[gmx-users] Index oh dihedral for dPCA

[mfat290]

Hi,
I want to do dPCA analysis but I don’t index backbone and khi dihedral in RNA. 
Gmx  mk_anandx  do this but in its out file there are many index that I don’t 
find my favorite dihedral. Please gave me some advice.
 Thank you.

-- 
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] thread-MPI compatibility requirement?

[Kevin Boyd]

Hi,

This isn't a problem. Thread-mpi is the built-in mpi parallelization
packaged with gromacs. What that message is saying is that Gromacs will use
the openmpi library on your system instead, which is what you want when
running on multiple nodes.


Kevin


On Wed, Aug 15, 2018 at 1:50 PM, Jost, Gabriele (ARC-TNC)[Supersmith] <
gabriele.j...@nasa.gov> wrote:

> Hello,
> I would like to install GROMACS on a cluster of Volta nodes. I have
> openmpi_3.1.1
> and
> pgi_openmpi_2.1.2
>
> available. For of them I get the message
>
> -- MPI is not compatible with thread-MPI. Disabling thread-MPI.
>
> However, I really would like to have this to take advantage of all 8 GPUs
>
> Have any of you encountered this problem?
>
> Thanks for your advice,
> Gabriele
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at https://na01.safelinks.
> protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%
> 2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%
> 7C01%7Ckevin.boyd%40uconn.edu%7Ccd4fc2fc237a4a64a39e08d602d7a489%
> 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636699522554318712
> sdata=Ixr0akDcvt%2BhCNJtjEE4Pi93JEhIQdpCq2yGVTBWdSM%3Dreserved=0
> before posting!
>
> * Can't post? Read https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists
> data=02%7C01%7Ckevin.boyd%40uconn.edu%7Ccd4fc2fc237a4a64a39e08d602d7a489%
> 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636699522554318712
> sdata=IEmufjCx%2B0ixIg%2FZQhwXvnfE2fOdNZp1mZVFgxRTdF8%3Dreserved=0
>
> * For (un)subscribe requests visit
> https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%
> 2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu%
> 7Ccd4fc2fc237a4a64a39e08d602d7a489%7C17f1a87e2a254eaab9df9d439034
> b080%7C0%7C0%7C636699522554318712sdata=poEmzQRCfPJgpozYD2L7zfiyRC8g9z
> oxRT7Stzf%2BKEs%3Dreserved=0 or send a mail to
> gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] thread-MPI compatibility requirement?

[Jost, Gabriele (ARC-TNC)[Supersmith]]

Hello,
I would like to install GROMACS on a cluster of Volta nodes. I have
openmpi_3.1.1
and
pgi_openmpi_2.1.2

available. For of them I get the message

-- MPI is not compatible with thread-MPI. Disabling thread-MPI.

However, I really would like to have this to take advantage of all 8 GPUs

Have any of you encountered this problem?

Thanks for your advice,
Gabriele

-- 
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] Estimating the required computer resource for a MD project

[Alex]

Dear all,
In accessing to a supercomputer facility, I have been asked to estimate how
much computer resource (time and processors) I would need for a MD
simulation project, so, I wonder how I can roughly overestimate what the
project need?
Just to give a hint/example below is the time accounting table given in the
end of the Gromacs *.log file for a 3 ns NpT equilibration for a system of
interest containing 51700 atoms haring 64 ranks (60 for PP + 4  for PME )
on two nodes.
The performance varies between 10 and 20 ns per day for such system.

 Computing:  Num   Num  CallWall time Giga-Cycles
 Ranks Threads  Count  (s) total sum%
-
 Domain decomp.601  3 134.862  18610.850   0.5
 DD comm. load 601  3   0.376 51.907   0.0
 DD comm. bounds   601  29901   3.861532.785   0.0
 Send X to PME 601301 163.956  22625.842   0.6
 Neighbor search   601  30001 211.374  29169.406   0.7
 Comm. coord.  601297 378.854  52281.547   1.3
 Force 601301   20351.0552808429.921  70.1
 Wait + Comm. F601301 961.324 132661.926   3.3
 PME mesh * 41301   26174.800 240806.816   6.0
 PME wait for PP *   1041.450   9581.289   0.2
 Wait + Recv. PME F6013014491.696 619850.624  15.5
 NB X/F buffer ops.6018940001 179.639  24790.085   0.6
 Write traj.   601330   0.483 66.585   0.0
 Update601301  44.996   6209.424   0.2
 Constraints   601301 204.982  28287.321   0.7
 Comm. energies601 31  32.308   4458.424   0.1
 Rest  58.136   8022.782   0.2
-
 Total  27217.9014006452.726 100.0
-
(*) Note that with separate PME ranks, the walltime column actually sums to
twice the total reported, but the cycle count total and % are correct.
-
 Breakdown of PME mesh computation
-
 PME redist. X/F416021430.989  13165.027   0.3
 PME spread 413016457.925  59412.576   1.5
 PME gather 413014496.692  41369.334   1.0
 PME 3D-FFT 416029933.436  91387.102   2.3
 PME 3D-FFT Comm.   416021543.890  14203.705   0.4
 PME solve Elec 413012298.771  21148.577   0.5
-

   Core t (s)   Wall t (s)(%)
   Time:  1741945.67327217.901 6400.0
 7h33:37
 (ns/day)(hour/ns)
Performance:9.5232.520

Thank you.
Regards,
Alex
-- 
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] GTP

[Justin Lemkul]

On 8/15/18 9:08 AM, Mahdi Sobati Nezhad wrote:

Excuse me I don't understand completely, I residue I see Gua and Ade. You
say I change Gua base with Ade base in the ATPs residue?!
What about my hydrogen bonds?!
Do my charges don't change?!


Additive force fields are constructed from building blocks. Look at the 
normal library of nucleosides and nucleotides in the force field. The 
sugar and phosphate parameters don't change as a function of the 
nucleobase. Just swap G for A in ATP and you will have GTP.


-Justin


Thanks for your help

On Wed, 15 Aug 2018 16:00 Justin Lemkul,  wrote:



On 8/15/18 3:05 AM, Mahdi Sobati Nezhad wrote:

hello
I'm working on a protein that contains GTP in its structure. I can't find
any force field that contains GTP's residue but I find a force field that
contains the ATPs residue! There is any way that I can convert ATP to

GTP?!

Or any other idea?!

Just replace the Ade base with Gua.

-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

* 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.



--
==

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

* 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] GTP

[Mahdi Sobati Nezhad]

Excuse me I don't understand completely, I residue I see Gua and Ade. You
say I change Gua base with Ade base in the ATPs residue?!
What about my hydrogen bonds?!
Do my charges don't change?!

Thanks for your help

On Wed, 15 Aug 2018 16:00 Justin Lemkul,  wrote:

>
>
> On 8/15/18 3:05 AM, Mahdi Sobati Nezhad wrote:
> > hello
> > I'm working on a protein that contains GTP in its structure. I can't find
> > any force field that contains GTP's residue but I find a force field that
> > contains the ATPs residue! There is any way that I can convert ATP to
> GTP?!
> > Or any other idea?!
>
> Just replace the Ade base with Gua.
>
> -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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Test particle insertion in designated coordinates gives Segmentation fault

[Zheng, Lingru]

Hello everyone,

I have a problem using tpic. Basically following the process here: 
https://groups.google.com/forum/#!topic/archive-gmx-users/hh2cq9ZtqgU

My system is a surface in contact with liquid water and within which there are 
some ions to balance the surface charge. There is a few nm space above the 
liquid water layer. I intend to insert water molecule into the water 
liquid-vapour interface. Here are my steps:

1. I equilibrated the whole system using NVT for 40ns, then use trjconv -sep to 
split the .trr file into a series of configuration files conf*.gro

2. I use a script to add the following cavity coordinates to the bottom of each 
of the conf*.gro file:
601INS  X 3551   2.565   2.196   5.050

3. I then load all of the conf*.gro into vmd, and 'save coordinates' to obtain 
a new trajectory: nvt_cavity.trr

4. I then modify the final configuration (.gro) from the NVT run by adding the 
following lines at the bottom, and save it as nvt_cavity.gro :
  601SOL  OW 3551   0.028  -0.033   0.000
  601SOLHW1 3552  -0.072  -0.033   0.000
  601SOLHW2 3553   0.044   0.066   0.000
  601INS   X 3554   2.565   2.196   5.050

5. I added an insert.itp file to the forcefield folder as otherwise gromacs 
cannot recognise the atom/molecule, it contains:
[ moleculetype ]
; molname nrexcl
INS 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge
1X  1  INS   X   1  0

6. I also add the following to the ffnonbonded.itp file (Here I am unsure)
[ atomtypes ]
 X   9  18.0 0. A   0.000.00

7. To the .top file I added two lines to the [molecules]:
SOL 1
INS  1

8. Then I run the following:
gmx grompp -f tpi.mdp -o tpi -pp tpi -c nvt_cavity.gro -p 
topol.top
gmx mdrun -v -deffnm tpi -rerun nvt_cavity.trr -tpid energy

It generates the .tpr file but gives 'Segmentation fault’. I do not understand 
why. Can anyone please help?

Below is my tpi.mdp file:

; Run parameters
integrator = tpic ; leap-frog integrator
nsteps = 1 ; run these many tpi's
dt  = 0.01
nstlist = 10 ; number of attempted insertions each nstep
rtpi = 0.05 ; radius of sphere for insertions (nm)

; Neighborsearching
cutoff-scheme   = group ; verlet scheme not valid for tpi
pbc = xyz ; 3-D PBC
rlist = 1.4 ; short-range neighborlist cutoff (in nm)

; Electrostatics and vdw
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
vdwtype = cutoff
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres; account for cut-off vdW scheme


I previously ran the tpi algorithm, it works  but the excess chemical potential 
varies significantly with nlist and nstep even for a 40ns length trajectory, so 
I am trying to use tpic to see if it would give more reliable results.

Thanks in advance for your help!
Lynn
-- 
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] Negative tilt factor

[Maureen M Kitheka]

Hi. I have a triclinic box whose beta angle is 123 making my tilt factor be a 
negative value. The rlist,rcoulomb and rvdw depend also on the tilt factor. 
This makes it hard to define the coulombic interactions and cut-offs of my 
simulation box. 

Is there any way on how to get around this?

Regards,

Maureen.
-- 
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] Combining two pdb

[Justin Lemkul]

On 8/15/18 8:11 AM, RAHUL SURESH wrote:

Hi. I tried combining two pdb's such that, 1-24res of PDB X with 25-72 res
of PDB Y. I used pymol to do this. I just aligned the protein in such a way
that the N terminal of one protein is near the C terminal of the other. I
haven't made any physical bonds between them and saved as pdb. I have
equilibriated the structure for 500ps and found normal, but when visualixed
in chimera or discovery studio, it shows a gap between the structure.

Is there any fault in the methodology that I follow?

That depends on how you generated the topology. What you see in 
visualization software is not necessarily real. The only way to know if 
bonds are there or not is to look at the topology.


-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

* 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] Combining two pdb

[RAHUL SURESH]

Hi. I tried combining two pdb's such that, 1-24res of PDB X with 25-72 res
of PDB Y. I used pymol to do this. I just aligned the protein in such a way
that the N terminal of one protein is near the C terminal of the other. I
haven't made any physical bonds between them and saved as pdb. I have
equilibriated the structure for 500ps and found normal, but when visualixed
in chimera or discovery studio, it shows a gap between the structure.

Is there any fault in the methodology that I follow?

-- 
*Regards,*
*Rahul *
-- 
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] Coordinates transformation

[Justin Lemkul]

On 8/15/18 5:47 AM, Yasser Almeida Hernández wrote:

Hi all,

I have two different simulations of a membrane protein in a E. coli 
model membrane, and I want to analyze the protein-lipids interactions, 
by generating 2D density maps. In each simulation, the protein 
moves/rotates different along the xy plane of the membrane, and ends 
up in a different orientation.


Is there a way to transform the coordinates of one simulation, ex. 
superposing one onto the other (taking the protein coordinates of the 
first simulation as reference) to have both in the same coordinates 
system and the proteins in the same orientation, so I can generate 
comparable 2D maps?




Use trjconv -fit rotxy+transxy

-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

* 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] GTP

[Justin Lemkul]

On 8/15/18 3:05 AM, Mahdi Sobati Nezhad wrote:

hello
I'm working on a protein that contains GTP in its structure. I can't find
any force field that contains GTP's residue but I find a force field that
contains the ATPs residue! There is any way that I can convert ATP to GTP?!
Or any other idea?!


Just replace the Ade base with Gua.

-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

* 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] How to search efficiently the mailing list.

[Justin Lemkul]

On 8/14/18 4:42 AM, Sergio Perez wrote:

Dear grommacs community!

I have some questions about gromacs and I wanted to search within the
mailing list in case the problem had already commed up. But I could not
search easily within a google group like you do in plumed or there was not
a single webpage with all the subjects like in vmd. The only thing found
usefull was to search in google like:

remd restart site:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/

Is there a better way? I don't want to be asking what has already been
asked.


Just add "site:mailman-1.sys.kth.se" to any Google search string.

-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

* 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] Overlapping frames within one .xtc

[Mark Abraham]

Hi,

Paul's answer is fully correct if you are using the (default) appending
upon restart from checkpoint. If you manage the restart or the filenames
yourself, then trjcat -overwrite can be needed because the first trajectory
can have additional frames after the time of the checkpoint (which mdrun
truncates if needed in the the appending-restart-from-checkpoint case).

Mark

On Wed, Aug 15, 2018 at 12:24 PM Sergio Perez 
wrote:

> Hello,
>
> I use gmx 2018.1 .I had just done a restart and I then thought that maybe I
> could have had that problem and I thought maybe that command could solve
> the problem if it had existed. I mean that if in the file there were
> overlapping frames they would be overwritten just as if you are doing
> trjcat on two files. But my problem is irrelevant if gromacs takes care of
> it preventively.
>
> Thanks a lot!
>
> Sergio
>
> On Wed, Aug 15, 2018 at 10:51 AM Paul bauer 
> wrote:
>
> > Hello,
> >
> > if you restart a run from the checkpoint file than any recent version of
> > GROMACS will make sure that there are no overlapping frames and that the
> > continuation is exact.
> > What were you trying to do on the command line when you wanted to
> > continue the run, and what version have you been using?
> >
> > Cheers
> >
> > Paul
> >
> > On 15/08/18 10:43, Sergio Perez wrote:
> > > Dear GMX comunity,
> > >
> > > I would like to know if a run is interrupted abruptly (killed by the
> > user)
> > > and then is restarted with -append option, is there any chance that
> > > overlapping frames are generated within the .xtc file?
> > >
> > > If this were to happen, would
> > >   gmx trjcat -f trj.xtc -o trj2.xtc -overwrite
> > >
> > > solve the problem?
> > >
> > > Thank you all very much in advance!
> > >
> > > Best,
> > >
> > > Sergio Pérez-Conesa
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/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] Overlapping frames within one .xtc

[Sergio Perez]

Hello,

I use gmx 2018.1 .I had just done a restart and I then thought that maybe I
could have had that problem and I thought maybe that command could solve
the problem if it had existed. I mean that if in the file there were
overlapping frames they would be overwritten just as if you are doing
trjcat on two files. But my problem is irrelevant if gromacs takes care of
it preventively.

Thanks a lot!

Sergio

On Wed, Aug 15, 2018 at 10:51 AM Paul bauer  wrote:

> Hello,
>
> if you restart a run from the checkpoint file than any recent version of
> GROMACS will make sure that there are no overlapping frames and that the
> continuation is exact.
> What were you trying to do on the command line when you wanted to
> continue the run, and what version have you been using?
>
> Cheers
>
> Paul
>
> On 15/08/18 10:43, Sergio Perez wrote:
> > Dear GMX comunity,
> >
> > I would like to know if a run is interrupted abruptly (killed by the
> user)
> > and then is restarted with -append option, is there any chance that
> > overlapping frames are generated within the .xtc file?
> >
> > If this were to happen, would
> >   gmx trjcat -f trj.xtc -o trj2.xtc -overwrite
> >
> > solve the problem?
> >
> > Thank you all very much in advance!
> >
> > Best,
> >
> > Sergio Pérez-Conesa
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Coordinates transformation

[Yasser Almeida Hernández]

Hi all,

I have two different simulations of a membrane protein in a E. coli 
model membrane, and I want to analyze the protein-lipids interactions, 
by generating 2D density maps. In each simulation, the protein 
moves/rotates different along the xy plane of the membrane, and ends up 
in a different orientation.


Is there a way to transform the coordinates of one simulation, ex. 
superposing one onto the other (taking the protein coordinates of the 
first simulation as reference) to have both in the same coordinates 
system and the proteins in the same orientation, so I can generate 
comparable 2D maps?


Thanks in advance.

Regards

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

--
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] Overlapping frames within one .xtc

[Paul bauer]

Hello,

if you restart a run from the checkpoint file than any recent version of 
GROMACS will make sure that there are no overlapping frames and that the 
continuation is exact.
What were you trying to do on the command line when you wanted to 
continue the run, and what version have you been using?


Cheers

Paul

On 15/08/18 10:43, Sergio Perez wrote:

Dear GMX comunity,

I would like to know if a run is interrupted abruptly (killed by the user)
and then is restarted with -append option, is there any chance that
overlapping frames are generated within the .xtc file?

If this were to happen, would
  gmx trjcat -f trj.xtc -o trj2.xtc -overwrite

solve the problem?

Thank you all very much in advance!

Best,

Sergio Pérez-Conesa



--
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] Overlapping frames within one .xtc

[Sergio Perez]

Dear GMX comunity,

I would like to know if a run is interrupted abruptly (killed by the user)
and then is restarted with -append option, is there any chance that
overlapping frames are generated within the .xtc file?

If this were to happen, would
 gmx trjcat -f trj.xtc -o trj2.xtc -overwrite

solve the problem?

Thank you all very much in advance!

Best,

Sergio Pérez-Conesa
-- 
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] .gro file

[hosein geraili]

I have a .gro file in which the atoms and the box size is a rectangular cube, 
and I need to change it to a cube. How can I do that?Best
-- 
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] GTP

[Mahdi Sobati Nezhad]

hello
I'm working on a protein that contains GTP in its structure. I can't find
any force field that contains GTP's residue but I find a force field that
contains the ATPs residue! There is any way that I can convert ATP to GTP?!
Or any other idea?!
(I work with gromos 43a1 force field)

thanks
-- 
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.