[gmx-users] addition of an isopeptide bond and its simulation

[Raag Saluja]

Hi!

 I need to study the effect of post-translational modifications on the
biophysical properties of my protein. This involves the addition of an
isopeptide bond to the primary chain of the C-terminal tail.

How may I add this isopeptide bond? And then which force field can I use to
simulate it?

Looking forward to your kind help!
Regards,
Raag
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[gmx-users] Hbond residence time

[Marcelo Depólo]

Hi all!


I have been looking into the autocorrelation function outputs of 'gmx
hbond' in order to calculate the residence time for my water hbond to a
specific heteroatom. It turns out that I couldn't find any detailed
explanation about each 'type' outputted. In my case:

Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 3.384  0.296   1.506   0.0290557
Backward   -0.183 -5.477-666.000
One-way 8.291  0.121  -0.716
Integral   0.802  1.247   5.075
Relaxation  0.767  1.303   5.185

Does anyone have a suggestion of what each of these types mean?

Thanks in advance!
--
Marcelo Depólo Polêto
DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770
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[gmx-users] Most suitable intervals of temperature in REMD

[Мижээ Батсайхан]

Dear gmx users,

Do you have a suggestions and discussions about most suitable temperature
intervals for REMD simulations of the peptides?

Best regards,
Mijee
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[gmx-users] User Defined Potentials

[Ommair Ishaque]

Hi,

I am Phd physics phd student at University of Delaware. I am using GROMACS
for calculation of solvation energy of argon or methane in water. But Our
water model has additional interaction terms other than already define in
GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*

And one of my senior colleagues was telling me in past, GROMACS had no
quaternion algorithm for rigid molecules. It handles rigid molecules using
SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
we will be able to use it for our water model (CC-5spol) which has at least
25 sites. *If there is now a means of truly propagating the motion of rigid
molecules without SHAKE/RATTLE/LINCS, this will be great.*

I am looking forward for your positive reply. Thanks

Ommair Ishaque
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Re: [gmx-users] HBond for F and S (Justin Lemkul)

[Marcelo Depólo]

Thanks, Justin!


It worked just fine.

I guess using a flag to include different atomtypes into the analyses would
be a nice feature for next GROMACS versions.

Cheers!
--
Marcelo Depólo Polêto
DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770
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[gmx-users] How to orientationally restrain a molecule?

[Michael Shirts]

I'm interested carrying out a long simulation of a thin, narrow protein.
Clearly, the volume-minimizing way to do this would be to put it in a thin,
narrow box of solvent.  The issue with this is that it could rotate around
and interact with itself. if the orientation of the protein changed
relative to the orientation of the box.

Is there a good way to restrain the orientation in GROMACS currently?  I
looked a little at the orientation restraint for NMR, but it didn't seem
like that would really work well (or at least, it was not obvious it would
work well), for restraining the overall orientation.  Am I missing
something?

Any other thoughts, suggestions for doing this?  Has anyone else done this?

Thanks!
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Re: [gmx-users] HBond for F and S

[Justin Lemkul]

On 4/24/17 3:15 PM, Marcelo Depólo wrote:

Hi,


Can gmx hbond also calculates hbonds between non-canonical atoms like S or
F as well? If so, how can I do it?



Without changing the code, the only way to do it is to rename the atoms in the 
topology as some type of oxygen, create a new .tpr file, and use that .tpr file 
for the hydrogen bond analysis.


-Justin

--
==

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

==
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[gmx-users] HBond for F and S

[Marcelo Depólo]

Hi,


Can gmx hbond also calculates hbonds between non-canonical atoms like S or
F as well? If so, how can I do it?

Cheers!
--
Marcelo
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Re: [gmx-users] cant load trajectory, low memory

[Justin Lemkul]

On 4/24/17 12:56 PM, abhisek Mondal wrote:

Hello,

I'm using the configurations generated by pulling run to re-box > resolvate

ion addition > EM > npt_umbrella(10ns) and forward.


So, please clarify me something. Am I following correct path ? Should I
have given a npt equilibration step prior to npt_umbrella step ?



Yes, as Mark said, you're essentially building all new simulation systems. 
Since this is part of an umbrella sampling series, be sure you're getting the 
same (or at least, very similar) number of water molecules in each box.


-Justin


Thank you.

On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham 
wrote:


Hi,

I already answered that. You're effectively starting again, so do that.

Mark

On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal 
wrote:


Ok, I got it this time.
But what kind of equilibration I'm to perform on these stripped

structures.

Should I perform normal NPT equilibration as done before generating
configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c

conf0.gro

-p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
page) and followed by mdrun step ?




On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar <

tasneemkausa...@gmail.com



wrote:


Create index group that have both protein and ACO. gmx make_ndx will

serve

this task.
Then create a pdb file file from gmx trjconv
Or you can choose system as output and delete ions and solvent from any
editor.



On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal <

abhisek.m...@gmail.com>

wrote:


Hello,

Alright. I have tried this but I'm stuck in the following scenario.
I'm using trjconv for getting pdb file of the protein-ligand complex

(used

for umbrella sampling).
trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr

This is giving me the following prompt:
Select group for output
Group 0 ( System) has 27051263 elements
Group 1 (Protein) has  1588 elements
Group 2 (  Protein-H) has  1245 elements
Group 3 (C-alpha) has   158 elements
Group 4 (   Backbone) has   474 elements
Group 5 (  MainChain) has   633 elements
Group 6 (   MainChain+Cb) has   784 elements
Group 7 (MainChain+H) has   785 elements
Group 8 (  SideChain) has   803 elements
Group 9 (SideChain-H) has   612 elements
Group10 (Prot-Masses) has  1588 elements
Group11 (non-Protein) has 27049675 elements
Group12 (  Other) has59 elements
Group13 (ACO) has59 elements
Group14 ( NA) has 16615 elements
Group15 ( CL) has 16615 elements
Group16 (  Water) has 27016386 elements
Group17 (SOL) has 27016386 elements
Group18 (  non-Water) has 34877 elements
Group19 (Ion) has 33230 elements
Group20 (ACO) has59 elements
Group21 ( NA) has 16615 elements
Group22 ( CL) has 16615 elements
Group23 ( Water_and_ions) has 27049616 elements
Group24 (

Now how can I be able to get both Protein+ACO as a pdb file ?
If I could get Protein+ACO, then I could strip the box size for

further

umbrella sampling procedure.

However, is it possible to go with the following way:
editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic

Please suggest me a way.

Thank you.

On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham <

mark.j.abra...@gmail.com>

wrote:


Hi,

Take a configuration of interest, strip the solvent, put it in a

box

you

think is good, and re-equilibrate just like you did before you

started.


Mark

On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <

abhisek.m...@gmail.com



wrote:


Hi,

Yes, I did when I started the simulation. The box size I used to

start

the

simulation was very big(I was dealing with an unknown sample).

After

successfully generating the configurations I realized that

further

work

could move faster if I could trim the box size little bit now.
So is there any way now to reduce the box size and proceed with

relevant

configurations towards PMF generation ?
Please suggest me a way here.

Thank you.

On Apr 24, 2017 12:22 AM, "Mark Abraham" <

mark.j.abra...@gmail.com



wrote:



Hi,

You get to choose the box size eg with editconf when you set up

your

simulation. It's not pre-defined ;-)

Mark

On Sun, 23 Apr 2017 20:28 abhisek Mondal <

abhisek.m...@gmail.com



wrote:



Hello,

Another thing I wanted to ask.
After generating configurations I found out that the

predefined

box

size

(used to reach so far) is excessively high.
Is it possible to trim the box size to perform further mdrun

during

umbrella sampling?

Please suggest me a way, it is taking very long time with

current

box

size.


Thank you.



On Apr 23, 2017 10:02 PM, "Mark Abraham" <

mark.j.abra...@gmail.com



wrote:



Hi,

You can only load a trajectory with fewer frames. Either

don't

write

so

many, or filter 

Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

Hello,

I'm using the configurations generated by pulling run to re-box > resolvate
> ion addition > EM > npt_umbrella(10ns) and forward.

So, please clarify me something. Am I following correct path ? Should I
have given a npt equilibration step prior to npt_umbrella step ?

Thank you.

On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham 
wrote:

> Hi,
>
> I already answered that. You're effectively starting again, so do that.
>
> Mark
>
> On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal 
> wrote:
>
> > Ok, I got it this time.
> > But what kind of equilibration I'm to perform on these stripped
> structures.
> > Should I perform normal NPT equilibration as done before generating
> > configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c
> conf0.gro
> > -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
> > page) and followed by mdrun step ?
> >
> >
> >
> >
> > On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar <
> tasneemkausa...@gmail.com
> > >
> > wrote:
> >
> > > Create index group that have both protein and ACO. gmx make_ndx will
> > serve
> > > this task.
> > > Then create a pdb file file from gmx trjconv
> > > Or you can choose system as output and delete ions and solvent from any
> > > editor.
> > >
> > >
> > >
> > > On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal <
> abhisek.m...@gmail.com>
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > Alright. I have tried this but I'm stuck in the following scenario.
> > > > I'm using trjconv for getting pdb file of the protein-ligand complex
> > > (used
> > > > for umbrella sampling).
> > > > trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
> > > >
> > > > This is giving me the following prompt:
> > > > Select group for output
> > > > Group 0 ( System) has 27051263 elements
> > > > Group 1 (Protein) has  1588 elements
> > > > Group 2 (  Protein-H) has  1245 elements
> > > > Group 3 (C-alpha) has   158 elements
> > > > Group 4 (   Backbone) has   474 elements
> > > > Group 5 (  MainChain) has   633 elements
> > > > Group 6 (   MainChain+Cb) has   784 elements
> > > > Group 7 (MainChain+H) has   785 elements
> > > > Group 8 (  SideChain) has   803 elements
> > > > Group 9 (SideChain-H) has   612 elements
> > > > Group10 (Prot-Masses) has  1588 elements
> > > > Group11 (non-Protein) has 27049675 elements
> > > > Group12 (  Other) has59 elements
> > > > Group13 (ACO) has59 elements
> > > > Group14 ( NA) has 16615 elements
> > > > Group15 ( CL) has 16615 elements
> > > > Group16 (  Water) has 27016386 elements
> > > > Group17 (SOL) has 27016386 elements
> > > > Group18 (  non-Water) has 34877 elements
> > > > Group19 (Ion) has 33230 elements
> > > > Group20 (ACO) has59 elements
> > > > Group21 ( NA) has 16615 elements
> > > > Group22 ( CL) has 16615 elements
> > > > Group23 ( Water_and_ions) has 27049616 elements
> > > > Group24 (
> > > >
> > > > Now how can I be able to get both Protein+ACO as a pdb file ?
> > > > If I could get Protein+ACO, then I could strip the box size for
> further
> > > > umbrella sampling procedure.
> > > >
> > > > However, is it possible to go with the following way:
> > > > editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
> > > >
> > > > Please suggest me a way.
> > > >
> > > > Thank you.
> > > >
> > > > On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Take a configuration of interest, strip the solvent, put it in a
> box
> > > you
> > > > > think is good, and re-equilibrate just like you did before you
> > started.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <
> > abhisek.m...@gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Yes, I did when I started the simulation. The box size I used to
> > > start
> > > > > the
> > > > > > simulation was very big(I was dealing with an unknown sample).
> > After
> > > > > > successfully generating the configurations I realized that
> further
> > > work
> > > > > > could move faster if I could trim the box size little bit now.
> > > > > > So is there any way now to reduce the box size and proceed with
> > > > relevant
> > > > > > configurations towards PMF generation ?
> > > > > > Please suggest me a way here.
> > > > > >
> > > > > > Thank you.
> > > > > >
> > > > > > On Apr 24, 2017 12:22 AM, "Mark Abraham" <
> mark.j.abra...@gmail.com
> > >
> > > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > You get to choose the box size eg with editconf when you set up
> > > your
> > > > > > > simulation. It's not pre-defined ;-)
> > > > > > >
> 

Re: [gmx-users] Gcc

[Anshul Lahariya]

Dear Joao,

U r right, it's my fault, but the thing is that i was tried lot of thing
but not found anything perfect. That's by , i was waiting from weekend for
one answer.

Regards,
Anshul

On Mon, Apr 24, 2017 at 2:53 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Dear Mark and by extension Anshul,
>
> I did make an assumption at the bottom of my previous email, and that was
> uncalled for (despite having good intentions, but that doesn't change
> anything). I apologize for that. That, however, does not overshadow the
> fact that I provided Anshul with all the necessary information in a most
> friendly, voluntary and professional way throughout three separate emails.
>
> Best regards,
> João
>
> On Mon, Apr 24, 2017 at 11:09 AM, Mark Abraham 
> wrote:
>
> > Hi Joao, Anshul and all,
> >
> > Let's all please remember to keep the environment friendly and
> > professional.
> >
> > That means not making assumptions about other people's intentions.
> Learning
> > complex things like simulation science take time, and people often make
> > mistakes when joining new communities, particularly if it's in a language
> > with which they are not fully familiar. :-)
> >
> > That also means remembering that everybody here is volunteering their
> time
> > to help others, and asking only for some of that time when you really
> need
> > it is important if you wish to keep others motivated to help you. Look
> for
> > your own answers first!
> >
> > Please all take a moment to review the thoughts at
> > http://www.gromacs.org/Support/Mailing_Lists (or suggest improvements!)
> >
> > Cheers,
> >
> > Mark
> >
> > On Mon, Apr 24, 2017 at 10:39 AM João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > Dear Anshul,
> > >
> > > I thought by movie you meant that you wanted to visually check the
> > > trajectory. ​For PyMOL, google search "pymol movie" produces about
> 31.000
> > > results in 0,31 seconds. The first hit is exactly what you want:
> > >
> > > https://pymolwiki.org/index.php/MovieSchool
> > >
> > > My previous email will still be valid as you'll first need to make
> PyMOL
> > > read your trajectory.
> > >
> > > - - -
> > >
> > > I know you want the exact array of commands you need to input in order
> to
> > > get a movie done, but I will not do that. I believe it is better to
> > provide
> > > the information from which you can learn on your own. It's a bit of the
> > old
> > > "give a man a fish and you feed him for a day; teach a man to fish and
> > you
> > > feed him for a lifetime" proverb. The fact you waited a full weekend
> > > instead of spending a couple of minutes searching and trying yourself
> > tells
> > > me that you're most likely just interested in the "fish", but I'll
> stick
> > to
> > > my belief that learning is better.
> > >
> > > /J
> > >
> > >
> > > On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya <
> > > anshullahariy...@gmail.com
> > > > wrote:
> > >
> > > > hello rahul,
> > > > can u tell me how to make movie??
> > > >
> > > >
> > > > On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> > > > joao.m.a.henriq...@gmail.com> wrote:
> > > >
> > > > > ​Plus, installing multiple version of the same software (e.g. gcc)
> is
> > > not
> > > > > problematic at all *when done by someone that knows what he/she is
> > > > doing*.
> > > > > Furthermore, I completely disagree with Vytautas Rakeviius final
> > > advice.
> > > > It
> > > > > wouldn't cross anyone's mind to change OS in order to use a
> different
> > > gcc
> > > > > version. That is ludicrous. I obviously don't recommend that an
> > > > > inexperienced user should start compiling stuff blindly on their
> > > machine,
> > > > > but that is just plain bad practice and impractical.
> > > > >
> > > > > But I digress, this is not really GROMACS related.
> > > > >
> > > > > A nice weekend to everyone!
> > > > > João
> > > > >
> > > > > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > > > > joao.m.a.henriq...@gmail.com> wrote:
> > > > >
> > > > > > You have (at the very least) three solutions regarding the movie:
> > > > > >
> > > > > > [1] Use gmx trjconv (see http://manual.gromacs.org/
> > > > documentation/5.1.4/
> > > > > > onlinehelp/gmx-trjconv.html) to generate a PDB file with the
> > desired
> > > > > > trajectory frames. Load and play it in PyMOL et voilà!
> > > > > >
> > > > > > [2] Install the GROMACS plugin for PyMOL, which will allow you
> > (among
> > > > > > other things) to directly read the trajectory files without
> having
> > to
> > > > > > resort to gmx trjconv (see https://pymolwiki.org/index.
> > > > > php/GROMACS_Plugin
> > > > > > ).
> > > > > >
> > > > > > [3] Use VMD which can read GROMACS trajectory output files
> straight
> > > out
> > > > > of
> > > > > > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> > > > > >
> > > > > > For details regarding gmx trjconv please read the documentation.
> It
> > > is
> > > > > > fairly trivial and only you know exactly what 

Re: [gmx-users] Gcc

[Anshul Lahariya]

Dear Joao,

U r right, it's my fault, but the thing is that i was tried lot of thing
but not found anything perfect. That's by , i was waiting from weekend for
one answer.


On Mon, Apr 24, 2017 at 2:53 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Dear Mark and by extension Anshul,
>
> I did make an assumption at the bottom of my previous email, and that was
> uncalled for (despite having good intentions, but that doesn't change
> anything). I apologize for that. That, however, does not overshadow the
> fact that I provided Anshul with all the necessary information in a most
> friendly, voluntary and professional way throughout three separate emails.
>
> Best regards,
> João
>
> On Mon, Apr 24, 2017 at 11:09 AM, Mark Abraham 
> wrote:
>
> > Hi Joao, Anshul and all,
> >
> > Let's all please remember to keep the environment friendly and
> > professional.
> >
> > That means not making assumptions about other people's intentions.
> Learning
> > complex things like simulation science take time, and people often make
> > mistakes when joining new communities, particularly if it's in a language
> > with which they are not fully familiar. :-)
> >
> > That also means remembering that everybody here is volunteering their
> time
> > to help others, and asking only for some of that time when you really
> need
> > it is important if you wish to keep others motivated to help you. Look
> for
> > your own answers first!
> >
> > Please all take a moment to review the thoughts at
> > http://www.gromacs.org/Support/Mailing_Lists (or suggest improvements!)
> >
> > Cheers,
> >
> > Mark
> >
> > On Mon, Apr 24, 2017 at 10:39 AM João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > Dear Anshul,
> > >
> > > I thought by movie you meant that you wanted to visually check the
> > > trajectory. ​For PyMOL, google search "pymol movie" produces about
> 31.000
> > > results in 0,31 seconds. The first hit is exactly what you want:
> > >
> > > https://pymolwiki.org/index.php/MovieSchool
> > >
> > > My previous email will still be valid as you'll first need to make
> PyMOL
> > > read your trajectory.
> > >
> > > - - -
> > >
> > > I know you want the exact array of commands you need to input in order
> to
> > > get a movie done, but I will not do that. I believe it is better to
> > provide
> > > the information from which you can learn on your own. It's a bit of the
> > old
> > > "give a man a fish and you feed him for a day; teach a man to fish and
> > you
> > > feed him for a lifetime" proverb. The fact you waited a full weekend
> > > instead of spending a couple of minutes searching and trying yourself
> > tells
> > > me that you're most likely just interested in the "fish", but I'll
> stick
> > to
> > > my belief that learning is better.
> > >
> > > /J
> > >
> > >
> > > On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya <
> > > anshullahariy...@gmail.com
> > > > wrote:
> > >
> > > > hello rahul,
> > > > can u tell me how to make movie??
> > > >
> > > >
> > > > On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> > > > joao.m.a.henriq...@gmail.com> wrote:
> > > >
> > > > > ​Plus, installing multiple version of the same software (e.g. gcc)
> is
> > > not
> > > > > problematic at all *when done by someone that knows what he/she is
> > > > doing*.
> > > > > Furthermore, I completely disagree with Vytautas Rakeviius final
> > > advice.
> > > > It
> > > > > wouldn't cross anyone's mind to change OS in order to use a
> different
> > > gcc
> > > > > version. That is ludicrous. I obviously don't recommend that an
> > > > > inexperienced user should start compiling stuff blindly on their
> > > machine,
> > > > > but that is just plain bad practice and impractical.
> > > > >
> > > > > But I digress, this is not really GROMACS related.
> > > > >
> > > > > A nice weekend to everyone!
> > > > > João
> > > > >
> > > > > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > > > > joao.m.a.henriq...@gmail.com> wrote:
> > > > >
> > > > > > You have (at the very least) three solutions regarding the movie:
> > > > > >
> > > > > > [1] Use gmx trjconv (see http://manual.gromacs.org/
> > > > documentation/5.1.4/
> > > > > > onlinehelp/gmx-trjconv.html) to generate a PDB file with the
> > desired
> > > > > > trajectory frames. Load and play it in PyMOL et voilà!
> > > > > >
> > > > > > [2] Install the GROMACS plugin for PyMOL, which will allow you
> > (among
> > > > > > other things) to directly read the trajectory files without
> having
> > to
> > > > > > resort to gmx trjconv (see https://pymolwiki.org/index.
> > > > > php/GROMACS_Plugin
> > > > > > ).
> > > > > >
> > > > > > [3] Use VMD which can read GROMACS trajectory output files
> straight
> > > out
> > > > > of
> > > > > > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> > > > > >
> > > > > > For details regarding gmx trjconv please read the documentation.
> It
> > > is
> > > > > > fairly trivial and only you know exactly what system you have 

Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

Hi,

I already answered that. You're effectively starting again, so do that.

Mark

On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal 
wrote:

> Ok, I got it this time.
> But what kind of equilibration I'm to perform on these stripped structures.
> Should I perform normal NPT equilibration as done before generating
> configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c conf0.gro
> -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
> page) and followed by mdrun step ?
>
>
>
>
> On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar  >
> wrote:
>
> > Create index group that have both protein and ACO. gmx make_ndx will
> serve
> > this task.
> > Then create a pdb file file from gmx trjconv
> > Or you can choose system as output and delete ions and solvent from any
> > editor.
> >
> >
> >
> > On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal 
> > wrote:
> >
> > > Hello,
> > >
> > > Alright. I have tried this but I'm stuck in the following scenario.
> > > I'm using trjconv for getting pdb file of the protein-ligand complex
> > (used
> > > for umbrella sampling).
> > > trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
> > >
> > > This is giving me the following prompt:
> > > Select group for output
> > > Group 0 ( System) has 27051263 elements
> > > Group 1 (Protein) has  1588 elements
> > > Group 2 (  Protein-H) has  1245 elements
> > > Group 3 (C-alpha) has   158 elements
> > > Group 4 (   Backbone) has   474 elements
> > > Group 5 (  MainChain) has   633 elements
> > > Group 6 (   MainChain+Cb) has   784 elements
> > > Group 7 (MainChain+H) has   785 elements
> > > Group 8 (  SideChain) has   803 elements
> > > Group 9 (SideChain-H) has   612 elements
> > > Group10 (Prot-Masses) has  1588 elements
> > > Group11 (non-Protein) has 27049675 elements
> > > Group12 (  Other) has59 elements
> > > Group13 (ACO) has59 elements
> > > Group14 ( NA) has 16615 elements
> > > Group15 ( CL) has 16615 elements
> > > Group16 (  Water) has 27016386 elements
> > > Group17 (SOL) has 27016386 elements
> > > Group18 (  non-Water) has 34877 elements
> > > Group19 (Ion) has 33230 elements
> > > Group20 (ACO) has59 elements
> > > Group21 ( NA) has 16615 elements
> > > Group22 ( CL) has 16615 elements
> > > Group23 ( Water_and_ions) has 27049616 elements
> > > Group24 (
> > >
> > > Now how can I be able to get both Protein+ACO as a pdb file ?
> > > If I could get Protein+ACO, then I could strip the box size for further
> > > umbrella sampling procedure.
> > >
> > > However, is it possible to go with the following way:
> > > editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
> > >
> > > Please suggest me a way.
> > >
> > > Thank you.
> > >
> > > On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Take a configuration of interest, strip the solvent, put it in a box
> > you
> > > > think is good, and re-equilibrate just like you did before you
> started.
> > > >
> > > > Mark
> > > >
> > > > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <
> abhisek.m...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Yes, I did when I started the simulation. The box size I used to
> > start
> > > > the
> > > > > simulation was very big(I was dealing with an unknown sample).
> After
> > > > > successfully generating the configurations I realized that further
> > work
> > > > > could move faster if I could trim the box size little bit now.
> > > > > So is there any way now to reduce the box size and proceed with
> > > relevant
> > > > > configurations towards PMF generation ?
> > > > > Please suggest me a way here.
> > > > >
> > > > > Thank you.
> > > > >
> > > > > On Apr 24, 2017 12:22 AM, "Mark Abraham"  >
> > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > You get to choose the box size eg with editconf when you set up
> > your
> > > > > > simulation. It's not pre-defined ;-)
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal  >
> > > > wrote:
> > > > > >
> > > > > > > Hello,
> > > > > > >
> > > > > > > Another thing I wanted to ask.
> > > > > > > After generating configurations I found out that the predefined
> > box
> > > > > size
> > > > > > > (used to reach so far) is excessively high.
> > > > > > > Is it possible to trim the box size to perform further mdrun
> > during
> > > > > > > umbrella sampling?
> > > > > > >
> > > > > > > Please suggest me a way, it is taking very long time with
> current
> > > box
> > > > > > size.
> > > > > > >
> > > > 

Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

Ok, I got it this time.
But what kind of equilibration I'm to perform on these stripped structures.
Should I perform normal NPT equilibration as done before generating
configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c conf0.gro
-p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
page) and followed by mdrun step ?




On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar 
wrote:

> Create index group that have both protein and ACO. gmx make_ndx will serve
> this task.
> Then create a pdb file file from gmx trjconv
> Or you can choose system as output and delete ions and solvent from any
> editor.
>
>
>
> On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal 
> wrote:
>
> > Hello,
> >
> > Alright. I have tried this but I'm stuck in the following scenario.
> > I'm using trjconv for getting pdb file of the protein-ligand complex
> (used
> > for umbrella sampling).
> > trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
> >
> > This is giving me the following prompt:
> > Select group for output
> > Group 0 ( System) has 27051263 elements
> > Group 1 (Protein) has  1588 elements
> > Group 2 (  Protein-H) has  1245 elements
> > Group 3 (C-alpha) has   158 elements
> > Group 4 (   Backbone) has   474 elements
> > Group 5 (  MainChain) has   633 elements
> > Group 6 (   MainChain+Cb) has   784 elements
> > Group 7 (MainChain+H) has   785 elements
> > Group 8 (  SideChain) has   803 elements
> > Group 9 (SideChain-H) has   612 elements
> > Group10 (Prot-Masses) has  1588 elements
> > Group11 (non-Protein) has 27049675 elements
> > Group12 (  Other) has59 elements
> > Group13 (ACO) has59 elements
> > Group14 ( NA) has 16615 elements
> > Group15 ( CL) has 16615 elements
> > Group16 (  Water) has 27016386 elements
> > Group17 (SOL) has 27016386 elements
> > Group18 (  non-Water) has 34877 elements
> > Group19 (Ion) has 33230 elements
> > Group20 (ACO) has59 elements
> > Group21 ( NA) has 16615 elements
> > Group22 ( CL) has 16615 elements
> > Group23 ( Water_and_ions) has 27049616 elements
> > Group24 (
> >
> > Now how can I be able to get both Protein+ACO as a pdb file ?
> > If I could get Protein+ACO, then I could strip the box size for further
> > umbrella sampling procedure.
> >
> > However, is it possible to go with the following way:
> > editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
> >
> > Please suggest me a way.
> >
> > Thank you.
> >
> > On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Take a configuration of interest, strip the solvent, put it in a box
> you
> > > think is good, and re-equilibrate just like you did before you started.
> > >
> > > Mark
> > >
> > > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Yes, I did when I started the simulation. The box size I used to
> start
> > > the
> > > > simulation was very big(I was dealing with an unknown sample). After
> > > > successfully generating the configurations I realized that further
> work
> > > > could move faster if I could trim the box size little bit now.
> > > > So is there any way now to reduce the box size and proceed with
> > relevant
> > > > configurations towards PMF generation ?
> > > > Please suggest me a way here.
> > > >
> > > > Thank you.
> > > >
> > > > On Apr 24, 2017 12:22 AM, "Mark Abraham" 
> > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You get to choose the box size eg with editconf when you set up
> your
> > > > > simulation. It's not pre-defined ;-)
> > > > >
> > > > > Mark
> > > > >
> > > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal 
> > > wrote:
> > > > >
> > > > > > Hello,
> > > > > >
> > > > > > Another thing I wanted to ask.
> > > > > > After generating configurations I found out that the predefined
> box
> > > > size
> > > > > > (used to reach so far) is excessively high.
> > > > > > Is it possible to trim the box size to perform further mdrun
> during
> > > > > > umbrella sampling?
> > > > > >
> > > > > > Please suggest me a way, it is taking very long time with current
> > box
> > > > > size.
> > > > > >
> > > > > > Thank you.
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham" <
> mark.j.abra...@gmail.com
> > >
> > > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > You can only load a trajectory with fewer frames. Either don't
> > > write
> > > > so
> > > > > > > many, or filter it with trjconv first.
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Sun, 23 Apr 2017 17:20 

Re: [gmx-users] cant load trajectory, low memory

[Tasneem Kausar]

If you are taking confout.gro as your starting input file, it will have all
water and ions of the previous simulation.

On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar 
wrote:

> Create index group that have both protein and ACO. gmx make_ndx will serve
> this task.
> Then create a pdb file file from gmx trjconv
> Or you can choose system as output and delete ions and solvent from any
> editor.
>
>
>
> On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal 
> wrote:
>
>> Hello,
>>
>> Alright. I have tried this but I'm stuck in the following scenario.
>> I'm using trjconv for getting pdb file of the protein-ligand complex (used
>> for umbrella sampling).
>> trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
>>
>> This is giving me the following prompt:
>> Select group for output
>> Group 0 ( System) has 27051263 elements
>> Group 1 (Protein) has  1588 elements
>> Group 2 (  Protein-H) has  1245 elements
>> Group 3 (C-alpha) has   158 elements
>> Group 4 (   Backbone) has   474 elements
>> Group 5 (  MainChain) has   633 elements
>> Group 6 (   MainChain+Cb) has   784 elements
>> Group 7 (MainChain+H) has   785 elements
>> Group 8 (  SideChain) has   803 elements
>> Group 9 (SideChain-H) has   612 elements
>> Group10 (Prot-Masses) has  1588 elements
>> Group11 (non-Protein) has 27049675 elements
>> Group12 (  Other) has59 elements
>> Group13 (ACO) has59 elements
>> Group14 ( NA) has 16615 elements
>> Group15 ( CL) has 16615 elements
>> Group16 (  Water) has 27016386 elements
>> Group17 (SOL) has 27016386 elements
>> Group18 (  non-Water) has 34877 elements
>> Group19 (Ion) has 33230 elements
>> Group20 (ACO) has59 elements
>> Group21 ( NA) has 16615 elements
>> Group22 ( CL) has 16615 elements
>> Group23 ( Water_and_ions) has 27049616 elements
>> Group24 (
>>
>> Now how can I be able to get both Protein+ACO as a pdb file ?
>> If I could get Protein+ACO, then I could strip the box size for further
>> umbrella sampling procedure.
>>
>> However, is it possible to go with the following way:
>> editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
>>
>> Please suggest me a way.
>>
>> Thank you.
>>
>> On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham 
>> wrote:
>>
>> > Hi,
>> >
>> > Take a configuration of interest, strip the solvent, put it in a box you
>> > think is good, and re-equilibrate just like you did before you started.
>> >
>> > Mark
>> >
>> > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal 
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > Yes, I did when I started the simulation. The box size I used to start
>> > the
>> > > simulation was very big(I was dealing with an unknown sample). After
>> > > successfully generating the configurations I realized that further
>> work
>> > > could move faster if I could trim the box size little bit now.
>> > > So is there any way now to reduce the box size and proceed with
>> relevant
>> > > configurations towards PMF generation ?
>> > > Please suggest me a way here.
>> > >
>> > > Thank you.
>> > >
>> > > On Apr 24, 2017 12:22 AM, "Mark Abraham" 
>> > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > You get to choose the box size eg with editconf when you set up your
>> > > > simulation. It's not pre-defined ;-)
>> > > >
>> > > > Mark
>> > > >
>> > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal 
>> > wrote:
>> > > >
>> > > > > Hello,
>> > > > >
>> > > > > Another thing I wanted to ask.
>> > > > > After generating configurations I found out that the predefined
>> box
>> > > size
>> > > > > (used to reach so far) is excessively high.
>> > > > > Is it possible to trim the box size to perform further mdrun
>> during
>> > > > > umbrella sampling?
>> > > > >
>> > > > > Please suggest me a way, it is taking very long time with current
>> box
>> > > > size.
>> > > > >
>> > > > > Thank you.
>> > > > >
>> > > > >
>> > > > >
>> > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham" <
>> mark.j.abra...@gmail.com>
>> > > > wrote:
>> > > > >
>> > > > > > Hi,
>> > > > > >
>> > > > > > You can only load a trajectory with fewer frames. Either don't
>> > write
>> > > so
>> > > > > > many, or filter it with trjconv first.
>> > > > > >
>> > > > > > Mark
>> > > > > >
>> > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal <
>> abhisek.m...@gmail.com>
>> > > > wrote:
>> > > > > >
>> > > > > > > Hi,
>> > > > > > > I'm having a problem loading trajectory file after umbrella
>> > > sampling.
>> > > > > The
>> > > > > > > file is so huge in size that the VMD finally runs out of
>> memory.
>> > > I'm
>> > > > > > > operating with 125gb of physical memory here though.
>> > 

Re: [gmx-users] cant load trajectory, low memory

[Tasneem Kausar]

Create index group that have both protein and ACO. gmx make_ndx will serve
this task.
Then create a pdb file file from gmx trjconv
Or you can choose system as output and delete ions and solvent from any
editor.



On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal 
wrote:

> Hello,
>
> Alright. I have tried this but I'm stuck in the following scenario.
> I'm using trjconv for getting pdb file of the protein-ligand complex (used
> for umbrella sampling).
> trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
>
> This is giving me the following prompt:
> Select group for output
> Group 0 ( System) has 27051263 elements
> Group 1 (Protein) has  1588 elements
> Group 2 (  Protein-H) has  1245 elements
> Group 3 (C-alpha) has   158 elements
> Group 4 (   Backbone) has   474 elements
> Group 5 (  MainChain) has   633 elements
> Group 6 (   MainChain+Cb) has   784 elements
> Group 7 (MainChain+H) has   785 elements
> Group 8 (  SideChain) has   803 elements
> Group 9 (SideChain-H) has   612 elements
> Group10 (Prot-Masses) has  1588 elements
> Group11 (non-Protein) has 27049675 elements
> Group12 (  Other) has59 elements
> Group13 (ACO) has59 elements
> Group14 ( NA) has 16615 elements
> Group15 ( CL) has 16615 elements
> Group16 (  Water) has 27016386 elements
> Group17 (SOL) has 27016386 elements
> Group18 (  non-Water) has 34877 elements
> Group19 (Ion) has 33230 elements
> Group20 (ACO) has59 elements
> Group21 ( NA) has 16615 elements
> Group22 ( CL) has 16615 elements
> Group23 ( Water_and_ions) has 27049616 elements
> Group24 (
>
> Now how can I be able to get both Protein+ACO as a pdb file ?
> If I could get Protein+ACO, then I could strip the box size for further
> umbrella sampling procedure.
>
> However, is it possible to go with the following way:
> editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
>
> Please suggest me a way.
>
> Thank you.
>
> On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Take a configuration of interest, strip the solvent, put it in a box you
> > think is good, and re-equilibrate just like you did before you started.
> >
> > Mark
> >
> > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal 
> > wrote:
> >
> > > Hi,
> > >
> > > Yes, I did when I started the simulation. The box size I used to start
> > the
> > > simulation was very big(I was dealing with an unknown sample). After
> > > successfully generating the configurations I realized that further work
> > > could move faster if I could trim the box size little bit now.
> > > So is there any way now to reduce the box size and proceed with
> relevant
> > > configurations towards PMF generation ?
> > > Please suggest me a way here.
> > >
> > > Thank you.
> > >
> > > On Apr 24, 2017 12:22 AM, "Mark Abraham" 
> > wrote:
> > >
> > > > Hi,
> > > >
> > > > You get to choose the box size eg with editconf when you set up your
> > > > simulation. It's not pre-defined ;-)
> > > >
> > > > Mark
> > > >
> > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal 
> > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Another thing I wanted to ask.
> > > > > After generating configurations I found out that the predefined box
> > > size
> > > > > (used to reach so far) is excessively high.
> > > > > Is it possible to trim the box size to perform further mdrun during
> > > > > umbrella sampling?
> > > > >
> > > > > Please suggest me a way, it is taking very long time with current
> box
> > > > size.
> > > > >
> > > > > Thank you.
> > > > >
> > > > >
> > > > >
> > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham"  >
> > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > You can only load a trajectory with fewer frames. Either don't
> > write
> > > so
> > > > > > many, or filter it with trjconv first.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal  >
> > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > > I'm having a problem loading trajectory file after umbrella
> > > sampling.
> > > > > The
> > > > > > > file is so huge in size that the VMD finally runs out of
> memory.
> > > I'm
> > > > > > > operating with 125gb of physical memory here though.
> > > > > > >
> > > > > > > Is there any way out of it ?
> > > > > > >
> > > > > > >
> > > > > > > Thank you
> > > > > > > --
> > > > > > > Abhisek Mondal
> > > > > > >
> > > > > > > *Senior Research Fellow*
> > > > > > >
> > > > > > > *Structural Biology and Bioinformatics Division*
> > > > > > > *CSIR-Indian Institute of Chemical Biology*
> > > > > > >
> > > > 

Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

Hi,

You need to make an index group (e.g. gmx select or gmx make_ndx) that has
the things you want (e.g. protein + ACO, or perhaps everything but
water+ions). See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume.
I'd guess your system has at least a factor of 10 more water than you need.
More like a factor of 100 ;-)

Mark

On Mon, Apr 24, 2017 at 11:52 AM abhisek Mondal 
wrote:

> Hello,
>
> Alright. I have tried this but I'm stuck in the following scenario.
> I'm using trjconv for getting pdb file of the protein-ligand complex (used
> for umbrella sampling).
> trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
>
> This is giving me the following prompt:
> Select group for output
> Group 0 ( System) has 27051263 elements
> Group 1 (Protein) has  1588 elements
> Group 2 (  Protein-H) has  1245 elements
> Group 3 (C-alpha) has   158 elements
> Group 4 (   Backbone) has   474 elements
> Group 5 (  MainChain) has   633 elements
> Group 6 (   MainChain+Cb) has   784 elements
> Group 7 (MainChain+H) has   785 elements
> Group 8 (  SideChain) has   803 elements
> Group 9 (SideChain-H) has   612 elements
> Group10 (Prot-Masses) has  1588 elements
> Group11 (non-Protein) has 27049675 elements
> Group12 (  Other) has59 elements
> Group13 (ACO) has59 elements
> Group14 ( NA) has 16615 elements
> Group15 ( CL) has 16615 elements
> Group16 (  Water) has 27016386 elements
> Group17 (SOL) has 27016386 elements
> Group18 (  non-Water) has 34877 elements
> Group19 (Ion) has 33230 elements
> Group20 (ACO) has59 elements
> Group21 ( NA) has 16615 elements
> Group22 ( CL) has 16615 elements
> Group23 ( Water_and_ions) has 27049616 elements
> Group24 (
>
> Now how can I be able to get both Protein+ACO as a pdb file ?
> If I could get Protein+ACO, then I could strip the box size for further
> umbrella sampling procedure.
>
> However, is it possible to go with the following way:
> editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
>
> Please suggest me a way.
>
> Thank you.
>
> On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Take a configuration of interest, strip the solvent, put it in a box you
> > think is good, and re-equilibrate just like you did before you started.
> >
> > Mark
> >
> > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal 
> > wrote:
> >
> > > Hi,
> > >
> > > Yes, I did when I started the simulation. The box size I used to start
> > the
> > > simulation was very big(I was dealing with an unknown sample). After
> > > successfully generating the configurations I realized that further work
> > > could move faster if I could trim the box size little bit now.
> > > So is there any way now to reduce the box size and proceed with
> relevant
> > > configurations towards PMF generation ?
> > > Please suggest me a way here.
> > >
> > > Thank you.
> > >
> > > On Apr 24, 2017 12:22 AM, "Mark Abraham" 
> > wrote:
> > >
> > > > Hi,
> > > >
> > > > You get to choose the box size eg with editconf when you set up your
> > > > simulation. It's not pre-defined ;-)
> > > >
> > > > Mark
> > > >
> > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal 
> > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Another thing I wanted to ask.
> > > > > After generating configurations I found out that the predefined box
> > > size
> > > > > (used to reach so far) is excessively high.
> > > > > Is it possible to trim the box size to perform further mdrun during
> > > > > umbrella sampling?
> > > > >
> > > > > Please suggest me a way, it is taking very long time with current
> box
> > > > size.
> > > > >
> > > > > Thank you.
> > > > >
> > > > >
> > > > >
> > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham"  >
> > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > You can only load a trajectory with fewer frames. Either don't
> > write
> > > so
> > > > > > many, or filter it with trjconv first.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal  >
> > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > > I'm having a problem loading trajectory file after umbrella
> > > sampling.
> > > > > The
> > > > > > > file is so huge in size that the VMD finally runs out of
> memory.
> > > I'm
> > > > > > > operating with 125gb of physical memory here though.
> > > > > > >
> > > > > > > Is there any way out of it ?
> > > > > > >
> > > > > > >
> > > > > > > Thank you
> > > > > > > --
> > > > > > > Abhisek Mondal
> > > > > > >
> > > > > > > *Senior Research Fellow*
> > > > 

Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

Hello,

Alright. I have tried this but I'm stuck in the following scenario.
I'm using trjconv for getting pdb file of the protein-ligand complex (used
for umbrella sampling).
trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr

This is giving me the following prompt:
Select group for output
Group 0 ( System) has 27051263 elements
Group 1 (Protein) has  1588 elements
Group 2 (  Protein-H) has  1245 elements
Group 3 (C-alpha) has   158 elements
Group 4 (   Backbone) has   474 elements
Group 5 (  MainChain) has   633 elements
Group 6 (   MainChain+Cb) has   784 elements
Group 7 (MainChain+H) has   785 elements
Group 8 (  SideChain) has   803 elements
Group 9 (SideChain-H) has   612 elements
Group10 (Prot-Masses) has  1588 elements
Group11 (non-Protein) has 27049675 elements
Group12 (  Other) has59 elements
Group13 (ACO) has59 elements
Group14 ( NA) has 16615 elements
Group15 ( CL) has 16615 elements
Group16 (  Water) has 27016386 elements
Group17 (SOL) has 27016386 elements
Group18 (  non-Water) has 34877 elements
Group19 (Ion) has 33230 elements
Group20 (ACO) has59 elements
Group21 ( NA) has 16615 elements
Group22 ( CL) has 16615 elements
Group23 ( Water_and_ions) has 27049616 elements
Group24 (

Now how can I be able to get both Protein+ACO as a pdb file ?
If I could get Protein+ACO, then I could strip the box size for further
umbrella sampling procedure.

However, is it possible to go with the following way:
editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic

Please suggest me a way.

Thank you.

On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham 
wrote:

> Hi,
>
> Take a configuration of interest, strip the solvent, put it in a box you
> think is good, and re-equilibrate just like you did before you started.
>
> Mark
>
> On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal 
> wrote:
>
> > Hi,
> >
> > Yes, I did when I started the simulation. The box size I used to start
> the
> > simulation was very big(I was dealing with an unknown sample). After
> > successfully generating the configurations I realized that further work
> > could move faster if I could trim the box size little bit now.
> > So is there any way now to reduce the box size and proceed with relevant
> > configurations towards PMF generation ?
> > Please suggest me a way here.
> >
> > Thank you.
> >
> > On Apr 24, 2017 12:22 AM, "Mark Abraham" 
> wrote:
> >
> > > Hi,
> > >
> > > You get to choose the box size eg with editconf when you set up your
> > > simulation. It's not pre-defined ;-)
> > >
> > > Mark
> > >
> > > On Sun, 23 Apr 2017 20:28 abhisek Mondal 
> wrote:
> > >
> > > > Hello,
> > > >
> > > > Another thing I wanted to ask.
> > > > After generating configurations I found out that the predefined box
> > size
> > > > (used to reach so far) is excessively high.
> > > > Is it possible to trim the box size to perform further mdrun during
> > > > umbrella sampling?
> > > >
> > > > Please suggest me a way, it is taking very long time with current box
> > > size.
> > > >
> > > > Thank you.
> > > >
> > > >
> > > >
> > > > On Apr 23, 2017 10:02 PM, "Mark Abraham" 
> > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You can only load a trajectory with fewer frames. Either don't
> write
> > so
> > > > > many, or filter it with trjconv first.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal 
> > > wrote:
> > > > >
> > > > > > Hi,
> > > > > > I'm having a problem loading trajectory file after umbrella
> > sampling.
> > > > The
> > > > > > file is so huge in size that the VMD finally runs out of memory.
> > I'm
> > > > > > operating with 125gb of physical memory here though.
> > > > > >
> > > > > > Is there any way out of it ?
> > > > > >
> > > > > >
> > > > > > Thank you
> > > > > > --
> > > > > > Abhisek Mondal
> > > > > >
> > > > > > *Senior Research Fellow*
> > > > > >
> > > > > > *Structural Biology and Bioinformatics Division*
> > > > > > *CSIR-Indian Institute of Chemical Biology*
> > > > > >
> > > > > > *Kolkata 700032*
> > > > > >
> > > > > > *INDIA*
> > > > > > --
> > > > > > 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.
> > > > > 

Re: [gmx-users] Gcc

[João Henriques]

Dear Mark and by extension Anshul,

I did make an assumption at the bottom of my previous email, and that was
uncalled for (despite having good intentions, but that doesn't change
anything). I apologize for that. That, however, does not overshadow the
fact that I provided Anshul with all the necessary information in a most
friendly, voluntary and professional way throughout three separate emails.

Best regards,
João

On Mon, Apr 24, 2017 at 11:09 AM, Mark Abraham 
wrote:

> Hi Joao, Anshul and all,
>
> Let's all please remember to keep the environment friendly and
> professional.
>
> That means not making assumptions about other people's intentions. Learning
> complex things like simulation science take time, and people often make
> mistakes when joining new communities, particularly if it's in a language
> with which they are not fully familiar. :-)
>
> That also means remembering that everybody here is volunteering their time
> to help others, and asking only for some of that time when you really need
> it is important if you wish to keep others motivated to help you. Look for
> your own answers first!
>
> Please all take a moment to review the thoughts at
> http://www.gromacs.org/Support/Mailing_Lists (or suggest improvements!)
>
> Cheers,
>
> Mark
>
> On Mon, Apr 24, 2017 at 10:39 AM João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > Dear Anshul,
> >
> > I thought by movie you meant that you wanted to visually check the
> > trajectory. ​For PyMOL, google search "pymol movie" produces about 31.000
> > results in 0,31 seconds. The first hit is exactly what you want:
> >
> > https://pymolwiki.org/index.php/MovieSchool
> >
> > My previous email will still be valid as you'll first need to make PyMOL
> > read your trajectory.
> >
> > - - -
> >
> > I know you want the exact array of commands you need to input in order to
> > get a movie done, but I will not do that. I believe it is better to
> provide
> > the information from which you can learn on your own. It's a bit of the
> old
> > "give a man a fish and you feed him for a day; teach a man to fish and
> you
> > feed him for a lifetime" proverb. The fact you waited a full weekend
> > instead of spending a couple of minutes searching and trying yourself
> tells
> > me that you're most likely just interested in the "fish", but I'll stick
> to
> > my belief that learning is better.
> >
> > /J
> >
> >
> > On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya <
> > anshullahariy...@gmail.com
> > > wrote:
> >
> > > hello rahul,
> > > can u tell me how to make movie??
> > >
> > >
> > > On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> > > joao.m.a.henriq...@gmail.com> wrote:
> > >
> > > > ​Plus, installing multiple version of the same software (e.g. gcc) is
> > not
> > > > problematic at all *when done by someone that knows what he/she is
> > > doing*.
> > > > Furthermore, I completely disagree with Vytautas Rakeviius final
> > advice.
> > > It
> > > > wouldn't cross anyone's mind to change OS in order to use a different
> > gcc
> > > > version. That is ludicrous. I obviously don't recommend that an
> > > > inexperienced user should start compiling stuff blindly on their
> > machine,
> > > > but that is just plain bad practice and impractical.
> > > >
> > > > But I digress, this is not really GROMACS related.
> > > >
> > > > A nice weekend to everyone!
> > > > João
> > > >
> > > > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > > > joao.m.a.henriq...@gmail.com> wrote:
> > > >
> > > > > You have (at the very least) three solutions regarding the movie:
> > > > >
> > > > > [1] Use gmx trjconv (see http://manual.gromacs.org/
> > > documentation/5.1.4/
> > > > > onlinehelp/gmx-trjconv.html) to generate a PDB file with the
> desired
> > > > > trajectory frames. Load and play it in PyMOL et voilà!
> > > > >
> > > > > [2] Install the GROMACS plugin for PyMOL, which will allow you
> (among
> > > > > other things) to directly read the trajectory files without having
> to
> > > > > resort to gmx trjconv (see https://pymolwiki.org/index.
> > > > php/GROMACS_Plugin
> > > > > ).
> > > > >
> > > > > [3] Use VMD which can read GROMACS trajectory output files straight
> > out
> > > > of
> > > > > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> > > > >
> > > > > For details regarding gmx trjconv please read the documentation. It
> > is
> > > > > fairly trivial and only you know exactly what system you have at
> > hand.
> > > > Some
> > > > > options will vary depending on that.
> > > > >
> > > > > - - -
> > > > >
> > > > > Regarding gcc, depending on your operating system you can either
> use
> > a
> > > > > package manager to install the desired version of gcc or compile it
> > > > > yourself. After installing it don't forget to make sure GROMACS
> knows
> > > > where
> > > > > to search for it, using the -DCMAKE_C_COMPILER=/path/to/gcc flag
> when
> > > > > running cmake (and probably also -DCMAKE_CXX_COMPILER=/path/to/
> c++).
> > 

Re: [gmx-users] Gcc

[Mark Abraham]

Hi Joao, Anshul and all,

Let's all please remember to keep the environment friendly and professional.

That means not making assumptions about other people's intentions. Learning
complex things like simulation science take time, and people often make
mistakes when joining new communities, particularly if it's in a language
with which they are not fully familiar. :-)

That also means remembering that everybody here is volunteering their time
to help others, and asking only for some of that time when you really need
it is important if you wish to keep others motivated to help you. Look for
your own answers first!

Please all take a moment to review the thoughts at
http://www.gromacs.org/Support/Mailing_Lists (or suggest improvements!)

Cheers,

Mark

On Mon, Apr 24, 2017 at 10:39 AM João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Dear Anshul,
>
> I thought by movie you meant that you wanted to visually check the
> trajectory. ​For PyMOL, google search "pymol movie" produces about 31.000
> results in 0,31 seconds. The first hit is exactly what you want:
>
> https://pymolwiki.org/index.php/MovieSchool
>
> My previous email will still be valid as you'll first need to make PyMOL
> read your trajectory.
>
> - - -
>
> I know you want the exact array of commands you need to input in order to
> get a movie done, but I will not do that. I believe it is better to provide
> the information from which you can learn on your own. It's a bit of the old
> "give a man a fish and you feed him for a day; teach a man to fish and you
> feed him for a lifetime" proverb. The fact you waited a full weekend
> instead of spending a couple of minutes searching and trying yourself tells
> me that you're most likely just interested in the "fish", but I'll stick to
> my belief that learning is better.
>
> /J
>
>
> On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya <
> anshullahariy...@gmail.com
> > wrote:
>
> > hello rahul,
> > can u tell me how to make movie??
> >
> >
> > On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > ​Plus, installing multiple version of the same software (e.g. gcc) is
> not
> > > problematic at all *when done by someone that knows what he/she is
> > doing*.
> > > Furthermore, I completely disagree with Vytautas Rakeviius final
> advice.
> > It
> > > wouldn't cross anyone's mind to change OS in order to use a different
> gcc
> > > version. That is ludicrous. I obviously don't recommend that an
> > > inexperienced user should start compiling stuff blindly on their
> machine,
> > > but that is just plain bad practice and impractical.
> > >
> > > But I digress, this is not really GROMACS related.
> > >
> > > A nice weekend to everyone!
> > > João
> > >
> > > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > > joao.m.a.henriq...@gmail.com> wrote:
> > >
> > > > You have (at the very least) three solutions regarding the movie:
> > > >
> > > > [1] Use gmx trjconv (see http://manual.gromacs.org/
> > documentation/5.1.4/
> > > > onlinehelp/gmx-trjconv.html) to generate a PDB file with the desired
> > > > trajectory frames. Load and play it in PyMOL et voilà!
> > > >
> > > > [2] Install the GROMACS plugin for PyMOL, which will allow you (among
> > > > other things) to directly read the trajectory files without having to
> > > > resort to gmx trjconv (see https://pymolwiki.org/index.
> > > php/GROMACS_Plugin
> > > > ).
> > > >
> > > > [3] Use VMD which can read GROMACS trajectory output files straight
> out
> > > of
> > > > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> > > >
> > > > For details regarding gmx trjconv please read the documentation. It
> is
> > > > fairly trivial and only you know exactly what system you have at
> hand.
> > > Some
> > > > options will vary depending on that.
> > > >
> > > > - - -
> > > >
> > > > Regarding gcc, depending on your operating system you can either use
> a
> > > > package manager to install the desired version of gcc or compile it
> > > > yourself. After installing it don't forget to make sure GROMACS knows
> > > where
> > > > to search for it, using the -DCMAKE_C_COMPILER=/path/to/gcc flag when
> > > > running cmake (and probably also -DCMAKE_CXX_COMPILER=/path/to/c++).
> > > > These paths are obviously fictitious and need to be changed with the
> > > right
> > > > ones.
> > > >
> > > > Best regards,
> > > > João
> > > >
> > > > On Fri, Apr 21, 2017 at 10:47 AM, Anshul Lahariya <
> > > > anshullahariy...@gmail.com> wrote:
> > > >
> > > >> okkk. it's fine...
> > > >>
> > > >>
> > > >> On Fri, Apr 21, 2017 at 1:06 PM, RAHUL SURESH <
> > drrahulsur...@gmail.com>
> > > >> wrote:
> > > >>
> > > >> > I am out
> > > >> > Can I say that to u on Monday.) ?
> > > >> > On Fri, 21 Apr 2017 at 10:28 AM, Anshul Lahariya <
> > > >> > anshullahariy...@gmail.com>
> > > >> > wrote:
> > > >> >
> > > >> > > yes rahul, i use pymol but dont know how to make movie
> > > >> > >
> > > >> > >
> > > >> > > On Fri, Apr 21, 2017 at 10:09 AM, 

Re: [gmx-users] Filling box with long linear molecules

[Mark Abraham]

Hi,

Not really. The general problem of filling space in a tight packing is
hard. Usable approaches include decreasing the VDW radius while inserting
molecules, using gmx genconf to start from an initially crystalline
configuration of suitable density that is then equilibrated for a long
time, using a much larger simulation cell that will later have its volume
reduced via pressure coupling, or dedicated software like
http://www.ime.unicamp.br/~martinez/packmol/home.shtml and various membrane
builders.

Mark

On Mon, Apr 24, 2017 at 10:46 AM Kamps, M.  wrote:

> Dear GMX users,
>
> I am working with polymers (~20 carbon atoms) in an enclosed box. In
> order to fill this box with polymers, I currently use an iteration of
> multiple steps.
>
> Currently, the polymers are created via an external code, and the
> resulting polymers are linear strings of polymers, with only a
> 'zig-zag' motion at the carbon atoms. Currently I am filling this box
> via the 'gmx insert-molecules -nmol X' command, where it will try to
> fill the box.
>
> Due to the orientation of the polymers, the box is considered full and
> GROMACS cannot add any more polymers. However, after performing a
> small relaxation the polymers will 'bend and twist' all around each
> other, resulting in lots of empty space. This process is repeated
> several times until gmx insert-molecules can no longer fit any more
> polymers in the box.
>
> My question, is there a more efficient way to do this? Can GROMACS
> insert-molecules while 'bending' the polymers?
>
> Kind regards,
>
> Mark
> --
> 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
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Filling box with long linear molecules

[Kamps, M.]

Dear GMX users,

I am working with polymers (~20 carbon atoms) in an enclosed box. In
order to fill this box with polymers, I currently use an iteration of
multiple steps.

Currently, the polymers are created via an external code, and the
resulting polymers are linear strings of polymers, with only a
'zig-zag' motion at the carbon atoms. Currently I am filling this box
via the 'gmx insert-molecules -nmol X' command, where it will try to
fill the box.

Due to the orientation of the polymers, the box is considered full and
GROMACS cannot add any more polymers. However, after performing a
small relaxation the polymers will 'bend and twist' all around each
other, resulting in lots of empty space. This process is repeated
several times until gmx insert-molecules can no longer fit any more
polymers in the box.

My question, is there a more efficient way to do this? Can GROMACS
insert-molecules while 'bending' the polymers?

Kind regards,

Mark
-- 
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.

Re: [gmx-users] Gcc

[João Henriques]

Dear Anshul,

I thought by movie you meant that you wanted to visually check the
trajectory. ​For PyMOL, google search "pymol movie" produces about 31.000
results in 0,31 seconds. The first hit is exactly what you want:

https://pymolwiki.org/index.php/MovieSchool

My previous email will still be valid as you'll first need to make PyMOL
read your trajectory.

- - -

I know you want the exact array of commands you need to input in order to
get a movie done, but I will not do that. I believe it is better to provide
the information from which you can learn on your own. It's a bit of the old
"give a man a fish and you feed him for a day; teach a man to fish and you
feed him for a lifetime" proverb. The fact you waited a full weekend
instead of spending a couple of minutes searching and trying yourself tells
me that you're most likely just interested in the "fish", but I'll stick to
my belief that learning is better.

/J


On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya  wrote:

> hello rahul,
> can u tell me how to make movie??
>
>
> On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > ​Plus, installing multiple version of the same software (e.g. gcc) is not
> > problematic at all *when done by someone that knows what he/she is
> doing*.
> > Furthermore, I completely disagree with Vytautas Rakeviius final advice.
> It
> > wouldn't cross anyone's mind to change OS in order to use a different gcc
> > version. That is ludicrous. I obviously don't recommend that an
> > inexperienced user should start compiling stuff blindly on their machine,
> > but that is just plain bad practice and impractical.
> >
> > But I digress, this is not really GROMACS related.
> >
> > A nice weekend to everyone!
> > João
> >
> > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > You have (at the very least) three solutions regarding the movie:
> > >
> > > [1] Use gmx trjconv (see http://manual.gromacs.org/
> documentation/5.1.4/
> > > onlinehelp/gmx-trjconv.html) to generate a PDB file with the desired
> > > trajectory frames. Load and play it in PyMOL et voilà!
> > >
> > > [2] Install the GROMACS plugin for PyMOL, which will allow you (among
> > > other things) to directly read the trajectory files without having to
> > > resort to gmx trjconv (see https://pymolwiki.org/index.
> > php/GROMACS_Plugin
> > > ).
> > >
> > > [3] Use VMD which can read GROMACS trajectory output files straight out
> > of
> > > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> > >
> > > For details regarding gmx trjconv please read the documentation. It is
> > > fairly trivial and only you know exactly what system you have at hand.
> > Some
> > > options will vary depending on that.
> > >
> > > - - -
> > >
> > > Regarding gcc, depending on your operating system you can either use a
> > > package manager to install the desired version of gcc or compile it
> > > yourself. After installing it don't forget to make sure GROMACS knows
> > where
> > > to search for it, using the -DCMAKE_C_COMPILER=/path/to/gcc flag when
> > > running cmake (and probably also -DCMAKE_CXX_COMPILER=/path/to/c++).
> > > These paths are obviously fictitious and need to be changed with the
> > right
> > > ones.
> > >
> > > Best regards,
> > > João
> > >
> > > On Fri, Apr 21, 2017 at 10:47 AM, Anshul Lahariya <
> > > anshullahariy...@gmail.com> wrote:
> > >
> > >> okkk. it's fine...
> > >>
> > >>
> > >> On Fri, Apr 21, 2017 at 1:06 PM, RAHUL SURESH <
> drrahulsur...@gmail.com>
> > >> wrote:
> > >>
> > >> > I am out
> > >> > Can I say that to u on Monday.) ?
> > >> > On Fri, 21 Apr 2017 at 10:28 AM, Anshul Lahariya <
> > >> > anshullahariy...@gmail.com>
> > >> > wrote:
> > >> >
> > >> > > yes rahul, i use pymol but dont know how to make movie
> > >> > >
> > >> > >
> > >> > > On Fri, Apr 21, 2017 at 10:09 AM, RAHUL SURESH <
> > >> drrahulsur...@gmail.com>
> > >> > > wrote:
> > >> > >
> > >> > > > You must use pymol
> > >> > > >
> > >> > > >
> > >> > > > On Fri, 21 Apr 2017 at 6:35 AM, Anshul Lahariya <
> > >> > > > anshullahariy...@gmail.com>
> > >> > > > wrote:
> > >> > > >
> > >> > > > > thanks rahul
> > >> > > > >
> > >> > > > >
> > >> > > > > and how to make md movie for 5ns by command.??
> > >> > > > >
> > >> > > > >
> > >> > > > > On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <
> > >> > drrahulsur...@gmail.com
> > >> > > >
> > >> > > > > wrote:
> > >> > > > >
> > >> > > > > > Yum apt-get gcc version
> > >> > > > > > Yum update
> > >> > > > > > Yum upgrade
> > >> > > > > > Yum install
> > >> > > > > >
> > >> > > > > >
> > >> > > > > > On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <
> > >> > > mark.j.abra...@gmail.com
> > >> > > > >
> > >> > > > > > wrote:
> > >> > > > > >
> > >> > > > > > > Hi,
> > >> > > > > > >
> > >> > > > > > > That's a good question for google or the forums of your
> > >> operating
> > >> > > > > system,
> > >> > > > > > > not here. :-)
> > 

Re: [gmx-users] Regarding finding orientation of angles of solvent with desired atom

[Dilip H N]

Hello,

I have simulated amino acid (eg., glycine) with water solvent mixture in
gromacs..
my question is ..
1] How can i find out the solvent orientation (angle made) ie.,angle made
by water (HOH) with respect to alpha carbon of amino acid (eg.,
glycine)...??
2] I have tried with gmx sorient command ..it gives me five outputs..sori,
snor, sord, scum, scount. With sori (it gives from solvent orientation -
cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
theta 0 to 1) , but with what respect is it giving i am not able to
understand...
3] I wanted to calculate the angle formed between water (HOH) and alpha
carbon of glycine. but if it consider the .gro file, i can calculate the
angle for only the last frame... but i want to calculate the angle for the
full frame (tpr/trr). How can i do it ...Can anybody kindly help me
regarding this..

Thank you...



   Sent with Mailtrack

<#>

On Mon, Apr 24, 2017 at 1:22 PM, Dilip H N 
wrote:

> Hello,
>
> I have simulated amino acid (eg., glycine) with water solvent mixture in
> gromacs..
> my question is ..
> 1] How can i find out the solvent orientation (angle made) ie.,angle made
> by water (HOH) with respect to alpha carbon of amino acid (eg.,
> glycine)...??
> 2] I have tried with gmx sorient command ..it gives me five outputs..sori,
> snor, sord, scum, scount. With sori (it gives from solvent orientation -
> cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
> theta 0 to 1) , but with what respect is it giving i am not able to
> understand...ie theta 1 and theta 2
> 3] I wanted to calculate the angle formed between water (HOH) and alpha
> carbon of glycine. but if it consider the .gro file, i can calculate the
> angle for only the last frame... but i want to calculate the angle for the
> full frame (tpr/trr). How can i do it sir...Can u kindly help me regarding
> this..
> Since i am referring one of ur research paper - [Glycine in aqueous
> solution: solvation shells, interfacial water, and vibrational spectroscopy
> from ab initio molecular dynamics]. and in other paper - [MONTE CARLO
> SIMULATION STUDIES OF THE SOLVATION OF IONS. 2. GLYCINE ZWITTERION] they
> have calculated the cos theta distribution functions...so i wanted to
> calculate ..
>
> Thank you sir...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> 
> <#m_1046049965356203242_>
>



-- 
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.

[gmx-users] Regarding finding orientation of angles of solvent with desired atom

[Dilip H N]

Hello,

I have simulated amino acid (eg., glycine) with water solvent mixture in
gromacs..
my question is ..
1] How can i find out the solvent orientation (angle made) ie.,angle made
by water (HOH) with respect to alpha carbon of amino acid (eg.,
glycine)...??
2] I have tried with gmx sorient command ..it gives me five outputs..sori,
snor, sord, scum, scount. With sori (it gives from solvent orientation -
cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
theta 0 to 1) , but with what respect is it giving i am not able to
understand...ie theta 1 and theta 2
3] I wanted to calculate the angle formed between water (HOH) and alpha
carbon of glycine. but if it consider the .gro file, i can calculate the
angle for only the last frame... but i want to calculate the angle for the
full frame (tpr/trr). How can i do it sir...Can u kindly help me regarding
this..
Since i am referring one of ur research paper - [Glycine in aqueous
solution: solvation shells, interfacial water, and vibrational spectroscopy
from ab initio molecular dynamics]. and in other paper - [MONTE CARLO
SIMULATION STUDIES OF THE SOLVATION OF IONS. 2. GLYCINE ZWITTERION] they
have calculated the cos theta distribution functions...so i wanted to
calculate ..

Thank you sir...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

<#>
-- 
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.

Re: [gmx-users] Gcc

[Mark Abraham]

Hi,

Please search for information before asking. Google has plenty of good hits
for "make md movie" for example.

Mark

On Mon, 24 Apr 2017 09:24 Anshul Lahariya 
wrote:

> hello rahul,
> can u tell me how to make movie??
>
>
> On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > ​Plus, installing multiple version of the same software (e.g. gcc) is not
> > problematic at all *when done by someone that knows what he/she is
> doing*.
> > Furthermore, I completely disagree with Vytautas Rakeviius final advice.
> It
> > wouldn't cross anyone's mind to change OS in order to use a different gcc
> > version. That is ludicrous. I obviously don't recommend that an
> > inexperienced user should start compiling stuff blindly on their machine,
> > but that is just plain bad practice and impractical.
> >
> > But I digress, this is not really GROMACS related.
> >
> > A nice weekend to everyone!
> > João
> >
> > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > You have (at the very least) three solutions regarding the movie:
> > >
> > > [1] Use gmx trjconv (see
> http://manual.gromacs.org/documentation/5.1.4/
> > > onlinehelp/gmx-trjconv.html) to generate a PDB file with the desired
> > > trajectory frames. Load and play it in PyMOL et voilà!
> > >
> > > [2] Install the GROMACS plugin for PyMOL, which will allow you (among
> > > other things) to directly read the trajectory files without having to
> > > resort to gmx trjconv (see https://pymolwiki.org/index.
> > php/GROMACS_Plugin
> > > ).
> > >
> > > [3] Use VMD which can read GROMACS trajectory output files straight out
> > of
> > > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> > >
> > > For details regarding gmx trjconv please read the documentation. It is
> > > fairly trivial and only you know exactly what system you have at hand.
> > Some
> > > options will vary depending on that.
> > >
> > > - - -
> > >
> > > Regarding gcc, depending on your operating system you can either use a
> > > package manager to install the desired version of gcc or compile it
> > > yourself. After installing it don't forget to make sure GROMACS knows
> > where
> > > to search for it, using the -DCMAKE_C_COMPILER=/path/to/gcc flag when
> > > running cmake (and probably also -DCMAKE_CXX_COMPILER=/path/to/c++).
> > > These paths are obviously fictitious and need to be changed with the
> > right
> > > ones.
> > >
> > > Best regards,
> > > João
> > >
> > > On Fri, Apr 21, 2017 at 10:47 AM, Anshul Lahariya <
> > > anshullahariy...@gmail.com> wrote:
> > >
> > >> okkk. it's fine...
> > >>
> > >>
> > >> On Fri, Apr 21, 2017 at 1:06 PM, RAHUL SURESH <
> drrahulsur...@gmail.com>
> > >> wrote:
> > >>
> > >> > I am out
> > >> > Can I say that to u on Monday.) ?
> > >> > On Fri, 21 Apr 2017 at 10:28 AM, Anshul Lahariya <
> > >> > anshullahariy...@gmail.com>
> > >> > wrote:
> > >> >
> > >> > > yes rahul, i use pymol but dont know how to make movie
> > >> > >
> > >> > >
> > >> > > On Fri, Apr 21, 2017 at 10:09 AM, RAHUL SURESH <
> > >> drrahulsur...@gmail.com>
> > >> > > wrote:
> > >> > >
> > >> > > > You must use pymol
> > >> > > >
> > >> > > >
> > >> > > > On Fri, 21 Apr 2017 at 6:35 AM, Anshul Lahariya <
> > >> > > > anshullahariy...@gmail.com>
> > >> > > > wrote:
> > >> > > >
> > >> > > > > thanks rahul
> > >> > > > >
> > >> > > > >
> > >> > > > > and how to make md movie for 5ns by command.??
> > >> > > > >
> > >> > > > >
> > >> > > > > On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <
> > >> > drrahulsur...@gmail.com
> > >> > > >
> > >> > > > > wrote:
> > >> > > > >
> > >> > > > > > Yum apt-get gcc version
> > >> > > > > > Yum update
> > >> > > > > > Yum upgrade
> > >> > > > > > Yum install
> > >> > > > > >
> > >> > > > > >
> > >> > > > > > On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <
> > >> > > mark.j.abra...@gmail.com
> > >> > > > >
> > >> > > > > > wrote:
> > >> > > > > >
> > >> > > > > > > Hi,
> > >> > > > > > >
> > >> > > > > > > That's a good question for google or the forums of your
> > >> operating
> > >> > > > > system,
> > >> > > > > > > not here. :-)
> > >> > > > > > >
> > >> > > > > > > Mark
> > >> > > > > > >
> > >> > > > > > > On Thu, 20 Apr 2017 12:42 Anshul Lahariya <
> > >> > > > anshullahariy...@gmail.com>
> > >> > > > > > > wrote:
> > >> > > > > > >
> > >> > > > > > > > hello,
> > >> > > > > > > >
> > >> > > > > > > > I want to change my gcc and want to install gcc version
> > >> later
> > >> > > than
> > >> > > > 5.
> > >> > > > > > > > what can i do so i can change the version of gcc to
> > >> gcc-4.9.4
> > >> > > > > > > > --
> > >> > > > > > > > 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 

Re: [gmx-users] Gcc

[Anshul Lahariya]

hello rahul,
can u tell me how to make movie??


On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> ​Plus, installing multiple version of the same software (e.g. gcc) is not
> problematic at all *when done by someone that knows what he/she is doing*.
> Furthermore, I completely disagree with Vytautas Rakeviius final advice. It
> wouldn't cross anyone's mind to change OS in order to use a different gcc
> version. That is ludicrous. I obviously don't recommend that an
> inexperienced user should start compiling stuff blindly on their machine,
> but that is just plain bad practice and impractical.
>
> But I digress, this is not really GROMACS related.
>
> A nice weekend to everyone!
> João
>
> On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > You have (at the very least) three solutions regarding the movie:
> >
> > [1] Use gmx trjconv (see http://manual.gromacs.org/documentation/5.1.4/
> > onlinehelp/gmx-trjconv.html) to generate a PDB file with the desired
> > trajectory frames. Load and play it in PyMOL et voilà!
> >
> > [2] Install the GROMACS plugin for PyMOL, which will allow you (among
> > other things) to directly read the trajectory files without having to
> > resort to gmx trjconv (see https://pymolwiki.org/index.
> php/GROMACS_Plugin
> > ).
> >
> > [3] Use VMD which can read GROMACS trajectory output files straight out
> of
> > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> >
> > For details regarding gmx trjconv please read the documentation. It is
> > fairly trivial and only you know exactly what system you have at hand.
> Some
> > options will vary depending on that.
> >
> > - - -
> >
> > Regarding gcc, depending on your operating system you can either use a
> > package manager to install the desired version of gcc or compile it
> > yourself. After installing it don't forget to make sure GROMACS knows
> where
> > to search for it, using the -DCMAKE_C_COMPILER=/path/to/gcc flag when
> > running cmake (and probably also -DCMAKE_CXX_COMPILER=/path/to/c++).
> > These paths are obviously fictitious and need to be changed with the
> right
> > ones.
> >
> > Best regards,
> > João
> >
> > On Fri, Apr 21, 2017 at 10:47 AM, Anshul Lahariya <
> > anshullahariy...@gmail.com> wrote:
> >
> >> okkk. it's fine...
> >>
> >>
> >> On Fri, Apr 21, 2017 at 1:06 PM, RAHUL SURESH 
> >> wrote:
> >>
> >> > I am out
> >> > Can I say that to u on Monday.) ?
> >> > On Fri, 21 Apr 2017 at 10:28 AM, Anshul Lahariya <
> >> > anshullahariy...@gmail.com>
> >> > wrote:
> >> >
> >> > > yes rahul, i use pymol but dont know how to make movie
> >> > >
> >> > >
> >> > > On Fri, Apr 21, 2017 at 10:09 AM, RAHUL SURESH <
> >> drrahulsur...@gmail.com>
> >> > > wrote:
> >> > >
> >> > > > You must use pymol
> >> > > >
> >> > > >
> >> > > > On Fri, 21 Apr 2017 at 6:35 AM, Anshul Lahariya <
> >> > > > anshullahariy...@gmail.com>
> >> > > > wrote:
> >> > > >
> >> > > > > thanks rahul
> >> > > > >
> >> > > > >
> >> > > > > and how to make md movie for 5ns by command.??
> >> > > > >
> >> > > > >
> >> > > > > On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <
> >> > drrahulsur...@gmail.com
> >> > > >
> >> > > > > wrote:
> >> > > > >
> >> > > > > > Yum apt-get gcc version
> >> > > > > > Yum update
> >> > > > > > Yum upgrade
> >> > > > > > Yum install
> >> > > > > >
> >> > > > > >
> >> > > > > > On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <
> >> > > mark.j.abra...@gmail.com
> >> > > > >
> >> > > > > > wrote:
> >> > > > > >
> >> > > > > > > Hi,
> >> > > > > > >
> >> > > > > > > That's a good question for google or the forums of your
> >> operating
> >> > > > > system,
> >> > > > > > > not here. :-)
> >> > > > > > >
> >> > > > > > > Mark
> >> > > > > > >
> >> > > > > > > On Thu, 20 Apr 2017 12:42 Anshul Lahariya <
> >> > > > anshullahariy...@gmail.com>
> >> > > > > > > wrote:
> >> > > > > > >
> >> > > > > > > > hello,
> >> > > > > > > >
> >> > > > > > > > I want to change my gcc and want to install gcc version
> >> later
> >> > > than
> >> > > > 5.
> >> > > > > > > > what can i do so i can change the version of gcc to
> >> gcc-4.9.4
> >> > > > > > > > --
> >> > > > > > > > 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
> >> > > > > > >