
> /J
>
> On Tue, Jun 6, 2017 at 3:27 PM, <mohammad.r0...@yahoo.com> wrote:
>
>> Hi All,
>> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp -
>> used as input into grompp to generate em.tpr
>> integrator  = steep ; Algorithm (steep = steepest descent
>> minimization)
>> emtol   = 1000.0; Stop minimization when the maximum
>> force < 1000.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps  = 5 ; Maximum number of (minimization) steps
>> to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist = 1 ; Frequency to update the neighbor
>> list and long range forces
>> cutoff-scheme   = Verlet
>> ns_type = grid  ; Method to determine neighbor
>> list (simple, grid)
>> coulombtype = PME   ; Treatment of long range
>> electrostatic interactions
>> rcoulomb= 1.0   ; Short-range electrostatic
>> cut-off
>> rvdw= 1.0   ; Short-range Van der Waals
>> cut-off
>> pbc = xyz   ; Periodic Boundary Conditions
>> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error
>> which said that the cutoff-scheme is not recognized. what should I write
>> instead of "cutoff-scheme" in this version?
>> Thanks,Mohammad
>> --
>> 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] mdp options in GROMACS 4.5.5

[João Henriques]

Hi!

I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
manual for that version (or the closest one).

Cheers,

/J

On Tue, Jun 6, 2017 at 3:27 PM,  wrote:

> Hi All,
> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used
> as input into grompp to generate em.tpr
> integrator  = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol   = 1000.0; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps  = 5 ; Maximum number of (minimization) steps
> to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor
> list and long range forces
> cutoff-scheme   = Verlet
> ns_type = grid  ; Method to determine neighbor
> list (simple, grid)
> coulombtype = PME   ; Treatment of long range
> electrostatic interactions
> rcoulomb= 1.0   ; Short-range electrostatic cut-off
> rvdw= 1.0   ; Short-range Van der Waals cut-off
> pbc = xyz   ; Periodic Boundary Conditions
> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error
> which said that the cutoff-scheme is not recognized. what should I write
> instead of "cutoff-scheme" in this version?
> Thanks,Mohammad
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

[João Henriques]

You haven't adjusted the temperature on the production mdp file, it's still
300 K.

J

On Mon, May 22, 2017 at 12:37 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear Gromacs,
> I am performing 370 K MD based on Justin's tutorial.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/lysozyme/index.html
>
>
> After "Step Five: Energy Minimization", I need to do NVT, NPT and a
> production run.
>
>
> I think I need to change 300 K to 370 K in three mdp files. Specifically,
>
>
> 1) In the NVT:
> ref_t = 370  370   ; reference temperature, one for each group, in
> K
> gen_temp = 370 ; temperature for Maxwell distribution
>
>
>
> 2)  In the NPT:
> ref_t = 370  370; reference temperature, one for each group, in K
>
>
> 3) In the production run:
> ref_t   = 300 300   ; reference temperature, one for
> each group, in K
>
>
> Can I ask if these are the adjustments I need to do, and if there are
> something else I need? Thank you.
>
>
> Yours sincerely
> Cheng
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Re: [gmx-users] HPC resources in Europe (preferably Northern/Central Europe)

[João Henriques]

Thank you very much Stéphane, I will certainly investigate this possibility.

Best regards,
João

On Mon, May 15, 2017 at 5:12 PM, ABEL Stephane  wrote:

> Hello,
>
> You could write a proposal to have access to the supercomputers of the
> PRACE consortium |1]. The access to the machines is free,
>
> [1] http://www.prace-ri.eu/
>
> Stéphane
>
>
> --
>
> Message: 3
> Date: Mon, 15 May 2017 14:45:00 +0200
> From: Jo?o Henriques 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] HPC resources in Europe (preferably
> Northern/CentralEurope)
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear users and developers,
>
> Our research group is having trouble finding enough computational resources
> to run our GROMACS simulations and it was decided that I would be in charge
> of finding new alternatives. I know this topic is not 100% GROMACS related
> in a strict sense, but I've seen threads about similar topics in the past
> and thought it would be a good idea to give it a shot, since there are
> many, many researchers and PIs who read/participate in this list.
>
> We have access to a couple of "supercomputers" in our area, but due to
> heavy booking and some other technical issues, several postdocs and
> students are struggling to get their simulations performed within in a
> reasonable amount of time. Does anyone know of any HPC clusters within the
> aforementioned geographic region which we could apply for/rent/buy computer
> time?
>
> Any input would be greatly appreciated.
>
> Thank you,
> Best regards,
> Jo?o
> --
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[gmx-users] HPC resources in Europe (preferably Northern/Central Europe)

[João Henriques]

Dear users and developers,

Our research group is having trouble finding enough computational resources
to run our GROMACS simulations and it was decided that I would be in charge
of finding new alternatives. I know this topic is not 100% GROMACS related
in a strict sense, but I've seen threads about similar topics in the past
and thought it would be a good idea to give it a shot, since there are
many, many researchers and PIs who read/participate in this list.

We have access to a couple of "supercomputers" in our area, but due to
heavy booking and some other technical issues, several postdocs and
students are struggling to get their simulations performed within in a
reasonable amount of time. Does anyone know of any HPC clusters within the
aforementioned geographic region which we could apply for/rent/buy computer
time?

Any input would be greatly appreciated.

Thank you,
Best regards,
João
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Re: [gmx-users] MD at different pH

[João Henriques]

P.S.: By "fully integrated" I meant that their modifications to Gromacs
were never submitted/added to the main public distribution. Their method is
obviously integrated with Gromacs, otherwise it wouldn't run, so it was a
poor choice of words. Plus it requires third-party software for the
Poisson-Boltzmann/Monte Carlo steps.

On Thu, May 4, 2017 at 3:02 PM, João Henriques <joao.m.a.henriq...@gmail.com
> wrote:

> Technically, Helmut Grubmüller's group is not the only performing
> constant-pH MD using Gromacs. António Baptista and Miguel Machuqueiro's
> groups in Portugal have done it with explicit solvent since 2002:
>
> http://aip.scitation.org/doi/abs/10.1063/1.1497164
>
> It is not fully integrated in Gromacs, making it difficult to use for
> someone outside the group, but I thought their names had to be mentioned
> given their extensive contribution to this field since its early days.
>
> /J
>
> On Thu, May 4, 2017 at 2:44 PM, Smith, Micholas D. <smit...@ornl.gov>
> wrote:
>
>> Although this is the gromacs mailing list, it should be mentioned that
>> "constant" pH simulations do exist...you just have to use a different MD
>> simulation packages (such as Amber or CHARMM) to allow protonation states
>> to change on the fly. See the following:
>>
>> http://pubs.acs.org/doi/abs/10.1021/ct2006314
>>
>> https://link.springer.com/article/10.1007/s00894-012-1680-0
>>
>> https://www.nature.com/articles/srep22523
>>
>> https://www.ncbi.nlm.nih.gov/pubmed/16878971?dopt=Abstract=npg
>>
>> https://www.ncbi.nlm.nih.gov/pubmed/21687785?dopt=Abstract=npg
>> (Ok So I was wrong, you can do it in gromacs, but you have to hack at the
>> lamba-dynamics stuff)
>>
>>
>> https://www.ncbi.nlm.nih.gov/pubmed/22694266?dopt=Abstract=npg
>>
>>
>> In general; however, Justin is right. It is much easier, and efficient to
>> just assign the protonation states at the onset and keep them fixed so that
>> you have a "fixed-pH"; however, if the sites are known to transistion from
>> protontated to deprotonated frequently in your solvent, than a  CpHMD
>> simulation can be used.
>>
>> Good Luck!
>>
>> ===
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
>> Lemkul <jalem...@vt.edu>
>> Sent: Thursday, May 04, 2017 8:29 AM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] MD at different pH
>>
>> On 5/4/17 1:02 AM, Anu George wrote:
>> > Through the simulation, I am trying to find out if the binding free
>> energy of the drug-protein complex is strong enough for the drug to be a
>> good inhibitor of the protein.
>> > so, does the pH of the simulation matter as in reality the active
>> monomer exists in acidic pH conditions?
>>
>> You have to model whatever the realistic conditions are, whether that's
>> in vivo
>> or in vitro.  This is part of good experimental design.  If your target
>> exists
>> in a mildly acidic microenvironment, that's what you should model.
>> Binding
>> thermodynamics do depend on protonation states (in some cases, quite
>> strongly)
>> so if you model one state and try to relate it to data that exist in
>> another,
>> you're comparing apples to oranges and you've wasted a lot of time and
>> resources.
>>
>> Also, dispel with the notion of "pH of the simulation" because such a
>> thing does
>> not exist.  You'll be modeling a constant protonation state and there are
>> no
>> dissociable protons floating around.  You're going to do a simulation
>> using the
>> dominant protonation state of a given set of molecules at a corresponding
>> experimental pH.
>>
>> -Justin
>>
>> > Thanks
>> > Anu George
>> >
>> > - Original Message -
>> > From: "Justin Lemkul" <jalem...@vt.edu>
>> > To: gmx-us...@gromacs.org
>> > Sent: Wednesday, May 3, 2017 8:15:33 PM
>> > Subject: Re: [gmx-users] MD at different pH
>> >
>> >
>> >
>> > On 5/3/17 10:04 AM, Anu George wrote:
>> >> Thanks Justin for the information.
>> >> But I had a further question regarding the simulation-if the active
>> monomer exists only in the acidic

Re: [gmx-users] MD at different pH

[João Henriques]

Technically, Helmut Grubmüller's group is not the only performing
constant-pH MD using Gromacs. António Baptista and Miguel Machuqueiro's
groups in Portugal have done it with explicit solvent since 2002:

http://aip.scitation.org/doi/abs/10.1063/1.1497164

It is not fully integrated in Gromacs, making it difficult to use for
someone outside the group, but I thought their names had to be mentioned
given their extensive contribution to this field since its early days.

/J

On Thu, May 4, 2017 at 2:44 PM, Smith, Micholas D.  wrote:

> Although this is the gromacs mailing list, it should be mentioned that
> "constant" pH simulations do exist...you just have to use a different MD
> simulation packages (such as Amber or CHARMM) to allow protonation states
> to change on the fly. See the following:
>
> http://pubs.acs.org/doi/abs/10.1021/ct2006314
>
> https://link.springer.com/article/10.1007/s00894-012-1680-0
>
> https://www.nature.com/articles/srep22523
>
> https://www.ncbi.nlm.nih.gov/pubmed/16878971?dopt=Abstract=npg
>
> https://www.ncbi.nlm.nih.gov/pubmed/21687785?dopt=Abstract=npg
> (Ok So I was wrong, you can do it in gromacs, but you have to hack at the
> lamba-dynamics stuff)
>
>
> https://www.ncbi.nlm.nih.gov/pubmed/22694266?dopt=Abstract=npg
>
>
> In general; however, Justin is right. It is much easier, and efficient to
> just assign the protonation states at the onset and keep them fixed so that
> you have a "fixed-pH"; however, if the sites are known to transistion from
> protontated to deprotonated frequently in your solvent, than a  CpHMD
> simulation can be used.
>
> Good Luck!
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: Thursday, May 04, 2017 8:29 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] MD at different pH
>
> On 5/4/17 1:02 AM, Anu George wrote:
> > Through the simulation, I am trying to find out if the binding free
> energy of the drug-protein complex is strong enough for the drug to be a
> good inhibitor of the protein.
> > so, does the pH of the simulation matter as in reality the active
> monomer exists in acidic pH conditions?
>
> You have to model whatever the realistic conditions are, whether that's in
> vivo
> or in vitro.  This is part of good experimental design.  If your target
> exists
> in a mildly acidic microenvironment, that's what you should model.  Binding
> thermodynamics do depend on protonation states (in some cases, quite
> strongly)
> so if you model one state and try to relate it to data that exist in
> another,
> you're comparing apples to oranges and you've wasted a lot of time and
> resources.
>
> Also, dispel with the notion of "pH of the simulation" because such a
> thing does
> not exist.  You'll be modeling a constant protonation state and there are
> no
> dissociable protons floating around.  You're going to do a simulation
> using the
> dominant protonation state of a given set of molecules at a corresponding
> experimental pH.
>
> -Justin
>
> > Thanks
> > Anu George
> >
> > - Original Message -
> > From: "Justin Lemkul" 
> > To: gmx-us...@gromacs.org
> > Sent: Wednesday, May 3, 2017 8:15:33 PM
> > Subject: Re: [gmx-users] MD at different pH
> >
> >
> >
> > On 5/3/17 10:04 AM, Anu George wrote:
> >> Thanks Justin for the information.
> >> But I had a further question regarding the simulation-if the active
> monomer exists only in the acidic pH, then will carrying out a simulation
> of the monomer with a drug  at neutral pH help?
> >
> > That depends on what your scientific goals/questions are and what you are
> > actually trying to model.
> >
> > -Justin
> >
> >> regards,
> >> Anu George
> >>
> >> - Original Message -
> >> From: "Justin Lemkul" 
> >> To: gmx-us...@gromacs.org
> >> Sent: Wednesday, May 3, 2017 5:37:33 PM
> >> Subject: Re: [gmx-users] MD at different pH
> >>
> >>
> >>
> >> On 5/2/17 11:31 PM, Anu George wrote:
> >>> Dear Gromacs users,
> >>> I am working on a tetramer(human beta-2 tryptase) protein which exist
> as an active monomer at an acidic pH of about 6..If I have to do a
> molecular dynamic simulation of the monomer with a small molecule,  should
> the simulation be carried out  at this pH ? what are the steps I should
> follow?
> >>
> >> Calculate the pKa values for titratable residues and select their
> dominant
> >> protonation states at that pH when running pdb2gmx.
> >>
> >> -Justin
> >>
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility