Re: [gmx-users] Atom positions change between topology generation and NVT equilibration

[Christian Blau]

Hi Max,

In the .mdp file that you uploaded you are using

constraints = h-bonds   ; bonds involving H are constrained

Is that the right file? Otherwise running without these constraints 
might help.



On the off-chance that happened: not using -ignh in grompp avoids 
re-placement of hydrogens.


Best,

Christian


On 2020-04-29 13:49, Max Winokan wrote:

My apologies for the missing images. Hopefully they are available along with 
the MDP in the following link: 
https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0

  


If anyone knows what could be going on, please let me know. Essentially the 
atom positions in the first NVT step are very different to the input topology, 
see my original email below.

  


Best,

  


Max

  


From:  on behalf of Max Winokan 

Reply to: 
Date: Wednesday, 29 April 2020 at 1:36 PM
To: 
Subject: [gmx-users] Atom positions change between topology generation and NVT 
equilibration

  


Dear GMX-Users,

  


I am running some simulations of unsolvated DNA base pair dimers, with a 
topology generated from a structure previously optimised with quantum 
mechanical models. Because these structures have been highly-optimised it is 
important that Gromacs begins the MD with these atom positions.

  


After generating the topology with pdb2gmx I get the structure file (gc.gro) 
with the configuration seen below (after_pdb2gmx.jpg):

  

  


This configuration matches the optimised input structure. However, when I 
examine the trajectory (.trr) produced by running my NVT simulation (the MDP 
file for which is attached), the first timestep is very different from the 
input gc.gro structure, as seen below (first_nvt_frame.jpg):

  

  


The discrepancy is largest with the hydrogen atoms (which are not constrained 
of course), but all the atoms have been slightly shifted from the input 
configuration. Please could someone fill me in on the source of these position 
changes, and how I can modify my methods to avoid these.

  


Thank you and best regards,

  


Max Winokan

  


PhD Candidate in Theoretical Physics

Leverhulme Quantum Biology Doctoral Training Centre University of Surrey

GU2 7XH Guildford

United Kingdom

Office: 03AZ04

Email: m.wino...@surrey.ac.uk

  

  


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Re: [gmx-users] debugging

[Christian Blau]

Hi Miro,


This can be of great help and a wonderful learning experience; at the 
same time also an enormous time-sink.


First, you did already do a bunch of very helpful work in trying to find 
the latest version, where things still work,  have the error be 
reproducible on a test system.


If you were to file an issue on gitlab here: 
https://gitlab.com/gromacs/gromacs/-/issues - note that we moved from 
redmine - with the test sytem attached, this would help tremendously in 
fixing the bug.



If you are up for the joy of debugging yourself and possibly provide 
your solution to gromacs, here are the steps that I would take:


0. check that this issue has not been already reported and solved (try 
the latest patch release (you did that), check in gitlab issues)


1. identify the smallest system where the issue occurs (or at least 
reasonably small, so that you can test quickly)


2. have a debug built of gromacs, using -DCMAKE_BUILD_TYPE=Debug

3. Set up a good build and debug environment. This in itself can take 
some time to find something that works well for the system that you're 
on. For a quick start gdb might work as well, more visual aids via IDEs 
like vscode and clion, ... are very useful.


4. Find the line where the error occurs (segfaults are kind of nice 
because they are very clear errors, often in a specific line and often a 
result of overlooked memory management (we're working our way through 
removing this via modernisation to modern C++ standards, but not there yet))


5. Look at the call hierarchy, try to understand the larger context that 
you're in.


6. Try to identify the smallest surrounding context in which the bug 
occurs, try to figure which function/class allocates the memory for the 
object that causes the segfault


If there are tests and the context is not too large:

  7. See if there are some tests written for this context. (usually 
there are corresponding .cpp files in the test folder where bugs occur), 
add a test that reproduces the buggy behaviour.


  8. Compile the tests, change code, then recompile tests until your 
test passes.


  9. Check that your intial case works, otherwise add more tests that 
catch the failing behaviour, fix, repeat


Otherwise:

Follow memory allocations, resizes, etc of the offending object, see if 
you can trigger the segfault earlier by trying to access memory that you 
know should be accessible.


Finally open a new merge-request on gitlab (see under 
https://gitlab.com/gromacs/gromacs/-/merge_requests), or create a merge 
request from the issue you had opened. Wait for comments and code-review.



Hope that gives you a feeling for the task on hand - I would personally 
definitely recommend at least looking *at* the source code and giving it 
a shot, also for the sake of getting a feel for the internal gears of 
GROMACS and just taking it as far as you can and have time.


Happy coding,

Christian

On 2020-04-28 12:16, Miro Astore wrote:


Hi all,

I am interested in how Gromacs works at the back end but I don't have much
C experience so this might be silly.

I have noticed that one of my systems that includes virtual sites parses
fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a
segmentation fault.
21169 Segmentation fault  (core dumped)
I'd like to try and debug this further. Should I try and go after this
myself?


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Re: [gmx-users] lincs warning

[Christian Blau]

Hi Afsane,


This might be an issue with the pressure coupling, depending on the 
compressibility you give for your system and the algorithm that you use 
for pressure coupling you might see quite large fluctuations in 
pressure. One idea might be to use temperature coupling to quickly 
dissipate large energies due to large fluctuations in box size. If 
you're not already using it you could try a robust temperature coupling 
with  v-rescale with tau-t = 0.1, which is usually recommendable. Using 
some steps to carefully anneal your system might help as well. To 
carefully heat your system from 0 to 300K in the first 100ps of the 
simulation you might use "annealing = single annealing-npoints = 2 
annealing-time = 0 100 annealing-temp = 0 300".


Then pressure-pre-equlibrating your system with the Berendsen barostat 
might be helpful, just don't use it for your production run.


Best,

Christian

On 2020-04-25 19:16, Afsane Farhadi wrote:

Hi gromacs users I generated a mixed box of methane and carbondioxide with 
insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and 
carbondioxide are optimized and the energy minimization of mixed gas  is ok 
(potential energy is about -2e+03))but when I want to run a npt run ,the lincs 
warning are showing( bond rotate more than 30 degree).I repeated energy 
minimization but it didn't work right Can any body help me please?

Sent from Yahoo Mail on Android

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Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

[Christian Blau]

Hi Yujie,


This sounds very much like something we should fix.

Can you file a bug report at https://redmine.gromacs.org/ where you can 
also upload the file that you are trying to run? Let me know if you have 
any trouble with uploading the report - I'm eager to know what happened.



Best,

Christian


On 2020-03-19 13:18, liuyujie714 wrote:

>I am guessing the issue a bit from the brief title, let me know if
>installing the external program required to run dssp as described below
>is addressing the issue or if this is something that used to work in
>GROMACS 2019 and suddenly stopped working, in which case I would need
>quite a bit more information.
>Dssp in gromacs relies on an external program to run which you can find
>here: http://swift.cmbi.ru.nl/gv/dssp , just installing GROMACS does not
>suffice.

Thanks Christian!
I post some information as following:
  This "gmx do_dssp" tool of gmx2020 will report an error 
"Segmentation fault" and no xpm and xvg file generated. I tesetd 2.0.4 
and later version of dssp. The gmx2018 and gmx 2019 can work correctly.
  Then I checked gmx_do_dssp.cpp code and found some parts of matrix 
changed a lot, I think this code may have a problem.

  Thanks
  Yujie Liu


liuyujie714
liuyujie...@gmail.com

 

签名由 网易邮箱大师  
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Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

[Christian Blau]

Hello Yujie Liu,


I am guessing the issue a bit from the brief title, let me know if 
installing the external program required to run dssp as described below 
is addressing the issue or if this is something that used to work in 
GROMACS 2019 and suddenly stopped working, in which case I would need 
quite a bit more information.


Dssp in gromacs relies on an external program to run which you can find 
here: http://swift.cmbi.ru.nl/gv/dssp , just installing GROMACS does not 
suffice.


The manual is hinting at this here:

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-do_dssp.html

There is a newer version available on github - see here: 
https://github.com/cmbi/dssp


which might compile better.


Best,

Christian


On 2020-03-19 11:48, liuyujie...@gmail.com wrote:
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Re: [gmx-users] mdp option periodic molecules

[Christian Blau]

Hi Johannnes,


That is correct.

Another confirmation of what you already suspect is found in the manual in

http://manual.gromacs.org/documentation/current/reference-manual/topologies/molecule-definition.html 



"Molecules can be made infinitely long by connecting to themselves over periodic boundaries. When such periodic 
molecules are present, an option in the mdp file needs to be set to tell GROMACS not to attempt to make molecules that 
are broken over periodic boundaries whole again."



Best,

Christian

On 2020-03-06 08:52, Johannes Hermann wrote:

Dear all,

could you please confirm if I understood the periodic molecules entry (I already browsed through the manual and 
mailing list):


I need "periodic molecules = yes", if a molecule interacts=connects to itself via covalent bonds over the periodic 
boundary.


I do NOT need "periodic molecules = yes", if a molecule interacts via non-covalent interactions to itself via PBs. In 
this case "periodic molecules = no" is the right choice.


Is that right?

Thanks in advance!

All the best

Johannes




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Re: [gmx-users] Listing residues in gromacs

[Christian Blau]

Hi Subhomoi,


Yes,

gmx select

can do that (see http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html) 




For what you want to do, it's beneficial to have a look at the selection syntax 
here

http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html 




Best,

Christian

On 2020-02-18 13:14, Subhomoi Borkotoky wrote:

Hi,

Is there any option in gromacs to list residues/atoms around a reference
group? I have checked trjorder , but it only gives number of molecules.

Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subho...@yahoo.com

https://scholar.google.co.in/citations?hl=en=1=bJz7GokJ

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Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU

[Christian Blau]

Hi Navneet,

This is achieved by setting the installation directory with cmake for the 
respective source code that you downloaded, then sourcing different GMXRC.

Install different GROMACS builds fromt the source code into seperate folders 
using something like

-DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2019.6

and for another version

-DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2020

Then,

"source /home/navneet/local/gromacs-2020/bin/GMXRC"

will give you GROMACS 2020, while

"source /home/navneet/local/gromacs-2019.6/bin/GMXRC"

will give you GROMACS2019.6.

Best,

Christian

On 2020-02-17 15:15, Navneet Kumar wrote:

Hello Everyone!

I have currently installed GROMACS 2018.8 and using it. But for some of my
previous work, I want to use the older version of GROMACS i.e 5.x.
I have installed the GROMACS using this method


sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF

-DCMAKE_C_COMPILER=/usr/bin/gcc-6
-DREGRESSIONTEST_PATH=/home/nitttr/Downloads/regressiontests-2018.8

everytime when I use GROMACS I start with command-

"source /usr/local/gromacs/bin/GMXRC"
How can I install some other version of gromacs and use simultaneously?


/

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Re: [gmx-users] (no subject)

[Christian Blau]

Hi Shakkira,


The simulation box deformation is described by six parameters that describe three basis box vectors with the following 
contraints,


 - the first box vector is aligned along the x-axis, with coordinates thus has 
coordinates (xx,0,0)

 - the second box vector is aligned in the x-y plane with coordinates (yx,yy,0)

 - the third box vector is free (zx,zy,zz)


The six parameters that you give in .mdp files are in the following order

xx, yy, zz, yx, zx, zy


The corrent box is then calculated as

box(t_start)+(t-t_start)*deform


For more information have a look at the gromacs manual mdp parameter 
description:

http://manual.gromacs.org/current/user-guide/mdp-options.html

under non-equilibrium MD:

   (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
   The velocities of deformation for the box elements: a(x) b(y) c(z)
   b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
   is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
   elements are corrected for periodicity. The coordinates are
   transformed accordingly. Frozen degrees of freedom are (purposely)
   also transformed. The time ts is set to t at the first step and at
   steps at which x and v are written to trajectory to ensure exact
   restarts. Deformation can be used together with semiisotropic or
   anisotropic pressure coupling when the appropriate
   compressibilities are set to zero. The diagonal elements can be
   used to strain a solid. The off-diagonal elements can be used to
   shear a solid or a liquid.


Best,

Christian

On 2020-02-16 12:12, shakira shukoor wrote:

   Hi all
Can anyone help me with the DEFORM option in Gromacs to change the box
values?



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Re: [gmx-users] genion without stdin

[Christian Blau]

Hello Matthias,


yes, if you use an indexfile with exactly one index group inside, this index 
group will be automatically picked.


(like

[ solvent ]

1001 1002 1003 1004 1005 1006 1007 1008 1009  ...

and nothing else


Best,

Christian


On 2020-02-13 11:49, Urban, Matthias wrote:

Hello mailinglist,


is there a way to prevent "gmx genion" from expecting input via stdin?


I am using gromacs v2020 with gmxapi.


Thanks in advance.


Cheers,


Matthias

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 80, 2. Re: Analysis with .sh file (Li, Shi)

[Christian Blau]

HI Riccardo,


in this case, it's the piping that does not work, so gromacs does not get the right 
"return". An alternative is

printf "10\n12\n"


Best,

Christian

On 2020-01-31 09:22, ric.co...@gmail.com wrote:

Dear all,

This is an example of a line I have been using on Gromacs 5.0.4:" echo
 "10" "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" and this is
 the error message I'm receiving from Gromacs: "Error in user input:
 Invalid selection '10 12 '
  B  Near '12'
  B B B  syntax error "
Regards,
Riccardo

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of
gromacs.org_gmx-users-requ...@maillist.sys.kth.se
Sent: jueves, 30 de enero de 2020 23:31
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 189, Issue 80

Send gromacs.org_gmx-users mailing list submissions to
gromacs.org_gmx-users@maillist.sys.kth.se

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When replying, please edit your Subject line so it is more specific than
"Re: Contents of gromacs.org_gmx-users digest..."


Today's Topics:

1. 3D monitors (tarzan p)
2. Re: Analysis with .sh file (Li, Shi)
3. Regarding rdf and number of molecules in the FSS of  tetramer
   (Ashma Khan)
4. Customize gromac FF for lipid parameters (Yogesh Sharma)
5. Re: Customize gromac FF for lipid parameters (Justin Lemkul)
6. Re: gromacs-2020 build gcc/nvcc error (Ryan Woltz)


--

Message: 1
Date: Thu, 30 Jan 2020 14:23:59 + (UTC)
From: tarzan p 
To: "gmx-us...@gromacs.org" 
Subject: [gmx-users] 3D monitors
Message-ID: <2141569556.1500215.1580394239...@mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

Hi all..Am looking for some good 3D monitors (either passive or active)Need
suggestions for some good 3D monitors for protein structure and interactions
visualization...
with best wishes


--

Message: 2
Date: Thu, 30 Jan 2020 09:50:09 -0500
From: "Li, Shi" 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Analysis with .sh file
Message-ID:

Content-Type: text/plain; charset="UTF-8"



Dear all,

I have recently upgrade my Gromacs to the 2019 version from the 5.0.4
and I found out that now that while I'm trying to use a .sh, as I was
doing in the version 5.0.4, now I'm receiving back an error since the
syntax is wrong. I'm wondering if someone could please help me.



What is the script in your .sh file? There is not enough information to find
out what goes wrong.




Regards,

Riccardo



--




--

Message: 3
Date: Thu, 30 Jan 2020 20:29:56 +0530
From: Ashma Khan 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding rdf and number of molecules in the FSS
of  tetramer
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Dear user's
I have calculated the rdf of urea molecules around the peptides for
different concentration of urea and obtained that peak height of first
solvation shell (FSS) decreases with increase in concentration of urea.
After that I have calculated the number of urea molecules in FSS and found
that urea molecules in the FSS increases with concentration of urea. There
is no correlation between the peak height of FSS and number of urea
molecules. Can anybody suggest me ? what is the reason The command I have
used is gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com
-seltype whole_res_com gmx select -f md.xtc -s md.tpr -os number.xvg -select
"resname URE and within 0.5 of group protein" -selrpos whole_res_com
-seltype whole_res_com


--
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh


--

Message: 4
Date: Fri, 31 Jan 2020 01:32:43 +0530
From: Yogesh Sharma 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Customize gromac FF for lipid parameters
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Hey everyone,
I have a membrane patch generated by charmm gui. I want to customize my
gromac forcefield in accordance with it. I want some suggestion in
extracting information from charmmff. I guess i need information to add in
ffbonded and ffnonbonded files. Can someone help me with it

I don't want to run simulations in charmmff



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Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

[Christian Blau]

Hi Michele,


Thanks for the input and suggestion!


I created a redmine issue using your observations that you can follow at 
https://redmine.gromacs.org/issues/3353



Best,

Christian

On 2020-01-23 11:03, Michele Pellegrino wrote:

Ok, I believe I have found the nature of this 'quirk' looking at the source 
code (as Berk suggested me to do).
I was assuming a format, but GROMACS is producing another: the .dat file in the 
output contains the values PLUS the coordinates for each bin, that is the first 
row and the first colum are not denisty values, but coordinates; hence the 
output matrix is indeed (n1+1)x(n2+1), the actual values being in 
grid[1:n1-1,1:n2-1] (0-start index convention).
So apparently is not a bug in the code, but just a misunderstanding of me as 
user; I double checked the documentation (both for 2019.04 and for the new 2020 
release) and I did not find any reference to the format of the output file: 
could it be a good idea to incude some indication in that regard?

Cheers,
Michele

* there is a typo in the original message (2:n2-2 instead of 1:n2-1)

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Michele Pellegrino 

Sent: 22 January 2020 22:58
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap 
doestnottmatchtprescribedtsize

I tried just now: it did not work: 1728 values expected, 1645 values in the 
.dat file.
I managed to make it work by defining the number of values in each direction as 
(in Python):
Nx = np.sqrt(Nda*Lx/Lz)
Nz = Nx*Lz/Lx
Nx = int( np.round(Nx) )
Nz = int( np.round(Nz) )
being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of 
the simulation box in the x (z) direction (np stands for numpy).
However, I believe this manipulation should not be necessary.

Cheers,
Michele

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of David van der Spoel 

Sent: 22 January 2020 22:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap 
doestnottmatchtprescribedtsize

Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:

Ok, thank you.
I am counting the elements assuming they are in an array organized in a row 
major fashion.

have you tried supplying -n1 47 -n2 35 to be able to check manually?

(by the way a resolution of 0.1 Angstrom is unlikely to give you a
smooth surface)

Scarica Outlook per Android

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Berk Hess 

Sent: Wednesday, January 22, 2020 6:34:47 PM
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed 
size

A grid element

I looked at the code and it directly uses n1 and n2 you provide. So I thought 
that it might be that the code reading the file has a limit on the number of 
characters on a line.

/Berk


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Michele Pellegrino 

Sent: Wednesday, January 22, 2020 5:07 PM
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed 
size


What do you mean by 'element'?

Anyway, part of the issue was in how I was reading the file; with a little 
modification of the script I reduced the mismatch, but it still persists.
Could it be because GROMACS forces a grid with same meshwith in x and (in my 
case) z direction, so that the used should impose either -n1 OR -n2 (but not 
both)? Or maybe the issue is just in the format of the .dat output file?

By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if 
that may help understanding the issue).

Thanks,
Michele


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Berk Hess 

Sent: 22 January 2020 16:49
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap does not match  
prescribed  size

How are you counting the elements? Lines with 3531 elements are very long, so 
they can easily exceed some limit.

/Berk


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Michele Pellegrino 

Sent: Tuesday, January 21, 2020 5:16 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size

Hello,


I am struggling a little bit with gmx densmap. I am trying to obtain a matrix 
with density values from the .dat file generated by the program; however the 
number of data in the output file does not match what I am expecting.

I tried to prescribe both the number of bins in each direction (-n1 and -n2 
options) and the grid size (-bin option), not at the same, of course:


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver 
y -n1 4772 -n2 3531


OR (equivalently):

Re: [gmx-users] specific heat calculation using "gmx dos"

[Christian Blau]

Hi Pragati,


Answers in short:

1. It's only c_v, you'll have to add VT \alpha_T^2/ \kappa_T to obtain c_p

2. I suggest you use the approach in the paper, running an NVT simulation and 
base all on the c_v estimate.

3. To check convergence, I suggest running the analysis again on shorter parts of your trajectory (1/2 of the data, 1/4 
of the data etc.)


4. You'll not see the quantum correction with this approach, your force-field might rely on entropy- enthalpy 
compensation. I would guess that you would obtain worse results with such an approach.



The DOS tool follows the supplementary material S(1)-S(17) in "Force Field Benchmark of Organic Liquids: Density, 
Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion 
Coefficient, and Dielectric Constant" by


Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, David van der Spoel. It's output "Heat 
capacity ... J/mol K" corresponds to equation (14) in above publication, the constant volume heat capacity c_v *with* 
quantum correction. To obtain c_p you would still need to apply (eqn 12).



Best,

Christian


On 2020-01-03 07:33, Pragati Sharma wrote:

  Dear all,

I am trying to calculate heat capacity of a polymeric system (30k atoms)
using gromacs.
I tried the classical way from the fluctuation dependent properties using
"gmx energy", but the values are not matching experimental values.

I want to use "gmx dos" program, but I have some confusions.

1. Does it gives only the quantum corrections in heat capacity, which
should be added to the one calculated from 'gmx energy' or  Does it gives
full heat capacity value including quantum corrections.

2. Should I have to run NVT simulations, run gmx dos, find Cv and the add
then calculate Cp, as given in the paper ( J. Chem. Theory Comput. 2012, 8,
61–74), *OR*
I can run a NPT simulation and calculate Cp from gmx dos.

3. gmx dos gives the Cp/Cv value in "dos.log" file. but is there any output
file to check its convergence. I mean how should I decide, how long the
trajectory I should take.

4. Cp can be calculated from the slope of enthalpy vs temp plot (dH/dT) (in
a small range of temp), what limitation does this approach have.

Thanks in advance.

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Re: [gmx-users] State of Matter

[Christian Blau]

Hi Sina,


You can have a look at order parameters of your system like angular distributions, orientations, local densities, etc. 
with analysis tools like gmx angle, h2order, order.



Best,

Christian

On 2020-01-20 12:02, Sina Omrani wrote:

Hi, I'm new to GROMACS and Molecular Dynamics and I'm sorry if it is a
witless question but how we can specify the state of a component (gas,
liquid or super critical) in MD simulations?

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Re: [gmx-users] gmx genconf

[Christian Blau]

Hi Alex,


It's not possible with genconf. genconf only ever outputs a single 
structure. If you provide a trajectory, each frame in the trajectory is 
matched with a grid position that is then output as a single structure.


If you're looking into this for the sake of visualisation, tools like 
vmd and pymol usually do provide the functionality to generate periodic 
images. If you're after some analysis, it's often better to make use of 
the symmetry properties in the analysis explicitly rather than doubling 
the data.



Best,

Christian

On 2020-01-15 19:10, Alex wrote:

Dear all,
I am aware of the "gmx genconf -f time.gro -nbox 2 2 2 -o 2times.gro" in
order to expand a gro file 2 times in all directions. I wonder if it is
possible to expand a xtc trajectory and outpout a larger trajectory in the
same way?

According to genconf man page I see that the input could be -trj.xtc, but
no trajectory as output has been mentioned there apparently.

Regards,
Alex

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Re: [gmx-users] Visualize replica exchange

[Christian Blau]

Hi Ahmed,


I don't know about VMD, but you can try

./gromacs/scripts/demux.pl


Best,

Christian

On 2020-01-09 15:01, hind ahmed wrote:

Dear All,

How can I visualize replica exchange in VMD?

Thanks

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Re: [gmx-users] Replica exchange probabilities and extend simulation

[Christian Blau]

Hi Ahmed,


If you have a look into "Optimal temperature ladders in replica exchange 
simulations", available here:

https://www.sciencedirect.com/science/article/pii/S000926140900356X

you will see that your exchange probabilities should be a bit higher. Then again, you might have to set up a lot more 
simulations, which you can get around with more advanced protocols like solute tempering (REST). These methods are 
implemented in PLUMED for example.



If you want further insight, I suggest using

demux.pl md.log

It's a good sign if you see single replicas walking through the whole temperature range, it's a bad sign if you see that 
some replicas only stay close to a certain temperature.



Best,

Christian


On 2020-01-09 14:58, hind ahmed wrote:

Dear All,

  Are these probabilities good? and how can I extend the simulation of 
replica-exchange?

Thanks

Replica exchange statistics
Repl  14999 attempts, 7500 odd, 7499 even
Repl  average probabilities:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  
.01  .01  .01  .01  .01  .01  .01  .01  .02  .02  .02  .01  .02  .02  .02  .02  
.02
Repl  number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  259  263  270  330   62   57   63   58   65   67   71   74   89   87  
 88  103  100  103   98   98  114   93  132  127  149  111  117  126  129  124  
145
Repl  average number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  
.01  .01  .01  .01  .01  .01  .02  .01  .02  .02  .02  .01  .02  .02  .02  .02  
.02


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Re: [gmx-users] cant compute msd

[Christian Blau]

Hi Devargya,


I believe it's the mixture of -mol and -o options at the same time that leads to the unexpected behaviour - there can 
only be one .xvg output for this tool and we'll see to having it fixed.


Do you get any diff_mol.xvg files instead?


The documentation states that

"If -mol is set, gmx msd plots the MSD for individual molecules (including
making molecules whole across periodic boundaries): for each individual
molecule a diffusion constant is computed for its center of mass. The chosen
index group will be split into molecules."


Best,

Christian


On 2020-01-08 11:12, Devargya Chakraborty wrote:

hi, when i am using the command
  gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg

after that choosing a group the following line is coming.
Select a group to calculate mean squared displacement for:
Group 0 ( System) has  5616 elements
Group 1 (  Other) has  5616 elements
Group 2 ( c2) has  2376 elements
Group 3 (   ntf2) has  3240 elements
Group 4 (  N) has   216 elements
Group 5 (  N) has   216 elements
Select a group: 3
Selected 3: 'ntf2'
Split group of 3240 atoms into 216 molecules
Reading frame5000 time 2.000   Killed

and i cant get the msd file any suggestion regarding this??

thank you

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Re: [gmx-users] How to rotate the molecule in box

[Christian Blau]

Hi Yeping,


The center of rotation is (0,0,0) for the rotate command, which is the lower left front corner of your box, and not the 
box center. That's why the molecule moves out of the box when rotating.


One (of conceivable more ways) to perform the rotation, is to use -center (0,0,0) to create a new structure, centered on 
the origin, then perform the rotation, and then shift the molecule back into the box center with -center only.



Best,

Christian


On 2019-12-30 14:44, sunyeping wrote:

Dear all,

By using the editconf command, we can build a box for the protein molecule, for 
example:

  gmx editconf -f complex.gro -o newbox.gro -c -d 1.2 -bt cubic

but how to rotate the molecule in the box? I tried to use "-rotate" option of 
the editconf command to do so, but I found part of the molecule goes out the pbc box 
after rotation. Please refer to the image at the following link:

https://drive.google.com/file/d/1P_yTeRSkHpeUTXSUZMlTw2AHZ17s0htv/view?usp=sharing

The molecule was orignally at position 1. I wanted to rotate the molecule 
around x and y axes by 45 degrees. After I ran the following command:

 gmx editconf -f newbox.gro -rotate 45 45 0 -bt o -o newbpx_1.gro

The molecule went to position 2. You can see part of the molecule are now out 
of the box.

Do you know how to rotate the molecule but keep it within the box?

Thank you in advance.

Yeping

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Christian Blau]

Hi Navnett,


gmx select will be your friend.


At the bottom of

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

you'll find some example commands. Something along the lines of

  gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much worth the 
effort reading through that documentation.


Best,

Chrsitian

On 2020-01-08 10:42, Navneet Kumar wrote:

Sorry, it should be 150-200 residues.

On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar  wrote:


Hello Everyone!


How to create an index group for Backbone/C-alpha for a specific set of
residues from protein? (Say Protein with 200 amino acid; want to create an
index group for the backbone of residues 150-210).
Regards
Navneet Kumar







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Re: [gmx-users] Make index command in gromacs

[Christian Blau]

Hi Shan,


gmx select gives you many more options to do complex arithmetic with selections 
that might help you here.


You can try using

gmx select -select "SELECTION STING"

you'll find lots of selection string examples at the bottom in here:

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



Best,

Christian


On 2020-01-07 23:33, Shan Jayasinghe wrote:

Dear Gromacs Users,

In my simulations, I have different sizes of water droplets.  I need
indexes of water molecules in each droplet separately. I am trying to make
the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
help regarding this matter.

Thank you.

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Re: [gmx-users] Trajectory guided by density maps

[Christian Blau]

Hi Ramon,


You would not need to keep your system constrained in the state that you started from to see a transition. Pushing state 
A , based on a crystal structure, into state B , described by a density, should give you just the transition you want.


If you would like to choose an arbitrary point "between" the two states, 
however, you would have to use maps of both states.


Best,

Christian

On 2019-12-12 12:37, Ramon Guixà wrote:

Hi Christian,

Ok, so If can't apply forces from two density maps at the same time then I
don't see how can I perform a guided transition.
I mean, I figured I would need to gradually switch on one map while
switching off the other, but for this I need to apply both restraints at
the same time right?

Do you see another way of doing this?

Best,
Ramon

On Thu, Dec 12, 2019 at 12:23 PM Christian Blau  wrote:


Hi Ramon,


This feature will be released in January ;) and is in a beta version, soon
to be release candidate, so you are
definitely an early adopter.

Most of the parameters are set by default in the .mdp file if you do not
set them yourself, you'll see them also in

http://manual.gromacs.org/2020-beta3/user-guide/mdp-options.html


It is hard to give very general advice on the parameters, but some things
to observe:

   - the force constant can have a very large range of values, try changing
the order of magnitude first, if you don't
have an idea, or try "adaptive force scaling"

   - the resolution parameter
density-guided-simulation-gaussian-transform-spreading-width is important
as well and
interplays with the force-constant - if this value is high (low
resolution), the forces will go down as well (there is
not so much force needed to make a blob be similar to anything)

   - density-guided-simulation-nst may be crucial for performance, the
blobbier the densities and / or previous value the
larger you can set this value. 20 or so is a good first guess for lots of
applications


For now you cannot apply forces from two density maps at the same time,
though this is an obvious possible extension for
a next release.

Since I just implemented the feature, I'll be interested in how things
work out for you and what is yet unclear in
documentation, etc..


Best,

Christian


On 2019-12-12 11:58, Ramon Guixà wrote:

Hi Christian,

thanks a lot for your answer. Good to know this makes sense to someone

else

too.
Now I have two questions out of ignorance (never used this newly
implemented feature before):

1) Can I apply two sets of forces (restraints) at the same time, namely

one

for each density map?
2) Would you have by any chance an example or a default set of values for
the density-guided options? I am not really sure how to use this feature
anyway...

Thanks!
R

On Thu, Dec 12, 2019 at 11:29 AM Christian Blau  wrote:


Hi Ramon,


This is definitely a way to obtain a transition path.

One things to consider here is that you deliberately "throw away"

already

perfect information about your target
structure, so it might be harder to reach. On the other hand you might

not

care to have an exact overlap with the
structures, so in this sense using the density might aid you in finding

a

more realistic transition path that is closer
to the lowest free energy barrier. If you're interested in that, using
very low resolution maps might even be beneficial.

I personally would be excited to hear about your findings.

Best,

Christian


On 2019-12-11 17:18, Ramon Guixà wrote:

Hi there,

I would like to use GROMACS to create a trajectory that goes from one
crystal structure to another crystal structure, both obtained from the

same

system using time resolved crystallography.

Would it be feasible to use the newly implemented density-guided
simulations parameters to guide this simulation by first fitting the
initial crystal structure its density map and then switching off these
restraints while switching on the density map restraints of the second
crystal structure? I figured this would in principle create a

trajectory

that better reflect the transition from one state to the other, but I

am

not even sure if this makes sense at all...

Thanks in advance for the guidance,
Ramon

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Re: [gmx-users] Trajectory guided by density maps

[Christian Blau]

Hi Ramon,


This feature will be released in January ;) and is in a beta version, soon to be release candidate, so you are 
definitely an early adopter.


Most of the parameters are set by default in the .mdp file if you do not set 
them yourself, you'll see them also in

http://manual.gromacs.org/2020-beta3/user-guide/mdp-options.html


It is hard to give very general advice on the parameters, but some things to 
observe:

 - the force constant can have a very large range of values, try changing the order of magnitude first, if you don't 
have an idea, or try "adaptive force scaling"


 - the resolution parameter density-guided-simulation-gaussian-transform-spreading-width is important as well and 
interplays with the force-constant - if this value is high (low resolution), the forces will go down as well (there is 
not so much force needed to make a blob be similar to anything)


 - density-guided-simulation-nst may be crucial for performance, the blobbier the densities and / or previous value the 
larger you can set this value. 20 or so is a good first guess for lots of applications



For now you cannot apply forces from two density maps at the same time, though this is an obvious possible extension for 
a next release.


Since I just implemented the feature, I'll be interested in how things work out for you and what is yet unclear in 
documentation, etc..



Best,

Christian


On 2019-12-12 11:58, Ramon Guixà wrote:

Hi Christian,

thanks a lot for your answer. Good to know this makes sense to someone else
too.
Now I have two questions out of ignorance (never used this newly
implemented feature before):

1) Can I apply two sets of forces (restraints) at the same time, namely one
for each density map?
2) Would you have by any chance an example or a default set of values for
the density-guided options? I am not really sure how to use this feature
anyway...

Thanks!
R

On Thu, Dec 12, 2019 at 11:29 AM Christian Blau  wrote:


Hi Ramon,


This is definitely a way to obtain a transition path.

One things to consider here is that you deliberately "throw away" already
perfect information about your target
structure, so it might be harder to reach. On the other hand you might not
care to have an exact overlap with the
structures, so in this sense using the density might aid you in finding a
more realistic transition path that is closer
to the lowest free energy barrier. If you're interested in that, using
very low resolution maps might even be beneficial.

I personally would be excited to hear about your findings.

Best,

Christian


On 2019-12-11 17:18, Ramon Guixà wrote:

Hi there,

I would like to use GROMACS to create a trajectory that goes from one
crystal structure to another crystal structure, both obtained from the

same

system using time resolved crystallography.

Would it be feasible to use the newly implemented density-guided
simulations parameters to guide this simulation by first fitting the
initial crystal structure its density map and then switching off these
restraints while switching on the density map restraints of the second
crystal structure? I figured this would in principle create a trajectory
that better reflect the transition from one state to the other, but I am
not even sure if this makes sense at all...

Thanks in advance for the guidance,
Ramon

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Re: [gmx-users] Trajectory guided by density maps

[Christian Blau]

Hi Ramon,


This is definitely a way to obtain a transition path.

One things to consider here is that you deliberately "throw away" already perfect information about your target 
structure, so it might be harder to reach. On the other hand you might not care to have an exact overlap with the 
structures, so in this sense using the density might aid you in finding a more realistic transition path that is closer 
to the lowest free energy barrier. If you're interested in that, using very low resolution maps might even be beneficial.


I personally would be excited to hear about your findings.

Best,

Christian


On 2019-12-11 17:18, Ramon Guixà wrote:

Hi there,

I would like to use GROMACS to create a trajectory that goes from one
crystal structure to another crystal structure, both obtained from the same
system using time resolved crystallography.

Would it be feasible to use the newly implemented density-guided
simulations parameters to guide this simulation by first fitting the
initial crystal structure its density map and then switching off these
restraints while switching on the density map restraints of the second
crystal structure? I figured this would in principle create a trajectory
that better reflect the transition from one state to the other, but I am
not even sure if this makes sense at all...

Thanks in advance for the guidance,
Ramon

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Re: [gmx-users] Chemical Shifts prediction using gmx chi -shift

[Christian Blau]

Hello Florent,


The tool is based on  "D. S. Wishart and A. M. Nip", "Protein Chemical Shift Analysis: A Practical Guide", "Biochem. 
Cell Biol.", 76, 1998, "153-163"


It reads chemical shift reference data on a phi-psi-angle grid from ca-shift.dat, cb-shift.dat, ha-shift.dat and 
co-shift.dat. The tool interpolates this data for the respective angle and sums it up. This sum is then normalized by 
the number of trajectory frames.



Best,

Christian


On 2019-12-06 17:39, Florent wrote:

Dear users,


I recently tried to use the -shift option of gmx chi, and I'm a bit confused 
about two things:

1) How does gromacs generate these results (chemical shift deviations from reference values)? The command-line 
documentation is of little help ("Compute chemical shifts from phi/psi angles")...


2) What are the reference values for Alanine and Tyrosine residues from? The calculation generates a log with a 
reference (Protein Chemical Shift Analysis: A Practical Guide), that does not contain any value for Alanine and 
Tyrosine residues while chemical shifts deviations are computed for those residues...



Any help or reference to a more complete documentation would be appreciated.


Best,


Florent


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Re: [gmx-users] Help installing do_x3dna

[Christian Blau]

Hi Salvador,


If you did not have any luck so far, trying to contact the author of the tool, 
Rajendra Kumar, directly might help:

https://scholar.google.com/citations?user=zYKuBCcJ=en


Best,
Christian

On 2019-11-21 21:00, Salvador Herrera-Velarde wrote:

Dear All,

I am trying to install do_x3dna in a Linux (Ubuntu Mint) computer where I
have already installed gromacs-2019.2.

I followed the steps in:
https://do-x3dna.readthedocs.io/en/latest/install_do_x3dna.html
but without success.

I executed the following command:
cmake .. -DGMX_PATH=/usr/local/gromacs/
-DFFTW_LIB=/home/shv/Gromacs/gromacs-2019.2/Build/src/external/build-fftw/fftwBuild-prefix/lib/
make
without warnings... then I executed
sudo make install
I got the following error
make: *** No rule to make target 'install'.  Stop.

I had checked the do_x3dna forum but it seems outdated and there is no much
information there.

Any suggestion of how to install do_x3dna would be greatly appreciated

Thanks a lot
s h.v

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Re: [gmx-users] How to calculate the spatial distribution function for the last 50ns of the trajectory?

[Christian Blau]

Hi Peiyin,


There is a related redmine entry that suggests this might be fixed in newer versions of GROMACS 
https://redmine.gromacs.org/issues/2189


(from GROMACS2018 on). If you are using a newer GROMACS version, to rule out that this is an issue related to .tng, can 
you try using the older .xtc format instead?



Best,
Chrstian

On 2019-12-05 03:13, Peiyin Lee wrote:

Dear users,

I have a simulation that has a 400 ns trajectory and I would like to
calculate the spatial distribution function of the last 50ns. I followed
the instructions on gmx_spatial manual and everything was ok if I run the
first 50ns of the trajectory instead of the last 50 ns. However, once I
changed the command from gmx_mpi trjconv -s md.tpr -f md.xtc -b 0 -e 5
-o b.tng -boxcenter tric -ur compact -pbc none
to gmx_mpi trjconv -s md.tpr -f md.xtc -b 35 -e 40 -o b.tng
-boxcenter tric -ur compact -pbc none
and then ran gmx_mpi trjconv -s md.tpr -f b.tng  -o c.tng -fit rot+trans
I would get an error saying:

WARNING: Incomplete frame: nr 0 time 0


WARNING no output, last frame read at t=0

I have checked my trajectory with gmx_check and the trajectory is fine. I
wonder why those two commands only work with -b 0, but not -b anyothertime.
Does anyone have an idea? Thank you in advance!

Regards,
Peiyin

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Re: [gmx-users] Maximising Hardware Performance on Local node: Optimal settings

[Christian Blau]

Hi Matt,


Here are a few bullet points that might help you, maybe other experts can 
contribute more.


If you're running on a single machine, using thread-mpi over mpi is a good 
choice.

"-pin on" might help you.

60k atoms is not very large, here are some other systems ready to benchmark https://www.mpibpc.mpg.de/grubmueller/bench 
that be able to tell you more about your performance on a range of systems.


It is normal that the GPU is not fully utilized; the newest GROMACS release should be able to make more use of the GPU, 
so you might want to try out the beta-3 version to get an idea, but please don't use for production, but wait till 
January when GROMACS-2020 is released.


If you want to maximise sampling, incorporate running multiple simulations simultaneously in your benchmark set (mdrun 
-multidir makes things easy here), most often this is what you actually want and can give you a drastic increase in 
output from your hardware (guessing a long shot, you might get 4 * 150 ns/day)



I assume you had already a look at this, but for reference check here:

http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mdrun.html
http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html

https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011


Best,

Christian

On 2019-12-04 17:53, Matthew Fisher wrote:

Dear all,

We're currently running some experiments with a new hardware configuration and 
attempting to maximise performance from it. Our system contains 1x V100 and 2x 12 
core (24 logical) Xeon Silver 4214 CPUs which, after optimisation of CUDA drivers 
& kernels etc., we've been able to get a performance of 210 ns/day for 60k 
atoms with GROMACS 2019.3 (allowing mdrun to select threads, which has surprised us 
as it only creates 24 OpenMP threads for our 48 logical core system). Furthermore 
we have a surprising amount of wasted GPU time. Therefore, we were wondering if 
anyone had any advice on how we could maximise our hardware output? We've enclosed 
the real cycle and time accounting display below.

Any help will be massively appreciated

Thanks,
Matt

  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 1 MPI rank, each using 24 OpenMP threads

  Computing:  Num   Num  CallWall time Giga-Cycles
  Ranks Threads  Count  (s) total sum%
-
  Neighbor search1   24  12501  32.590   1716.686   3.2
  Launch GPU ops.1   24252 105.169   5539.764  10.2
  Force  1   241250001 140.283   7389.414  13.6
  Wait PME GPU gather1   241250001  79.714   4198.902   7.7
  Reduce GPU PME F   1   241250001  25.159   1325.260   2.4
  Wait GPU NB local  1   241250001 264.961  13956.769  25.7
  NB X/F buffer ops. 1   242487501 177.862   9368.871  17.3
  Write traj.1   24252   5.748302.799   0.6
  Update 1   241250001  81.151   4274.601   7.9
  Constraints1   241250001  70.231   3699.389   6.8
  Rest  47.521   2503.167   4.6
-
  Total   1030.389  54275.623 100.0
-

Core t (s)   Wall t (s)(%)
Time:24729.331 1030.389 2400.0
  (ns/day)(hour/ns)
Performance:  209.6300.114

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Re: [gmx-users] npt.tpr protein-lig

[Christian Blau]

Hi Iman,


Great that you checked the notes!

The oscillatory period is estimated only from the masses and the force constant for the bond, see 
https://socratic.org/questions/frequency-of-vibration-of-two-masses-connected-by-a-spring ; note that the oscillation 
period = 2pi/\omega. To be on the conservative save side with the leap-frog algorithm, this then may not exceed 10 times 
your time-step to prevent integration errors that yield very unphysical results.


In your case, it seems that the parameters you are using for UNL seem to have a very large force constant on the bond 
between the atom types for C5 and C6 in your UNL parameters. One first step would be to re-check that the parameters you 
are using are fine and that you don't have an energy unit conversion error (note that GROMACS uses SI units) or that a 
Carbon atom type does not have the correct mass.


If you are reasonably convinced that your parameters are okay, reducing the timestep to 1fs from the 2fs that you have 
set currently (halving the performance of your run) might be an option, using constraints = all-bonds another. In 
general the latter is less preferable, unless your force-field was parametrized with this.


For temperature coupling you should use v-rescale instead of Berendsen in production runs, but that shouldn't affect the 
warning.


Best,

Christian

On 2019-12-02 13:02, Iman Katouzian wrote:

Good day,

I have generated npt.tpr for my protein ligand and changed my npt.mdp file
according to the suggestions by GROMACS for using Brendsen and h-bonds for
constraints finally I encounter this NOTE which I think will cause further
problems in my md run :
  NOTE 1 [file topol.top, line 18260]:
   The bond in molecule-type UNL between atoms 6 C5 and 7 C6 has an
   estimated oscillational period of 1.8e-02 ps, which is less than 10 times
   the time step of 2.0e-03 ps.
   Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group Protein_UNL is 4960.82
Number of degrees of freedom in T-Coupling group Water_and_ions is 77850.18
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm

I would appreciate it if someone tells me what I need to do with my system
I think it may be related to the time step of my simulaiton and frames as I
searched the similar issues.

thanks


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Re: [gmx-users] Problem with GROMAC 2019.4

[Christian Blau]

HI Avneel,


In general, using the latest stable version is always the first thing to recommend, because this is where your issue 
might have already been fixed.



Do you also get the same "unsafe srcdir value" when running make? It'd be 
interesting to know what system you are using.


I assume you tried a bunch of things already in the past two weeks, but on the chance that  you did not already you 
might try:


  - try building in a directory with no whitespaces or other special characters in the directory name (usually should 
not be an issue, but "unsafe srcdir value" hints at this)


  - using ninja as a build system (use cmake -GNinja , then type ninja instead 
of make)

  - trying different fft libraries (fftw, mkl, fftpack)


Also, it'd be great to hear back to know what solved the issue.


Best,

Christian

On 2019-12-04 08:42, Avi Hundal wrote:

Hi all,

I've been trying to get GROMAC 2019.4 to work on my computer with GPU
acceleration for over 2 weeks, without success and without trying to bother
you all here.  Scouring the archives, someone else had the same exact issue
I have (
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg33675.html
).

The problem occurs after entering "make".  I haven't been able to find a
solution, and the person who previously had this problem was suggested to
upgrade to the newest stable version at that time.  Any suggestions?  Thank
you!

Regards,

Avneel S. Hundal

Email: havn...@gmail.com

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Re: [gmx-users] the a.u. unit in the RMS distribution graph

[Christian Blau]

Hello Lalehan and Justin,


Thanks for the suggestion! The following patch : 
https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that.


Best,
Christian

On 2019-11-29 14:23, Justin Lemkul wrote:



On 11/29/19 7:18 AM, Christian Blau wrote:

Hello Lalehan,


a.u. stands for "arbitrary units".

The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per 
length-interval.




I would suggest that all histograms that GROMACS produces actually be labeled reasonably in the code - using a.u. is 
itself arbitrary because it has multiple possible meanings. If it's a raw histogram, we should be using "Frequency" 
and if normalized, "Probability."


-Justin


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Re: [gmx-users] the a.u. unit in the RMS distribution graph

[Christian Blau]

Hello Lalehan,


a.u. stands for "arbitrary units".

The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per 
length-interval.



Best,

Christian

On 2019-11-29 12:57, Lalehan Ozalp wrote:

Hello everyone, I ran a cluster analysis for a 10 ns simulation and
produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg file,
I see "a. u." in the y axis which I couldn't entirely understand. Is it
supposed to stand for atomic unit for length or mass or something else? I
provide the file as an example.

Thank you in advance.

Lalehan


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Re: [gmx-users] Magnetic effects in a classical force field

[Christian Blau]

Dear Yogesh,


This question strays indeed a bit from the forum topic though being valid. In short - the effect is too small to be 
considered.


The interaction terms in a force field are usually developed as approximations to the the non-relativistic coulomb 
molecular Hamiltonian operator. In this operator, the magnetic field is neglected as giving too little of a 
contribution. This means that also related quantum effects like spin-orbit coupling are not taken into account. These 
effects are vanish in relation to all other approximations during molecular dynamics simulations.



Best,

Christian

On 11/26/19 9:37 AM, atb files wrote:
 

 
 Hello experts,The question may be little bit off the forum guidelines. But still I wanted to ask, since I cannot find more experts at one place other than this forum. The force on the moving charge is given as:F = q(E+v * B)Where q is the charge, v is velocity of charged particle, and B is magnetic field due to motion of charges around a given charge. I hope I am not wrong in any of these definitions. Since in MD simulation charges are moving with certain velocity, why we do not consider magnetic effects in the potential energy function (or so called force field) ?Thank you for your answers in advance. - YogeshSent using Zoho Mail
 
 
 
 

 
 


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Re: [gmx-users] Superparamagnetism

[Christian Blau]

Dear Amin,


Superparamagnetism can not be simulated easily with GROMACS.

Some challenges you'll face are the following:

 - Usual superparamagnetic materials like iron oxide nanoparticles require a quantum chemistry parametrization that 
will be hard to approximate with classical force field


 - Magnetic fields are currently not implemented in GROMACS

 - Evaluating Néel relaxation times might be hard, because they range from nanoseconds to years and only the nano to 
microsecond range will be accessible to your simulation


 - You could estimate these times via Néel-Arrhenius with free-energy estimation or enhanced sampling methods, however 
I don't know of any reaction coordinate that is implemented at the moment in any of the packages that could help you 
with that like PLUMED or COLVARS.



Best,

Christian


On 11/22/19 1:54 PM, Amin Rouy wrote:

Hi everyone,

Is it possible to simulate* superparamagnetism*  in Gromacs?

thanks for answer.

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Re: [gmx-users] droplet

[Christian Blau]

Hi Alex,


I'm not sure this is really something for the GROMACS mailing list and I'm guessing the question you were asking - What 
is the expected behaviour of the solvent accessible surface area of a droplet with temperature?


Here is a "back-of-the envelope" estimate: The easiest model of a droplet is an effective harmonic potential that keeps 
together a bunch of molecules at the center of the coordinate system. A molecule at x has then the effective potential 
energy (chemical potential) E(x) = k * x^2, yielding a Boltzmann distribution of particle positions at a given 
temperature proportional to exp(-(kx^2)/(k_b T)). The droplet boundary is an iso-contour of this distribution - 
proportional to 1/T - the surface area is thus proportional to (1/T)^2. In an equilibrium situation you would expect 
your droplet SASA to go with T^(-2). Because quenching includes non-equilibrium effects, you might observe an exponent > -2.



Best,

Christian

On 11/18/19 10:28 PM, Alex wrote:

Dear all,
The surface area (calculated by gmx sasa) of a droplet of a molecule,
reduces during temperature quenching, I wonder if anybody has an idea to
explain that by calculation a meaningful quantity of the droplet?

Thank you
Alex

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Re: [gmx-users] eelctric field

[Christian Blau]

Hi Amin,


Sorry for the late answer - when calculating the pressure, no information about the electric field is used (as it should 
be). To obtain the pressure as if no electric field were applied, running another simulation with the field switched off 
is the only way.



Best,

Christian

On 11/15/19 3:20 PM, Amin Rouy wrote:

Dear Christian,

Thank you for the answer.  My last question I hope:

I just noticed that the pressure I get in y and z directions seem physical
and correct, but the x direction of pressure is a big negative number and
not reasonable (Pres-ZZ = -400 bar). (I had applied the filed in x
direction and I have NVT ensemble). So I think the way Gromacs calculates
the pressure in presence applied field does not take into account the field
effect, am I correct?

On Fri, Nov 15, 2019 at 11:17 AM Christian Blau  wrote:


Hello Amin,


Though the forces are present during the simulation the additional work on
the system that is exerted via the electric
field is not output as an additional energy term in GROMACS.

I believe the pressure deviations that you observe are due to two
different effects:

  - the pressure fluctuates much more than energies, like coulomb
interactions, etc., especially in small systems.
The question here would be if the deviation between the perturbed and
unperturbed system that you observe is larger than
the deviation between two unperturbed systems

  - the electric field indirectly influences the pressure. I would
expect this effect to be usually small, but if you
imagine a system consisting only of the same number of positively and
negatively charged ions, applying the electric
field along z-direction will cause half of them to move upwards and the
other half downwards along the z-direction,
which will in turn affect the pressure.


Best,

Christian

On 11/13/19 3:39 PM, Amin Rouy wrote:

Dear Christian,

Thank you for your reply. However, still it is not fully clear to me.

Lets

only talk about gmx energy.  How it happens that I get from gmx energy
similar values of energies (LJ, columbs, total energies) while a

different

pressure, with and without applied filed? The total energy should be
different as a result of an additional energy due to applied filed on

each

atom.

On Wed, Nov 13, 2019 at 3:10 PM Christian Blau  wrote:


Hello Amin,


When you apply an electric field during the simulation by setting the

mdp

parameters like E-x =... as you describe,
nothing more happens than that each atom experiences an additional force
that is "atom charge * field strength". The
energy terms or virial (that then would relate to pressure coupling) are
not influenced by this. If these terms differ
between a simulation with electric field and one without, then only
because the system as a whole responds to the
applied electric field.

gmx potential on the other hand is an analysis tool that is per se
unrelated on how you chose to apply an electric field
during your simulation or not. However, when applying an electric field,
you would expect a different result from an
analysis with gmx potential than without electric field, because your
system will respond to the applied electric field.


Best,

Christian

On 11/13/19 2:44 PM, Amin Rouy wrote:

Hi,

I am using gromacs 5.0.4. I apply a uniform electric field in x

direction

of my box (no walls),
E-x= 1  10  0, and simulation runs without error.
I notice that the values of electrostatic interactions I get from the
simulation is the same as without the an electric field. Which is

strange,

but according to previous questions in the gromacs forum this is true:
''gmx potential only calculates the electric field and potential of the
system. It does not take into account the applied field.''

Now, my question is are the other quantities obtaining from gmx energy

take

into account field effect? e.g. pressure of the system.

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Re: [gmx-users] Regarding LSI calculation

[Christian Blau]

Hi Omar,


Though I don't know of any GROMACS tool that can calculate the local structure 
index, some third-party tool might help, like

https://pypi.org/project/iOrder/


The input file format for above tool is .xyz which you can obtain from a 
GROMACS trajectory using the MDAnalysis tools here:

https://www.mdanalysis.org/docs/documentation_pages/coordinates/XYZ.html#xyz-format


Best,

Christian

On 11/11/19 4:40 AM, Omkar Singh wrote:

Hi everyone,
  I want to find out LSI (local structural Index) for my protein water
system. Can anybody help me regarding this issue?

Thank you

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Re: [gmx-users] Potential bug in IMD implementation (Interactive Molecular Dynamics)

[Christian Blau]

Hi Xavier,


Bugs are usually best reported via "redmine.gromacs.org". You can self-report when registering there. In this case I 
just went ahead and filed the bug report, if you want to add information to the bug report and check how things are 
developing you can check here:


https://redmine.gromacs.org/issues/3209

There, you can also attach files to the bug report. The most helpful thing for fixing a GROMACS bug is a complete set of 
input files (at least the .tpr though) that reliably reproduces the bug. (Ideally the tiniest system you can conceive, 
but any system is much much better than none)



The video that you linked is also extremely nice to have and helpful

Thanks for the report!

Best,

Christian


On 11/19/19 11:11 AM, Xavier Martinez wrote:

Dear gmx users,

I came across a bug that is reproducible when using the IMD implementation in several versions of Gromacs including 
2019.3 and different operating systems.


This bug occurs with the following steps:

- Run an IMD simulation (gmx mdrun -imdwait -imdpull -imdterm -s mysim.tpr)

- Connect to the simulation using VMD (or other visualization tool that 
implements the IMD protocol)

- Pause the simulation from VMD ("detach sim" button)

- Reconnect to the simulation

The expected behavior is to have the same performance before and after pausing 
the simulation.

The actual behavior is a slower and stuttering simulation. Note that this bug 
does not occur when using NAMD.

See an example of the bug here: https://www.youtube.com/watch?v=_gZ6wA7c4b8 



An error line appears in the gromacs window: "IMD: Failed to shutdown socket. Did the client already disconnect?" and 
"IMD: Error in file gromacs-2019.3/src/gromacs/imd/imdsocket.cpp on line 293."


How should I proceed to help this bug getting fixed ?

Best regards,

Xavier Martinez, Ph.D

CNRS-IBPC LBT, Paris



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Re: [gmx-users] applied electirc field with use potential

[Christian Blau]

Hi Amin,


It's me again :)

Yes, applying an electric field mixes well with any other potentials you apply.

When you use an additional electric field by using the .mdp options, there is already an additional force added to all 
the forces on the atoms that makes the system respond to an electric field. You would not have to modify any other 
potential to include an external electric field.



Best,

Christian

On 11/14/19 10:59 AM, Amin Rouy wrote:

Hi,

I have a system with a user-potential.
-Can I use an external applied field?
-Can I modify my user potential to include the external field?

thank you for help,

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Re: [gmx-users] eelctric field

[Christian Blau]

Hello Amin,


Though the forces are present during the simulation the additional work on the system that is exerted via the electric 
field is not output as an additional energy term in GROMACS.


I believe the pressure deviations that you observe are due to two different 
effects:

    - the pressure fluctuates much more than energies, like coulomb interactions, etc., especially in small systems. 
The question here would be if the deviation between the perturbed and unperturbed system that you observe is larger than 
the deviation between two unperturbed systems


    - the electric field indirectly influences the pressure. I would expect this effect to be usually small, but if you 
imagine a system consisting only of the same number of positively and negatively charged ions, applying the electric 
field along z-direction will cause half of them to move upwards and the other half downwards along the z-direction, 
which will in turn affect the pressure.



Best,

Christian

On 11/13/19 3:39 PM, Amin Rouy wrote:

Dear Christian,

Thank you for your reply. However, still it is not fully clear to me. Lets
only talk about gmx energy.  How it happens that I get from gmx energy
similar values of energies (LJ, columbs, total energies) while a different
pressure, with and without applied filed? The total energy should be
different as a result of an additional energy due to applied filed on each
atom.

On Wed, Nov 13, 2019 at 3:10 PM Christian Blau  wrote:


Hello Amin,


When you apply an electric field during the simulation by setting the mdp
parameters like E-x =... as you describe,
nothing more happens than that each atom experiences an additional force
that is "atom charge * field strength". The
energy terms or virial (that then would relate to pressure coupling) are
not influenced by this. If these terms differ
between a simulation with electric field and one without, then only
because the system as a whole responds to the
applied electric field.

gmx potential on the other hand is an analysis tool that is per se
unrelated on how you chose to apply an electric field
during your simulation or not. However, when applying an electric field,
you would expect a different result from an
analysis with gmx potential than without electric field, because your
system will respond to the applied electric field.


Best,

Christian

On 11/13/19 2:44 PM, Amin Rouy wrote:

Hi,

I am using gromacs 5.0.4. I apply a uniform electric field in x direction
of my box (no walls),
E-x= 1  10  0, and simulation runs without error.
I notice that the values of electrostatic interactions I get from the
simulation is the same as without the an electric field. Which is

strange,

but according to previous questions in the gromacs forum this is true:
''gmx potential only calculates the electric field and potential of the
system. It does not take into account the applied field.''

Now, my question is are the other quantities obtaining from gmx energy

take

into account field effect? e.g. pressure of the system.

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Re: [gmx-users] eelctric field

[Christian Blau]

Hello Amin,


When you apply an electric field during the simulation by setting the mdp parameters like E-x =... as you describe, 
nothing more happens than that each atom experiences an additional force that is "atom charge * field strength". The 
energy terms or virial (that then would relate to pressure coupling) are not influenced by this. If these terms differ 
between a simulation with electric field and one without, then only because the system as a whole responds to the 
applied electric field.


gmx potential on the other hand is an analysis tool that is per se unrelated on how you chose to apply an electric field 
during your simulation or not. However, when applying an electric field, you would expect a different result from an 
analysis with gmx potential than without electric field, because your system will respond to the applied electric field.



Best,

Christian

On 11/13/19 2:44 PM, Amin Rouy wrote:

Hi,

I am using gromacs 5.0.4. I apply a uniform electric field in x direction
of my box (no walls),
E-x= 1  10  0, and simulation runs without error.
I notice that the values of electrostatic interactions I get from the
simulation is the same as without the an electric field. Which is strange,
but according to previous questions in the gromacs forum this is true:
''gmx potential only calculates the electric field and potential of the
system. It does not take into account the applied field.''

Now, my question is are the other quantities obtaining from gmx energy take
into account field effect? e.g. pressure of the system.

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Re: [gmx-users] Script to merge protein and ligand topology for BAR calculation?

[Christian Blau]

Hi Billy,


I cannot offer a script for the merging of the topologies, but depending 
on the transformation you want to carry out, I can suggest using pmx


http://pmx.mpibpc.mpg.de/webserver.html


for preparing dual topologies for alchemical free energy calculations 
that are GROMACS-compatible.



Best,

Christian

On 2019-11-11 07:22, Billy Williams-Noonan wrote:

Hi Experts,

I have a protein .itp file

I -also- have the dual ligand .itp file to perform a relative alchemical
transformation

Both are compatible with GROMACS, and use AMBER/GAFF parameters.

I need a script that can easily merge the two together. Have been doing on
Excel. I was wondering if anyone would be kind enough to please share?

FESetup is good, but the input requires correct atom naming for Amber (not
GROMACS) and this is a pain to get right.

Cheers,
Billy


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Re: [gmx-users] (no subject)

[Christian Blau]

Hello Shakuntala,


If you already have the trajectories, you have to post-process at least once to filter the data down to a manageable 
size, and once to do the periodic boundary condition fix precisely as you described.


If you set up a new simulation you may use "nstxout-compressed" to control the output frequency for your xtc file. It is 
very unlikely that you will need a .trr file, so you can even set nstxout, nstvout and nstfout to zero. Starting your 
post-processing from a xtc should speed up your analysis process.



On another note: Please fill in a subject line in your emails, it makes it easier to search and keep track of the 
ongoing discussions.



Best,

Christian


On 11/7/19 3:12 PM, shakuntala dhurua wrote:

I would like to calculate rmsd of protein system, but there is much time
taking for trjcat of all simulated trajectories (.trr file) then generated
.xtc file by using -center -pbc mol flag. from this .xtc file i use to
calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
want to ask here is any other way is available to directly calculate rmsd
without using trjcat or less time taking method.

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Re: [gmx-users] gmx trjorder

[Christian Blau]

Hello Akash,


Not knowing much more about your this system, this looks reasonable to me and 
should give you the count you just described.


Best,

Christian

On 11/7/19 2:44 PM, Pandya, Akash wrote:

Hi,

I would like to calculate the number of ligand molecules within 0.5 nm of a 
particular amino acid in my protein. I came across the gmx trjorder command (as 
shown below).


gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -nshell nshell1.xvg -b 
2 -e 4 -na 10 -r 0.5


I have 10 atoms in my ligand. I wanted to ask how accurate is this command in 
trying to calculate what I want?


Akash


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Re: [gmx-users] Stochastic Dynamics nsttcouple

[Christian Blau]

Hi John,


Thanks for the suggestion! Find a patch here that updates the mdp documentation 
to clarify the issue you had with nsttcoupl:

https://gerrit.gromacs.org/c/gromacs/+/14157


Let me know if things are still unclear.


Best,

Christian

On 11/7/19 1:38 PM, John Whittaker wrote:

Hi Justin,

Thank you very much for the response. That's the conclusion I kept coming
to, but I'm happy to know it for sure now.

I'm not sure if others have been confused by this in the past, but it
would have saved me some trouble had I known that explicitly from the
beginning; any chance this note can be added to the documentation (at
least the mdp options page)?

Thanks again,

John



On 11/6/19 10:40 AM, John Whittaker wrote:

Hi all,

Please correct me if this is the wrong list for this particular
question.

I have been messing around with the stochastic dynamics integrator in
version 5.1 (yes, it's relatively ancient, but I am testing some things
involving AdResS) and I can't wrap my head around something:

In the src/gromacs/mdlib/update.cpp file, I cannot find a moment when
the
parameter "nsttcouple" is used in order to determine when the thermostat
is applied. I'm not sure if this is a stupid question, but are the
friction and noise applied at each step, regardless of the value of
nsttcouple?

I understand that tcoupl is ignored when the SD integrator is used, but
does this mean that nsttcouple is ignored, too?

Yes. Formally, the SD integrator does not apply an explicit thermostat
algorithm; velocities are updated based on the friction coefficient
specified in the .mdp file. nsttcoupl is only relevant when tcoupl is
active, which it is not when using SD.

-Justin


I am by no means an expert in C++ so I could have easily misunderstood
or
missed something, but this question has been plaguing me for a couple
days. Any help I can get to better understand this is much appreciated!

Best,

John





--
==

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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Re: [gmx-users] Load Imbalance

[Christian Blau]

Hello Shradheya,


If you want to enforce dynamic load balancing you can use gmx mdrun -dlb yes instead of 
the default "auto".

However, as I read from the output, your system was not balanced because it was not needed and the overhead of 
re-distributing atoms might outperform the gain from it.



Best,

Christian


On 11/7/19 12:14 PM, Shradheya R.R. Gupta wrote:

Respected Researchers,
How to balance the MD simulations? Below is the report.





*Dynamic load balancing report: DLB was off during the run due to low
measured imbalance. Average load imbalance: 1.4%. The balanceable part of
the MD step is 70%, load imbalance is computed from this. Part of the total
run time spent waiting due to load imbalance: 1.0%.*

Thank you
Shradheya Gupta
DBT-BIF University of Rajasthan

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Re: [gmx-users] Time step mismatch.

[Christian Blau]

Hello Maryam,


trjconv might help here. There are two ways I can interpret time step in your 
email.

 1. the integration time step dt - if you changed this one I would not recommend that you concatenate the trajectories 
(though also possible), but treat this as independent simulation setup, because this will mean a different approximation 
to the underlying physics.


 there is an option in trjconv  -timestep  (0) Change time step 
between input frames (ps)

 2. the output frequency

 There, the trjconv options -skip    (1) Only write every nr-th frame
                                                   -dt  (0) Only write 
frame when t MOD dt = first time (ps)

 should help to generate trajectories that have matching spacing time.


Best,

Christian


On 11/6/19 11:15 AM, Maryam wrote:

Dear gmx users,

I have two xtc files generated from my simulation with two different
time steps. I had to change the time step/mdp options because of disc
size. After the simulation, I tried to use trjcat to combine the two xtc
files so I can perform analsis on the trajectory. But I get this warning  :

Timesteps at t=1.4028e+07 don't match (1200, 1500), How do I fix this?
is it possible to rewrite the time step after the simulation?Thanks in
advance.

Best regards,

Maryam





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Re: [gmx-users] gmx gangle in a for loop

[Christian Blau]

Hello Alex,


What works for me is setting '$i' within singe quotation marks, e.g.,

'group '$i' and name C10 plus group '$i' and name C20'


Note that this is more of a bash escaping quotes issue and only a GROMACS issue insofar as the selection syntax requires 
the quotes.



Best,

Christian

On 11/6/19 3:32 AM, Alex wrote:

Dear all,
Could one kindly let me know how $i should come in gmx gangle used in a for
loop to avoid syntax errors?
I tested different flavors like "$i", "${i}", ..., and still the problem is
here.

#!/bin/bash/
for i in {1..1000}
do
 gmx gangle -g1 vector -group1 'group $i and name C10 plus group $i
and name C20' -g2 vector -group2 'cog of group 0 plus cog of group $i' -n
ind.ndx -f ind.xtc -s ind.tpr -oav aver$i.xvg -oh hist$i.xvg
done

Thank you
Alex

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Re: [gmx-users] Output from gmx h2order

[Christian Blau]

Hello Decai,


h2order works in the following way:

  - all water molecules are put into the simulation box by applying periodic boundary conditions so that the first 
water molecule atom is in the simulation box


  - the simulation system is sliced along z (0,0,1) direction (default, can be 
changed)

  - each water molecule contributes it's dipole to the slice sum of dipole moments - this is what you see in the output 
columns mux, muy, muz. These dipoles are calculated as  \sum charge * positionVector. The dipole moments are averaged 
per slice over all water molecules and frames


  - the cosine with normal is calculated as the average normalized inner product of the dipole vector with the "normal" 
- in the default case z direction, .e.g, average[dipole . (0,0,1) / sqrt(dipole.dipole)]



Best,

Christian



On 11/1/19 8:00 PM, Decai Yu wrote:

Hi, All
There are four columns from the output of gmx h2order, mux, muy, myz,
cosine with normal.
What are they? Can anyone further explain?
Decai Yu

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Re: [gmx-users] Simulated Annealing General Procedure

[Christian Blau]

Hello Neena,


The outline you give appears reasonable for exploring peptide conformations. It is very hard to judge appropriateness 
though without knowing what you are trying to learn from your system.


The unspecified position restraints might defeat the purpose of the simulated annealing if you keep too much of your 
system fixed. It's good to prevent chirality changes however, and back-bone position restraints are the right choice if 
you are interested in side-chain conformation changes.



If you are not tied to simulated annealing, but just want to explore your peptide conformations, the following methods 
are also useful:


 - if you know the reaction coordinate that your are interested in, e.g., a distance between residues, an angle or 
dihedral, then I suggest you try the "accelerated weighted histogram" (AWH) module. It may benefit your sampling a lot, 
because it ensures in a near optimal way that your system visits all conformations along a given reaction coordinate, 
e..g, all C-alpha - C-alpha distances between two residues in a given range


 - if you don't know the reaction coordinate, then Temperature-replica exchange for small peptide systems or flooding 
with essential dynamics sampling might be useful.



Best,

Christian

On 10/29/19 5:08 PM, Neena Susan Eappen wrote:

Hello gromacs users,

My goal is to do a better conformational sampling of my peptides using 
simulated annealing. Is my following procedure correct?

1- Energy minimization
2- NVT equilibration with position restraints say at 600 K for 100 ps
3- Simulated annealing with position restraints to cool down from 600 K to 300 
K for 152 ps, with no velocity generation
4- Production simulation at 300 K for 10 ns without position restraints, with 
no velocity generation
5- Another step of energy minimization
6- Then repeat steps 2-6 multiple times with initially minimized structure from 
step 1

Many thanks,
Neena

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Re: [gmx-users] (no subject)

[Christian Blau]

Hello Saranya,

Now again with readable formatting. Also note that it is very useful to people 
on gmx-useres to  specify the subject when writing emails, because it makes it 
easier to search, reply, and handle multiple discussion threads.

This error means that during the nvt equilibrium high forces occurred that made 
it impossible to resolve the bond constraints. The very high forces occurred 
most likely are due to some high tension in the system.

As indicated in the error message you can:
 - Reduce the time step of your run initially to relax the structure first.
 - Check the output PDB structure at the site where the error occurred (atoms 
217 and 218), possibly removing or displacing the offending water molecule 
manually
 - Check that you used a well relaxed structure from energy minimisation

Best,
Christian

On 11/1/19 7:48 AM, saranya wrote:

Hello everyone,
while running nvt equilibration i am getting the error as:
Step 12, time 0.024 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 92522.640625 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 277278   58.90.1090  74.2482  0.1090
 281282   35.80.1098  73.5336  0.1090
 281283  119.30.1097  74.0780  0.1090
 281284   63.50.1097  74.2253  0.1090

step 12: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step12b.pdb to ./#step12b.pdb.1#

Back Off! I just backed up step12c.pdb to ./#step12c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)



how can i resolve this error...?

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*

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Re: [gmx-users] how to perform analysis in faster with multicore/processor

[Christian Blau]

Hello Nikhil,


Currently there is no "in-built" way to do this. (we thought of this before and there is some basic infrastructure for 
this in the trajectory analysis framework, but in short - no)


However, if you have many trajectories you can run analysis of all trajectories in parallel to speed up the time to 
obtaining a result. One possible way to automate this parallelisation would be to set up a makefile for your analysis 
and then run with -j (numberOfProcessors), see for a rough outline on how this would work 
https://stackoverflow.com/questions/19822435/multiple-targets-from-one-recipe-and-parallel-execution/ 




Best,

Christian


On 10/29/19 11:35 AM, Nikhil Maroli wrote:

Is there any way to speed up the gromacs analysis or any way to use
multiprocessor for gromacs trajectory analysis.? I have to analyze
trajectories of 10 ps intervals upto 1 microsecond. (I do not want to
reduce time interval for many reason)

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