[gmx-users] using gmx density for making a radial density plot of a vesicle

[SRINIVAS MUSHNOORI]

Dear gromacs users,

I'm trying to make a radial density profile function (NOT an rdf) from the
center of my vesicle. I'm trying to use the following command:

gmx density -f vesicle.gro -o density.xvg -s vesicle.tpr -center

I want it to make a radial density profile from the center of mass of the
vesicle along an outward pointing radial vector. But the result I get with
the above command is incorrect, it appears as a monomodal bell curve. Since
it is a bilayered vesicle, it should be a bimodal distribution. I know that
this functionality exists for a flat bilayer along the normal vector to the
bilayer surface, but unsure how to do this for a spherical vesicle. Please
assist in helping me figure out what the right way to do this is?

Thanks!

Sincerely
Srinivas Mushnoori
Dept of Chemical and Biochemical Engineering
Rutgers University
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Re: [gmx-users] RDF of a group around CNT axis

[SRINIVAS MUSHNOORI]

If I understand you correctly: you want to calculate the RDF of a certain
group (NOT part of the nanotube) around the central axis of a nanotube?

The way I do these calculations is to use the gmx trjconv tool to isolate a
trajectory file of ONLY the gropus I am interested in and run my
calculations on that.
If you expect to see one peak but see many that might mean that the RDF is
picking up groups that you don't want it to.

Hope that helps,
Srinivas

On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani 
wrote:

> Dear experts,
> I want to calculate rdf of a certain group around the axis of a cnt, but I
> do not know what are the proper parameters to choose in the command-line.
> To test the parameters, I calculated the rdf of cnt itself around its axis
> which must be a sharp peak at the cnt radius.
> I tested the following: (both selection groups of reference and rdf are
> CNT)
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
>
> BUT all the results are the same!!! and surprisingly they have multiple
> sharp peaks at different ranges, which I expected just one peak at the
> radius of the CNT 
> It is notable that the CNT is aligned to z axis.
> (the first two peaks are listed below):
>
>   0.000 211939.438
>   0.002 53771.996
>   0.004 11278.401
>   0.006 3935.633
>   0.008 1782.280
>   0.010  809.616
>   0.012  584.723
>   0.014  536.531
>   0.016  292.361
>   0.018  149.929
>   0.020   94.455
>   0.022   00.000
>   ...
>   ...
>   ...
>   0.11800.000
>   0.1200.375
>   0.1222.212
>   0.1240.725
>   0.1266.069
>   0.128   36.545
>   0.130  114.868
>   0.132  278.390
>   0.134 1669.916
>   0.136 2360.069
>   0.138  346.139
>   0.140  183.770
>   0.142   39.277
>
> Could you please explain to me that what should I do?
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Re: [gmx-users] Using backward.py with Gromacs 5.x?

[SRINIVAS MUSHNOORI]

Thank you, Peter. I will post on the forum.

On Mon, Jan 23, 2017 at 3:44 AM, Peter Kroon <p.c.kr...@rug.nl> wrote:

> Hi Srinivas,
>
>
> You're probably better off asking this on the Martini forum
> (cgmartini.nl). What I would suggest for now (as a quick fix) is to
> define bash aliases for grompp and mdrun, and have them point to gmx
> grompp and gmx mdrun respectively. There might be more subtle effects as
> well though. You have been warned.
>
>
> Peter
>
>
> On 22-01-17 20:12, SRINIVAS MUSHNOORI wrote:
> > Dear GROMACS users,
> >
> > I'm attempting to backmap from a MARTINI CG representation to a CHARMM AA
> > representation for my biomolecular system.
> >
> > The command I am using is:
> > **./initram.sh -f FNF150-40out.gro -o charmm_FNF150-40.gro -to charmm36
> -p
> > FNF150-40.top**
> >
> >
> > And the output I get is:
> > **Checking dependencies:backward.py ...
> > /md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.pygrompp
> ...
> > Missing dependency: grompp**
> >
> >
> > Now doing a bit of googling seemed to shed some light on the issue:
> GROMACS
> > 5.x domes not seem to use a separate executable called "grompp" or even
> > "mdrun" for that matter. Instead it simply uses one executable called
> gmx.
> > Changing the dependency to the path of my gmx executable inside
> initram.sh
> > and then attempting to run it gives me the following error:
> > **Checking dependencies:backward.py ...
> > /md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backw
> ard.py/usr/local/gromacs/bin/gmx
> > <http://backward.py/usr/local/gromacs/bin/gmx>
> > ... /usr/local/gromacs/bin/gmxTraceback (most recent call last):  File
> > "/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
> > 644, in struc =
> > Structure(options["-f"].value,strict=options["-strict"].value)  File
> > "/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
> > 411, in __init__crsp.append(crsp[-1])IndexError: list index out of
> > range*
> > *
> > I am unsure how to go about running the script. Any assistance on the
> > matter will be immensely helpful.
> >
> > Thank you!
> >
> > Sincerely yours,
> >
> > Srinivas Mushnoori
>
>
>
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[gmx-users] Using backward.py with Gromacs 5.x?

[SRINIVAS MUSHNOORI]

Dear GROMACS users,

I'm attempting to backmap from a MARTINI CG representation to a CHARMM AA
representation for my biomolecular system.

The command I am using is:
**./initram.sh -f FNF150-40out.gro -o charmm_FNF150-40.gro -to charmm36 -p
FNF150-40.top**


And the output I get is:
**Checking dependencies:backward.py ...
/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.pygrompp ...
Missing dependency: grompp**


Now doing a bit of googling seemed to shed some light on the issue: GROMACS
5.x domes not seem to use a separate executable called "grompp" or even
"mdrun" for that matter. Instead it simply uses one executable called gmx.
Changing the dependency to the path of my gmx executable inside initram.sh
and then attempting to run it gives me the following error:
**Checking dependencies:backward.py ...
/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py/usr/local/gromacs/bin/gmx
<http://backward.py/usr/local/gromacs/bin/gmx>
... /usr/local/gromacs/bin/gmxTraceback (most recent call last):  File
"/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
644, in struc =
Structure(options["-f"].value,strict=options["-strict"].value)  File
"/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
411, in __init__crsp.append(crsp[-1])IndexError: list index out of
range*
*
I am unsure how to go about running the script. Any assistance on the
matter will be immensely helpful.

Thank you!

Sincerely yours,

Srinivas Mushnoori
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[gmx-users] Backmapping from MARTINI to AA in GROMACS 5.1.1: initram.sh error

[SRINIVAS MUSHNOORI]

Dear GROMACS users,

I'm attempting to backmap from a MARTINI CG representation to a CHARMM AA
representation for my biomolecular system.

The command I am using is:

*./initram.sh -f FNF150-40out.gro -o charmm_FNF150-40.gro -to charmm36 -p
FNF150-40.top*


And the output I get is:




*Checking dependencies:backward.py ...
/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.pygrompp ...
Missing dependency: grompp*


Now doing a bit of googling seemed to shed some light on the issue: GROMACS
5.x domes not seem to use a separate executable called "grompp" or even
"mdrun" for that matter. Instead it simply uses one executable called gmx.
Changing the dependency to the path of my gmx executable inside initram.sh
and then attempting to run it gives me the following error:









*Checking dependencies:backward.py ...
/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py/usr/local/gromacs/bin/gmx
... /usr/local/gromacs/bin/gmxTraceback (most recent call last):  File
"/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
644, in struc =
Structure(options["-f"].value,strict=options["-strict"].value)  File
"/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.00/backward.py", line
411, in __init__crsp.append(crsp[-1])IndexError: list index out of
range*

I am unsure how to go about running the script. Any assistance on the
matter will be immensely helpful.

Thank you!

Sincerely yours,

Srinivas Mushnoori
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