[gmx-users] two peptides in simulation tend to stick together

[MD]

Hi Gromacs folks,

I was trying a simulation to look at a protein (35kDa) and a peptide (10
amino acids)interaction. I prepped one pdb file containing both the protein
and the peptide. The original position of the peptide is in a hydrophobic
pocket of the protein from a docking result. I used 1-10 to number the
peptide and I kept the original protein numbering system (23-336) as it is,
and they are both named chain A. However after the simulation I found quite
some structures have the #10 of the peptide trying to get close to #23 of
the protein. I used the tutorial mdp file and the protein and peptide are
easy to start with (no modified residues). I wonder if I am missing some
parameters setting up at the starting point? Or by simply naming them with
different chain names will fix the problem?

Thank you in advance,

MD
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Re: [gmx-users] Formatting of spacing in .top and .itp files

[Justin Lemkul]

On 4/12/18 2:12 PM, Andrew DeYoung wrote:

Hi,

I am running Gromacs 4.5.5.  In that rather old version, there is a
binary called g_x2top -- I think it is now called something else -- to
generate "a primitive topology from a coordinate file."

When I use g_x2top with my (custom) force field, g_x2top generates a
nicely formatted topology file (either .top or .itp).  Here is a
snippet from the nicely formatted topology (assuming you display the
text in a fixed width font):

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
8197   113   129 1
   11297   113   114 1
   11297   113   129 1
82989983 1
829899   115 1

(Only atom indices and a function type are printed because I used the
option -noparam in g_x2top.)

But, what if I want to generate my own .top or .itp text file, using
for example Fortran, Perl, or Python?  Are .top and .itp fixed-spaced
file formats?  In other words, do I have to nicely align the columns
as g_x2top does?  Or can I just use any number of spaces to delimit
the columns, like in the following example?

[ dihedrals ]
81 97 113 129 1
112 97 113 114 1
112 97 113 129 1
82 98 99 83 1
82 98 99 115 1

I have tried this ugly formatting, and it seems to give the same
results as the nice formatting.  But can anyone confirm that .top and
.itp are NOT fixed-spaced file formats (unlike .pdb and .gro for
example)?


GROMACS topologies are free format.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Formatting of spacing in .top and .itp files

[Andrew DeYoung]

Hi,

I am running Gromacs 4.5.5.  In that rather old version, there is a
binary called g_x2top -- I think it is now called something else -- to
generate "a primitive topology from a coordinate file."

When I use g_x2top with my (custom) force field, g_x2top generates a
nicely formatted topology file (either .top or .itp).  Here is a
snippet from the nicely formatted topology (assuming you display the
text in a fixed width font):

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
   8197   113   129 1
  11297   113   114 1
  11297   113   129 1
   82989983 1
   829899   115 1

(Only atom indices and a function type are printed because I used the
option -noparam in g_x2top.)

But, what if I want to generate my own .top or .itp text file, using
for example Fortran, Perl, or Python?  Are .top and .itp fixed-spaced
file formats?  In other words, do I have to nicely align the columns
as g_x2top does?  Or can I just use any number of spaces to delimit
the columns, like in the following example?

[ dihedrals ]
81 97 113 129 1
112 97 113 114 1
112 97 113 129 1
82 98 99 83 1
82 98 99 115 1

I have tried this ugly formatting, and it seems to give the same
results as the nice formatting.  But can anyone confirm that .top and
.itp are NOT fixed-spaced file formats (unlike .pdb and .gro for
example)?

Thanks for your time,
Andrew DeYoung
Carnegie Mellon University
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Re: [gmx-users] changing the time frame for simmulation

[neelam wafa]

okay got it.
with dt =2fs250 nsteps are for 5 ns simmulation.

On Thu, 12 Apr 2018 10:35 pm Justin Lemkul,  wrote:

>
>
> On 4/12/18 1:33 PM, neelam wafa wrote:
> > Thank you sir justin.
> > I am confused a bit. Kindly tell me which one of the following is right
> for
> > 5 ns.
> > nsteps =500; 500=5000 ps (5ns)
> >
> > or
> >
> > nsteps  = 250 ;  2*250= 5000 ps (5ns).
>
> Depends on dt. Please consider what the units are. This is a trivial
> calculation and is actually explained exactly in the comment field of
> the file you posted previously (and in the tutorial from which you got
> the file).
>
> -Justin
>
> > On Thu, 12 Apr 2018 10:13 pm Justin Lemkul,  wrote:
> >
> >>
> >> On 4/12/18 4:11 AM, neelam wafa wrote:
> >>> Dear gmx users,
> >>>
> >>> I have run the md simmulation of my protein ligand complex for 1ns
> >>> following the conditions used in tutorial by sir Justin. Now I want to
> >> run
> >>> the simmulations for 5ns and 10 ns. How have set it like this:
> >>> integrator  = md; leap-frog integrator
> >>> nsteps  = 500; 2 * 500 = 1 ps (10 ns)
> >>> dt  = 0.002 ; 2 fs
> >>>
> >>> Is it right?
> >> Yes.
> >>
> >>> Is it needed to change the output control as well. It is in this form
> >>>Output control
> >>> nstxout = 0 ; suppress .trr output
> >>> nstvout = 0 ; suppress .trr output
> >>> nstenergy   = 5000  ; save energies every 10.0 ps
> >>> nstlog  = 5000  ; update log file every 10.0 ps
> >>> nstxout-compressed  = 5000  ; write .xtc trajectory every 10.0 ps
> >>>
> >>> Please also guide me is it enough to run the last production md for 10
> ns
> >>> with the npt and nvt run unchanged or I have change the time frame of
> the
> >>> equliberation steps as well.
> >> You do not need to change the amount of equilibration.
> >>
> >>> Further how can I set the parameters for a 5ns simmulation?
> >> It's the same math that you did above.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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> posting!
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Re: [gmx-users] changing the time frame for simmulation

[Justin Lemkul]

On 4/12/18 1:33 PM, neelam wafa wrote:

Thank you sir justin.
I am confused a bit. Kindly tell me which one of the following is right for
5 ns.
nsteps =500; 500=5000 ps (5ns)

or

nsteps  = 250 ;  2*250= 5000 ps (5ns).


Depends on dt. Please consider what the units are. This is a trivial 
calculation and is actually explained exactly in the comment field of 
the file you posted previously (and in the tutorial from which you got 
the file).


-Justin


On Thu, 12 Apr 2018 10:13 pm Justin Lemkul,  wrote:



On 4/12/18 4:11 AM, neelam wafa wrote:

Dear gmx users,

I have run the md simmulation of my protein ligand complex for 1ns
following the conditions used in tutorial by sir Justin. Now I want to

run

the simmulations for 5ns and 10 ns. How have set it like this:
integrator  = md; leap-frog integrator
nsteps  = 500; 2 * 500 = 1 ps (10 ns)
dt  = 0.002 ; 2 fs

Is it right?

Yes.


Is it needed to change the output control as well. It is in this form
   Output control
nstxout = 0 ; suppress .trr output
nstvout = 0 ; suppress .trr output
nstenergy   = 5000  ; save energies every 10.0 ps
nstlog  = 5000  ; update log file every 10.0 ps
nstxout-compressed  = 5000  ; write .xtc trajectory every 10.0 ps

Please also guide me is it enough to run the last production md for 10 ns
with the npt and nvt run unchanged or I have change the time frame of the
equliberation steps as well.

You do not need to change the amount of equilibration.


Further how can I set the parameters for a 5ns simmulation?

It's the same math that you did above.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] changing the time frame for simmulation

[neelam wafa]

Thank you sir justin.
I am confused a bit. Kindly tell me which one of the following is right for
5 ns.
nsteps =500; 500=5000 ps (5ns)

or

nsteps  = 250 ;  2*250= 5000 ps (5ns).

On Thu, 12 Apr 2018 10:13 pm Justin Lemkul,  wrote:

>
>
> On 4/12/18 4:11 AM, neelam wafa wrote:
> > Dear gmx users,
> >
> > I have run the md simmulation of my protein ligand complex for 1ns
> > following the conditions used in tutorial by sir Justin. Now I want to
> run
> > the simmulations for 5ns and 10 ns. How have set it like this:
> > integrator  = md; leap-frog integrator
> > nsteps  = 500; 2 * 500 = 1 ps (10 ns)
> > dt  = 0.002 ; 2 fs
> >
> > Is it right?
>
> Yes.
>
> > Is it needed to change the output control as well. It is in this form
> >   Output control
> > nstxout = 0 ; suppress .trr output
> > nstvout = 0 ; suppress .trr output
> > nstenergy   = 5000  ; save energies every 10.0 ps
> > nstlog  = 5000  ; update log file every 10.0 ps
> > nstxout-compressed  = 5000  ; write .xtc trajectory every 10.0 ps
> >
> > Please also guide me is it enough to run the last production md for 10 ns
> > with the npt and nvt run unchanged or I have change the time frame of the
> > equliberation steps as well.
>
> You do not need to change the amount of equilibration.
>
> > Further how can I set the parameters for a 5ns simmulation?
>
> It's the same math that you did above.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 168, Issue 45

[Justin Lemkul]

On 4/12/18 2:55 AM, za...@tezu.ernet.in wrote:

Dear Mark

Thank you for the kind response.

H with +0.418 charge and N with -0.845 charge is contributing towards
coulomb 14 interaction. So what is the amount of interaction between one
single H and N (3 bonds apart)? Kindly correct me if I am wrong.


Simply calculate it with Coulomb's Law and apply the 1-4 electrostatic 
scaling factor (if your force field uses one).


-Justin


Here is my Gdm topology

[ moleculetype ]
; name  nrexcl
GDM 3

[ atoms ]
;   nrtype   resnr  residuatomcgnr  charge  MASS
  1  C1GND   C1   1  1.027  13.019
  2 NT1GND   N2   2  -0.845 14.0067
  3  H1GND   H3   2  0.418  1.008
  4  H1GND   H4   2  0.418  1.008
  5 NT1GND   N5   3  -0.845 14.0067
  6  H1GND   H6   3   0.418 1.008
  7  H1GND   H7   3  0.418  1.008
  8 NT1GND   N8   4  -0.845 14.0067
  9  H1GND   H9   4  0.418  1.008
  10 H1GND   H10  4  0.418  1.008


  [ bonds ]
 1 2  2  0.1340  1.0500e+07
 1 5  2  0.1340  1.0500e+07
 1 8  2  0.1340  1.0500e+07
 2 3  2  0.1000  1.8700e+07
 2 4  2  0.1000  1.8700e+07
 5 6  2  0.1000  1.8700e+07
 5 7  2  0.1000  1.8700e+07
 8 9  2  0.1000  1.8700e+07
 810  2  0.1000  1.8700e+07


  [ angles ]
 1 2 32  120.00  390.00
 1 2 42  120.00  390.00
 1 5 62  120.00  390.00
 1 5 72  120.00  390.00
 1 8 92  120.00  390.00
 1 8102  120.00  390.00
 3 2 42  120.00  445.00
 6 5 72  120.00  445.00
 9 8102  120.00  445.00
 2 1 52  120.00  670.00
 5 1 82  120.00  670.00
 8 1 22  120.00  670.00


[ pairs ]
;  aiaj funct   c0   c1
 2 6 1 0.00e+00 0.00e+00
 2 7 1 0.00e+00 0.00e+00
 2 9 1 0.00e+00 0.00e+00
 210 1 0.00e+00 0.00e+00
 5 3 1 0.00e+00 0.00e+00
 5 4 1 0.00e+00 0.00e+00
 5 9 1 0.00e+00 0.00e+00
 510 1 0.00e+00 0.00e+00
 8 3 1 0.00e+00 0.00e+00
 8 4 1 0.00e+00 0.00e+00
 8 6 1 0.00e+00 0.00e+00
 8 7 1 0.00e+00 0.00e+00

  [ dihedrals ]
;  aiajakal   gromos type
 2 1 5 6  1 180.000   33.5  2
 2 1 5 7  1 180.000   33.5  2
 2 1 8 9  1 180.000   33.5  2
 2 1 810  1 180.000   33.5  2
 5 1 2 3  1 180.000   33.5  2
 5 1 2 4  1 180.000   33.5  2
 5 1 8 9  1 180.000   33.5  2
 5 1 810  1 180.000   33.5  2
 8 1 2 3  1 180.000   33.5  2
 8 1 2 4  1 180.000   33.5  2

Thank you

Regards
Zaved Hazarika
PhD Scholar
Dept.of Molecular Biology and Biotechnology
Tezpur University
India


Hi,

Presumably Gdm has atoms connected by three adjacent bonds that generally
have negative potential, and there's enough Gdm to make the total for the
system negative. It's generally a good idea to understand how the topology
you're using for Gdm works.

Mark

On Tue, Apr 10, 2018 at 2:23 PM  wrote:


Dear Gromacs Users

I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl) with
gromos54a7 ff. Simulations have been performed for 100ns each at 298K,
350K and 450K.

The Average Coulomb-14 Energies are as follows:

ricin in water (298K) : 3.42E+04 (positive value)
ricin in water (350K) : 3.41E+04 (positive value)
ricin in water (450K) : 3.40E+04 (positive value)

ricin + GdmCl  (298K)  :-3.16E+06 (negative value)
ricin + GdmCl  (350K) : -3.17E+06 (negative value)
ricin + GdmCl  (450K) : -3.17E+06 (negative value)

Can anyone suggest me why there is a (10 to the power 10) fold
difference
of average Coulomb-14 energy of ricin in presence of water and ricin in
presence of GdmCl?

Thank You

Regards

Zaved



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Re: [gmx-users] changing the time frame for simmulation

[Justin Lemkul]

On 4/12/18 4:11 AM, neelam wafa wrote:

Dear gmx users,

I have run the md simmulation of my protein ligand complex for 1ns
following the conditions used in tutorial by sir Justin. Now I want to run
the simmulations for 5ns and 10 ns. How have set it like this:
integrator  = md; leap-frog integrator
nsteps  = 500; 2 * 500 = 1 ps (10 ns)
dt  = 0.002 ; 2 fs

Is it right?


Yes.


Is it needed to change the output control as well. It is in this form
  Output control
nstxout = 0 ; suppress .trr output
nstvout = 0 ; suppress .trr output
nstenergy   = 5000  ; save energies every 10.0 ps
nstlog  = 5000  ; update log file every 10.0 ps
nstxout-compressed  = 5000  ; write .xtc trajectory every 10.0 ps

Please also guide me is it enough to run the last production md for 10 ns
with the npt and nvt run unchanged or I have change the time frame of the
equliberation steps as well.


You do not need to change the amount of equilibration.


Further how can I set the parameters for a 5ns simmulation?


It's the same math that you did above.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] GPU Command

[Mark Abraham]

Hi,

On Thu, Apr 12, 2018 at 4:47 PM  wrote:

> Dear Gromacs Users
>
> We have a GPU Server (Intel(R) Xeon(R) CPU E5-2609 v4 @ 1.70GHz, 16 cores)
> with 2 NVIDIA Tesla P100 (12GB) cards.
>
> What should be my final mdrun command so that it should utilize both the
> cards for the run? (As of now it detects both the cards, but auto selects
> only 1)
>
> As of now I am using the following command:
>
> gmx_mpi mdrun -v -deffnm run -gpu_id 0 1
>

You mentioned auto selection of GPU usage, but you are selecting the GPU
usage here, and you are requiring it to use only GPU 0. If you would look
at the examples in the user guide you would see how to use -gpu_id. If you
want permit mdrun to use its auto-selection, then don't use -gpu_id.


> I am using Gromacs 2016.4 version.
>
> For gromacs installation, used the following:
>
> CC=/usr/bin/mpicc F77=/usr/bin/f77 CXX=/usr/bin/mpicxx
> MPICC=/usr/bin/mpicc CMAKE_PREFIX_PATH=/soft/fftw337/lib cmake ..
> -DFFTWF_INCLUDE_DIR=/soft/fftw337/include
> -DFFTWF_LIBRARIES=/soft/fftw337/lib/libfftw3.so
> -DCMAKE_INSTALL_PREFIX=/soft/gmx164 -DGMX_X11=OFF
> -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc
> -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON
> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_SIMD=SSE2 -DGMX_SIMD=AVX2_256
> -DGMX_USE_RDTSCP=OFF -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>

Use only one GMX_SIMD setting - the one that matches the capabilities of
the CPU.


> Do I need to provide any other option (openMPI) while installing groamcs?
>

You already chose to use your MPI library.

Mark


> Thank You
>
> Regards
> Zaved Hazarika
> PhD Scholar
> Dept.of Molecular Biology and Biotechnology
> Tezpur University
> Indi
>
>
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[gmx-users] GPU Command

[zaved]

Dear Gromacs Users

We have a GPU Server (Intel(R) Xeon(R) CPU E5-2609 v4 @ 1.70GHz, 16 cores)
with 2 NVIDIA Tesla P100 (12GB) cards.

What should be my final mdrun command so that it should utilize both the
cards for the run? (As of now it detects both the cards, but auto selects
only 1)

As of now I am using the following command:

gmx_mpi mdrun -v -deffnm run -gpu_id 0 1

I am using Gromacs 2016.4 version.

For gromacs installation, used the following:

CC=/usr/bin/mpicc F77=/usr/bin/f77 CXX=/usr/bin/mpicxx
MPICC=/usr/bin/mpicc CMAKE_PREFIX_PATH=/soft/fftw337/lib cmake ..
-DFFTWF_INCLUDE_DIR=/soft/fftw337/include
-DFFTWF_LIBRARIES=/soft/fftw337/lib/libfftw3.so
-DCMAKE_INSTALL_PREFIX=/soft/gmx164 -DGMX_X11=OFF
-DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc
-DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_SIMD=SSE2 -DGMX_SIMD=AVX2_256
-DGMX_USE_RDTSCP=OFF -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda

Do I need to provide any other option (openMPI) while installing groamcs?

Thank You

Regards
Zaved Hazarika
PhD Scholar
Dept.of Molecular Biology and Biotechnology
Tezpur University
Indi


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Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

[Joe Jordan]

Since gmx trjconv does not work with dynamic selections, you can either
feed the index file to trjconv and manually pick which frames to dump or
write a script that calls trjconv to dump the atoms you want for each
timestep you want.

On Thu, Apr 12, 2018 at 10:04 AM, Dilip.H.N 
wrote:

> The -on option too gives the output as in index format, which i don't want.
> I want it in a .gro file and not as in an index file format.In gmx select
> options the output files are written in .xvg/.ndx.dat format only...
> i want the output to be written like the following:-
>
> frame t= 0.000
>  1543
> 1GLY  N1   1.206   1.052   1.131
> 1GLY H12   1.266   1.070   1.215
> 1GLY H23   1.270   1.019   1.056
> 1GLY H34   1.134   0.981   1.155
> 1GLY CA5   1.158   1.191   1.103
> 1GLYHA16   1.086   1.211   1.181
> 1GLYHA27   1.127   1.205   1.001
> 1GLY  C8   1.276   1.289   1.123
> 1GLYOT19   1.252   1.408   1.108
> 1GLYOT2   10   1.392   1.257   1.149
>   253SOL OW  764   1.085   0.998   0.837
>   253SOLHW1  765   0.998   0.982   0.883
>   253SOLHW2  766   1.109   0.919   0.781
>   252SOL OW  761   0.848   1.089   0.990
>   252SOLHW1  762   0.767   1.098   1.049
>   252SOLHW2  763   0.881   1.180   0.965
> .
> .
> frame t= 1.000
>  1543
> 1GLY  N1   1.229   1.032   1.106
> 1GLY H12   1.277   1.040   1.198
> 1GLY H23   1.290   0.979   1.041
> 1GLY H34   1.145   0.976   1.127
> 1GLY CA5   1.198   1.175   1.059
> 1GLYHA16   1.128   1.213   1.132
> 1GLYHA27   1.175   1.175   0.953
> 1GLY  C8   1.309   1.273   1.082
> 1GLYOT19   1.282   1.393   1.056
> 1GLYOT2   10   1.417   1.237   1.137
>   155SOL OW  470   1.005   1.448   1.113
>   155SOLHW1  471   1.103   1.445   1.095
>   155SOLHW2  472   0.957   1.477   1.030
>   388SOL OW 1169   1.307   1.001   1.370
>   388SOLHW1 1170   1.329   1.053   1.452 etc...
>
> Any suggestions are appreciated.
>
> Thank you.
> ‌
>  Sent with Mailtrack
>  signaturevirality&>
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
>
> On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan  wrote:
>
> > You need -on for gmx select to write out the index file.
> >
> > On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N 
> > wrote:
> >
> > > I tried the following two ways ie., with gmx select and with gmx
> trjorder
> > >
> > > 1) when i give the command :-
> > > gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro
> > -nshell
> > > -r 0.35
> > >
> > > i got an output file, it has all the water molecules (i have 511 water
> > > molecules in my system) for each time frame but it has arranged
> according
> > > to the smallest distance to atoms in the reference group. (but i want
> > only
> > > those water molecules within 0.35nm of nitrogen of glycine molecule.)
> > >
> > > 2) in this command:-
> > > gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close
> > to
> > > name N" resname SOL and within 0.35 of group protein'
> > >
> > > i am getting an .dat file which has only the coordinates and the format
> > on
> > > as in index file format.
> > >
> > > Actually, i wanted the format in which the gmx trjorder output gives
> (as
> > in
> > > my case, order.gro), but i want only those water molecules which are
> > within
> > > 3.5 nm of the nitrogen atom of glycine molecule for each time frame.
> > >
> > > Any suggestions are appreciated.
> > >
> > > Thank you.
> > >
> > > ‌
> > >  Sent with Mailtrack
> > >  > signature_campaign=
> > > signaturevirality&>
> > >
> > > ---
> > > With Best Regards,
> > >
> > > Dilip.H.N
> > > PhD Student.
> > >
> > > On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger <
> hoemb...@brandeis.edu>
> > > wrote:
> > >
> > > > You can use either gmx trjorder with the nshell parameter (if it is
> as
> > > > simple as within Xnm of Y, use nshell parameter, see manual) or gmx
> > > select
> > > > (if you need some more complex selection).
> > > >
> > > > On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N <
> cy16f01.di...@nitk.edu.in>
> > > > wrote:
> > > >
> > > > > Hello all,
> > > > >
> > > > > I want to get the water molecules which are at a certain distance
> > (say
> > > > all
> > > > > the water molecules which are within 0.35nm of the Nitrogen atom of
> > > > glycine
> > > > > molecule). How can i get this all the coordinates.?
> > > > >
> > > > > Any specific commands..??
> > > > >
> > > > >
> > > > > Thank you.
> > > > >
> > > > > ---
> > > > > With Best Regards,
> > > > >
> > > > > Dilip.H.N
> > > > > PhD Student.
> > > > >  Sent with Mailtrack

[gmx-users] changing the time frame for simmulation

[neelam wafa]

Dear gmx users,

I have run the md simmulation of my protein ligand complex for 1ns
following the conditions used in tutorial by sir Justin. Now I want to run
the simmulations for 5ns and 10 ns. How have set it like this:
integrator  = md; leap-frog integrator
nsteps  = 500; 2 * 500 = 1 ps (10 ns)
dt  = 0.002 ; 2 fs

Is it right?
Is it needed to change the output control as well. It is in this form
 Output control
nstxout = 0 ; suppress .trr output
nstvout = 0 ; suppress .trr output
nstenergy   = 5000  ; save energies every 10.0 ps
nstlog  = 5000  ; update log file every 10.0 ps
nstxout-compressed  = 5000  ; write .xtc trajectory every 10.0 ps

Please also guide me is it enough to run the last production md for 10 ns
with the npt and nvt run unchanged or I have change the time frame of the
equliberation steps as well.

Further how can I set the parameters for a 5ns simmulation?

Thanks in advance.

Regards
-- 
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Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

[Dilip.H.N]

The -on option too gives the output as in index format, which i don't want.
I want it in a .gro file and not as in an index file format.In gmx select
options the output files are written in .xvg/.ndx.dat format only...
i want the output to be written like the following:-

frame t= 0.000
 1543
1GLY  N1   1.206   1.052   1.131
1GLY H12   1.266   1.070   1.215
1GLY H23   1.270   1.019   1.056
1GLY H34   1.134   0.981   1.155
1GLY CA5   1.158   1.191   1.103
1GLYHA16   1.086   1.211   1.181
1GLYHA27   1.127   1.205   1.001
1GLY  C8   1.276   1.289   1.123
1GLYOT19   1.252   1.408   1.108
1GLYOT2   10   1.392   1.257   1.149
  253SOL OW  764   1.085   0.998   0.837
  253SOLHW1  765   0.998   0.982   0.883
  253SOLHW2  766   1.109   0.919   0.781
  252SOL OW  761   0.848   1.089   0.990
  252SOLHW1  762   0.767   1.098   1.049
  252SOLHW2  763   0.881   1.180   0.965
.
.
frame t= 1.000
 1543
1GLY  N1   1.229   1.032   1.106
1GLY H12   1.277   1.040   1.198
1GLY H23   1.290   0.979   1.041
1GLY H34   1.145   0.976   1.127
1GLY CA5   1.198   1.175   1.059
1GLYHA16   1.128   1.213   1.132
1GLYHA27   1.175   1.175   0.953
1GLY  C8   1.309   1.273   1.082
1GLYOT19   1.282   1.393   1.056
1GLYOT2   10   1.417   1.237   1.137
  155SOL OW  470   1.005   1.448   1.113
  155SOLHW1  471   1.103   1.445   1.095
  155SOLHW2  472   0.957   1.477   1.030
  388SOL OW 1169   1.307   1.001   1.370
  388SOLHW1 1170   1.329   1.053   1.452 etc...

Any suggestions are appreciated.

Thank you.
‌
 Sent with Mailtrack


---
With Best Regards,

Dilip.H.N
PhD Student.

On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan  wrote:

> You need -on for gmx select to write out the index file.
>
> On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N 
> wrote:
>
> > I tried the following two ways ie., with gmx select and with gmx trjorder
> >
> > 1) when i give the command :-
> > gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro
> -nshell
> > -r 0.35
> >
> > i got an output file, it has all the water molecules (i have 511 water
> > molecules in my system) for each time frame but it has arranged according
> > to the smallest distance to atoms in the reference group. (but i want
> only
> > those water molecules within 0.35nm of nitrogen of glycine molecule.)
> >
> > 2) in this command:-
> > gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close
> to
> > name N" resname SOL and within 0.35 of group protein'
> >
> > i am getting an .dat file which has only the coordinates and the format
> on
> > as in index file format.
> >
> > Actually, i wanted the format in which the gmx trjorder output gives (as
> in
> > my case, order.gro), but i want only those water molecules which are
> within
> > 3.5 nm of the nitrogen atom of glycine molecule for each time frame.
> >
> > Any suggestions are appreciated.
> >
> > Thank you.
> >
> > ‌
> >  Sent with Mailtrack
> >  signature_campaign=
> > signaturevirality&>
> >
> > ---
> > With Best Regards,
> >
> > Dilip.H.N
> > PhD Student.
> >
> > On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger 
> > wrote:
> >
> > > You can use either gmx trjorder with the nshell parameter (if it is as
> > > simple as within Xnm of Y, use nshell parameter, see manual) or gmx
> > select
> > > (if you need some more complex selection).
> > >
> > > On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N 
> > > wrote:
> > >
> > > > Hello all,
> > > >
> > > > I want to get the water molecules which are at a certain distance
> (say
> > > all
> > > > the water molecules which are within 0.35nm of the Nitrogen atom of
> > > glycine
> > > > molecule). How can i get this all the coordinates.?
> > > >
> > > > Any specific commands..??
> > > >
> > > >
> > > > Thank you.
> > > >
> > > > ---
> > > > With Best Regards,
> > > >
> > > > Dilip.H.N
> > > > PhD Student.
> > > >  Sent with Mailtrack
> > > >  > > signature_campaign=
> > > > signaturevirality&>
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Marc 

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

[Joe Jordan]

You need -on for gmx select to write out the index file.

On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N 
wrote:

> I tried the following two ways ie., with gmx select and with gmx trjorder
>
> 1) when i give the command :-
> gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro -nshell
> -r 0.35
>
> i got an output file, it has all the water molecules (i have 511 water
> molecules in my system) for each time frame but it has arranged according
> to the smallest distance to atoms in the reference group. (but i want only
> those water molecules within 0.35nm of nitrogen of glycine molecule.)
>
> 2) in this command:-
> gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close to
> name N" resname SOL and within 0.35 of group protein'
>
> i am getting an .dat file which has only the coordinates and the format on
> as in index file format.
>
> Actually, i wanted the format in which the gmx trjorder output gives (as in
> my case, order.gro), but i want only those water molecules which are within
> 3.5 nm of the nitrogen atom of glycine molecule for each time frame.
>
> Any suggestions are appreciated.
>
> Thank you.
>
> ‌
>  Sent with Mailtrack
>  signaturevirality&>
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
>
> On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger 
> wrote:
>
> > You can use either gmx trjorder with the nshell parameter (if it is as
> > simple as within Xnm of Y, use nshell parameter, see manual) or gmx
> select
> > (if you need some more complex selection).
> >
> > On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N 
> > wrote:
> >
> > > Hello all,
> > >
> > > I want to get the water molecules which are at a certain distance (say
> > all
> > > the water molecules which are within 0.35nm of the Nitrogen atom of
> > glycine
> > > molecule). How can i get this all the coordinates.?
> > >
> > > Any specific commands..??
> > >
> > >
> > > Thank you.
> > >
> > > ---
> > > With Best Regards,
> > >
> > > Dilip.H.N
> > > PhD Student.
> > >  Sent with Mailtrack
> > >  > signature_campaign=
> > > signaturevirality&>
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Marc Hoemberger
> > Ph.D. Candidate, Biochemistry and Biophysics,
> > Laboratory of Dorothee Kern
> > MS-009, 415 South St.
> > Brandeis University
> > Waltham, MA, 02453
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.




-- 
Joe Jordan
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 168, Issue 45

[zaved]

Dear Mark

Thank you for the kind response.

H with +0.418 charge and N with -0.845 charge is contributing towards
coulomb 14 interaction. So what is the amount of interaction between one
single H and N (3 bonds apart)? Kindly correct me if I am wrong.

Here is my Gdm topology

[ moleculetype ]
; name  nrexcl
GDM 3

[ atoms ]
;   nrtype   resnr  residuatomcgnr  charge  MASS
 1  C1GND   C1   1   1.027  13.019
 2 NT1GND   N2   2   -0.845 14.0067
 3  H1GND   H3   2   0.418  1.008
 4  H1GND   H4   2   0.418  1.008
 5 NT1GND   N5   3   -0.845 14.0067
 6  H1GND   H6   3   0.418  1.008
 7  H1GND   H7   3   0.418  1.008
 8 NT1GND   N8   4   -0.845 14.0067
 9  H1GND   H9   4   0.418  1.008
 10 H1GND   H10  4   0.418  1.008


 [ bonds ]
1 2  2  0.1340  1.0500e+07
1 5  2  0.1340  1.0500e+07
1 8  2  0.1340  1.0500e+07
2 3  2  0.1000  1.8700e+07
2 4  2  0.1000  1.8700e+07
5 6  2  0.1000  1.8700e+07
5 7  2  0.1000  1.8700e+07
8 9  2  0.1000  1.8700e+07
810  2  0.1000  1.8700e+07


 [ angles ]
1 2 32  120.00  390.00
1 2 42  120.00  390.00
1 5 62  120.00  390.00
1 5 72  120.00  390.00
1 8 92  120.00  390.00
1 8102  120.00  390.00
3 2 42  120.00  445.00
6 5 72  120.00  445.00
9 8102  120.00  445.00
2 1 52  120.00  670.00
5 1 82  120.00  670.00
8 1 22  120.00  670.00


[ pairs ]
;  aiaj funct   c0   c1
2 6 1 0.00e+00 0.00e+00
2 7 1 0.00e+00 0.00e+00
2 9 1 0.00e+00 0.00e+00
210 1 0.00e+00 0.00e+00
5 3 1 0.00e+00 0.00e+00
5 4 1 0.00e+00 0.00e+00
5 9 1 0.00e+00 0.00e+00
510 1 0.00e+00 0.00e+00
8 3 1 0.00e+00 0.00e+00
8 4 1 0.00e+00 0.00e+00
8 6 1 0.00e+00 0.00e+00
8 7 1 0.00e+00 0.00e+00

 [ dihedrals ]
;  aiajakal   gromos type
2 1 5 6  1 180.000   33.5  2
2 1 5 7  1 180.000   33.5  2
2 1 8 9  1 180.000   33.5  2
2 1 810  1 180.000   33.5  2
5 1 2 3  1 180.000   33.5  2
5 1 2 4  1 180.000   33.5  2
5 1 8 9  1 180.000   33.5  2
5 1 810  1 180.000   33.5  2
8 1 2 3  1 180.000   33.5  2
8 1 2 4  1 180.000   33.5  2

Thank you

Regards
Zaved Hazarika
PhD Scholar
Dept.of Molecular Biology and Biotechnology
Tezpur University
India

> Hi,
>
> Presumably Gdm has atoms connected by three adjacent bonds that generally
> have negative potential, and there's enough Gdm to make the total for the
> system negative. It's generally a good idea to understand how the topology
> you're using for Gdm works.
>
> Mark
>
> On Tue, Apr 10, 2018 at 2:23 PM  wrote:
>
>> Dear Gromacs Users
>>
>> I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl) with
>> gromos54a7 ff. Simulations have been performed for 100ns each at 298K,
>> 350K and 450K.
>>
>> The Average Coulomb-14 Energies are as follows:
>>
>> ricin in water (298K) : 3.42E+04 (positive value)
>> ricin in water (350K) : 3.41E+04 (positive value)
>> ricin in water (450K) : 3.40E+04 (positive value)
>>
>> ricin + GdmCl  (298K)  :-3.16E+06 (negative value)
>> ricin + GdmCl  (350K) : -3.17E+06 (negative value)
>> ricin + GdmCl  (450K) : -3.17E+06 (negative value)
>>
>> Can anyone suggest me why there is a (10 to the power 10) fold
>> difference
>> of average Coulomb-14 energy of ricin in presence of water and ricin in
>> presence of GdmCl?
>>
>> Thank You
>>
>> Regards
>>
>> Zaved



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Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

[Dilip.H.N]

I tried the following two ways ie., with gmx select and with gmx trjorder

1) when i give the command :-
gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro -nshell
-r 0.35

i got an output file, it has all the water molecules (i have 511 water
molecules in my system) for each time frame but it has arranged according
to the smallest distance to atoms in the reference group. (but i want only
those water molecules within 0.35nm of nitrogen of glycine molecule.)

2) in this command:-
gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close to
name N" resname SOL and within 0.35 of group protein'

i am getting an .dat file which has only the coordinates and the format on
as in index file format.

Actually, i wanted the format in which the gmx trjorder output gives (as in
my case, order.gro), but i want only those water molecules which are within
3.5 nm of the nitrogen atom of glycine molecule for each time frame.

Any suggestions are appreciated.

Thank you.

‌
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---
With Best Regards,

Dilip.H.N
PhD Student.

On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger 
wrote:

> You can use either gmx trjorder with the nshell parameter (if it is as
> simple as within Xnm of Y, use nshell parameter, see manual) or gmx select
> (if you need some more complex selection).
>
> On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N 
> wrote:
>
> > Hello all,
> >
> > I want to get the water molecules which are at a certain distance (say
> all
> > the water molecules which are within 0.35nm of the Nitrogen atom of
> glycine
> > molecule). How can i get this all the coordinates.?
> >
> > Any specific commands..??
> >
> >
> > Thank you.
> >
> > ---
> > With Best Regards,
> >
> > Dilip.H.N
> > PhD Student.
> >  Sent with Mailtrack
> >  signature_campaign=
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>
>
>
> --
> Marc Hoemberger
> Ph.D. Candidate, Biochemistry and Biophysics,
> Laboratory of Dorothee Kern
> MS-009, 415 South St.
> Brandeis University
> Waltham, MA, 02453
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Re: [gmx-users] How to post a reply on user list?

[RAHUL SURESH]

Hi.

Think you are doing the right way.

Try replying to this mail.

On Thu, Apr 12, 2018 at 11:35 AM, sanjeet kumar singh ch16d012 <
ch16d...@smail.iitm.ac.in> wrote:

>   Respected Sir,
>  I wanted to know that after posting a question on the
> list and getting a answer for that, from where i can post a reply on the
> user list if i want to discuss some more issues related to that
> particular question. I know that the question is silly but i am not able to
> find how to reply?
>
> Thanking You,
> SK
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*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] How to post a reply on user list?

[sanjeet kumar singh ch16d012]

  Respected Sir,
 I wanted to know that after posting a question on the
list and getting a answer for that, from where i can post a reply on the
user list if i want to discuss some more issues related to that
particular question. I know that the question is silly but i am not able to
find how to reply?

Thanking You,
SK
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