Re: [gmx-users] High pressure variation during NPT equilibration oftProtein-ligand system.

[Braden Kelly]

Did you equilibrate the system? Typically you discard the initial values. You 
discard by adding "-b 200" to the gmx energy command line call. This doesn't 
include the first 200 Pico seconds in the averaging. 200 only is an example... 
I prefer more.

Another point is that you don't seem to have run for very long. I suggest 
plotting the potential energy and density of the system. You will know you have 
reached equilibrium  when they flatline around a value. Only include the values 
after equilibrium has been reached in you averaging.

Best of luck,


Get Outlook for Android

From: Seketoulie Keretsu
Sent: Tuesday, May 21, 1:36 a.m.
Subject: [gmx-users] High pressure variation during NPT equilibration 
ofProtein-ligand system.
To: gromacs.org_gmx-users@maillist.sys.kth.se


Dear Experts, I am performing a protein-ligand stimulation in gromacs 2018. The 
pressure value showed wild variation between -800 to 500 bar and showed an 
average pressure value of -139 bar. The reference is 1 bar. I have used the 
"lysozyme in water" simulation tutorial by Justin A. Lemkul as a reference. The 
tutorial mentioned that 7.5 (+- 160) bar was reasonable for the system. I'm not 
sure if the value I am getting in my simulation results (-139 bar variation in 
pressure) are reasonable. Kindly advise. How do i justify this ? References and 
suggestions will be appreciated. Thank you. Regards, Seketoulie Note: The 
pressure values from the NPT are given below: # This file was created Tue May 
14 21:24:43 2019 # Created by: # :-) GROMACS - gmx energy, 2018.4 (-: # # 
Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # 
Working dir: /home/biopo5/tutorial/Project4/JAK1/cmp49_jak1 # Command line: # 
gmx energy -f nvt.edr -o pressure.xvg # gmx energy is part of
  G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @ 
title "GROMACS Energies" @ xaxis label "Time (ps)" @ yaxis label "(bar)" @TYPE 
xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype 
view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Pressure" 0.00 
-3931.674805 1.00 528.706482 2.00 27.634497 3.00 -130.418900 
4.00 -491.462982 5.00 3.087336 6.00 -246.631638 7.00 -86.932167 
8.00 -453.551422 9.00 -46.325455 10.00 270.657562 11.00 
-432.105682 12.00 -578.059326 13.00 -397.159760 14.00 180.598190 
15.00 -159.344788 16.00 -122.911415 17.00 470.059418 18.00 
-375.501251 19.00 -310.881561 20.00 68.639618 21.00 157.454422 
22.00 -619.447388 23.00 -130.864059 24.00 58.016773 25.00 
-132.054276 26.00 114.288574 27.00 -108.022186 28.00 -235.894424 
29.00 -398.703217 30.00 252.965332 31.00 -269.996368 32.00 
-58.09
 6252 33.00 -291.578918 34.00 15.896652 35.00 53.429890 36.00 
43.522858 37.00 -442.695190 38.00 111.608665 39.00 -12.626378 
40.00 -136.936111 41.00 182.577164 42.00 -68.747620 43.00 
121.546547 44.00 127.403526 45.00 -248.055176 46.00 184.869797 
47.00 162.962906 48.00 -387.420013 49.00 228.167648 50.00 
348.351471 51.00 -462.909180 52.00 -234.574936 53.00 -224.565689 
54.00 311.879456 55.00 -404.242920 56.00 -740.461182 57.00 
38.036850 58.00 -677.158447 59.00 -117.842407 60.00 -20.302151 
61.00 -558.201233 62.00 218.174881 63.00 -269.575531 64.00 
-153.398697 65.00 178.027954 66.00 -193.050797 67.00 -590.598694 
68.00 -487.503754 69.00 171.980606 70.00 84.821785 71.00 
-219.844803 72.00 -228.680954 73.00 -145.632614 74.00 47.675121 
75.00 -310.033478 76.00 -705.341248 77.00 212.275406 78.00 
24.035654 79
 .00 -221.810410 80.00 -189.725708 81.00 217.696289 82.00 
427.632660 83.00 249.210770 84.00 -405.385956 85.00 78.898247 
86.00 -19.268747 87.00 85.342247 88.00 155.808731 89.00 
2.646250 90.00 -284.466888 91.00 152.030930 92.00 280.804352 
93.00 -182.475830 94.00 -268.784149 95.00 -470.018829 96.00 
-163.642685 97.00 291.026855 98.00 -982.940430 99.00 155.447800 
100.00 77.415077 -- 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 

Re: [gmx-users] High pressure variation during NPT equilibration of Protein-ligand system.

[David van der Spoel]

Den 2019-05-21 kl. 07:36, skrev Seketoulie Keretsu:

Dear Experts,

I am performing a protein-ligand stimulation in gromacs 2018. The
pressure value showed wild variation between -800 to 500 bar and
showed an average pressure value of -139 bar. The reference is 1 bar.
I have used the "lysozyme in water" simulation tutorial by Justin A.
Lemkul as a reference. The tutorial mentioned that 7.5 (+- 160) bar
was reasonable for the system. I'm not sure if the value I am getting
in my simulation results (-139 bar variation in pressure) are
reasonable. Kindly advise. How do i justify this ?

References and suggestions will be appreciated. Thank you.
This is normal. It will average out in a longer simulation. Larger boxes 
have less fluctuations in general.




Regards,
Seketoulie

Note: The pressure values from the NPT are given below:

# This file was created Tue May 14 21:24:43 2019
# Created by:
#  :-) GROMACS - gmx energy, 2018.4 (-:
#
# Executable:   /usr/local/gromacs/bin/gmx
# Data prefix:  /usr/local/gromacs
# Working dir:  /home/biopo5/tutorial/Project4/JAK1/cmp49_jak1
# Command line:
#   gmx energy -f nvt.edr -o pressure.xvg
# gmx energy is part of G R O M A C S:
#
# Gromacs Runs One Microsecond At Cannonball Speeds
#
@title "GROMACS Energies"
@xaxis  label "Time (ps)"
@yaxis  label "(bar)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Pressure"
 0.00  -3931.674805
 1.00  528.706482
 2.00   27.634497
 3.00  -130.418900
 4.00  -491.462982
 5.003.087336
 6.00  -246.631638
 7.00  -86.932167
 8.00  -453.551422
 9.00  -46.325455
10.00  270.657562
11.00  -432.105682
12.00  -578.059326
13.00  -397.159760
14.00  180.598190
15.00  -159.344788
16.00  -122.911415
17.00  470.059418
18.00  -375.501251
19.00  -310.881561
20.00   68.639618
21.00  157.454422
22.00  -619.447388
23.00  -130.864059
24.00   58.016773
25.00  -132.054276
26.00  114.288574
27.00  -108.022186
28.00  -235.894424
29.00  -398.703217
30.00  252.965332
31.00  -269.996368
32.00  -58.096252
33.00  -291.578918
34.00   15.896652
35.00   53.429890
36.00   43.522858
37.00  -442.695190
38.00  111.608665
39.00  -12.626378
40.00  -136.936111
41.00  182.577164
42.00  -68.747620
43.00  121.546547
44.00  127.403526
45.00  -248.055176
46.00  184.869797
47.00  162.962906
48.00  -387.420013
49.00  228.167648
50.00  348.351471
51.00  -462.909180
52.00  -234.574936
53.00  -224.565689
54.00  311.879456
55.00  -404.242920
56.00  -740.461182
57.00   38.036850
58.00  -677.158447
59.00  -117.842407
60.00  -20.302151
61.00  -558.201233
62.00  218.174881
63.00  -269.575531
64.00  -153.398697
65.00  178.027954
66.00  -193.050797
67.00  -590.598694
68.00  -487.503754
69.00  171.980606
70.00   84.821785
71.00  -219.844803
72.00  -228.680954
73.00  -145.632614
74.00   47.675121
75.00  -310.033478
76.00  -705.341248
77.00  212.275406
78.00   24.035654
79.00  -221.810410
80.00  -189.725708
81.00  217.696289
82.00  427.632660
83.00  249.210770
84.00  -405.385956
85.00   78.898247
86.00  -19.268747
87.00   85.342247
88.00  155.808731
89.002.646250
90.00  -284.466888
91.00  152.030930
92.00  280.804352
93.00  -182.475830
94.00  -268.784149
95.00  -470.018829
96.00  -163.642685
97.00  291.026855
98.00  -982.940430
99.00  155.447800
   100.00   77.415077




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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] High pressure variation during NPT equilibration of Protein-ligand system.

[Seketoulie Keretsu]

Dear Experts,

I am performing a protein-ligand stimulation in gromacs 2018. The
pressure value showed wild variation between -800 to 500 bar and
showed an average pressure value of -139 bar. The reference is 1 bar.
I have used the "lysozyme in water" simulation tutorial by Justin A.
Lemkul as a reference. The tutorial mentioned that 7.5 (+- 160) bar
was reasonable for the system. I'm not sure if the value I am getting
in my simulation results (-139 bar variation in pressure) are
reasonable. Kindly advise. How do i justify this ?

References and suggestions will be appreciated. Thank you.

Regards,
Seketoulie

Note: The pressure values from the NPT are given below:

# This file was created Tue May 14 21:24:43 2019
# Created by:
#  :-) GROMACS - gmx energy, 2018.4 (-:
#
# Executable:   /usr/local/gromacs/bin/gmx
# Data prefix:  /usr/local/gromacs
# Working dir:  /home/biopo5/tutorial/Project4/JAK1/cmp49_jak1
# Command line:
#   gmx energy -f nvt.edr -o pressure.xvg
# gmx energy is part of G R O M A C S:
#
# Gromacs Runs One Microsecond At Cannonball Speeds
#
@title "GROMACS Energies"
@xaxis  label "Time (ps)"
@yaxis  label "(bar)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Pressure"
0.00  -3931.674805
1.00  528.706482
2.00   27.634497
3.00  -130.418900
4.00  -491.462982
5.003.087336
6.00  -246.631638
7.00  -86.932167
8.00  -453.551422
9.00  -46.325455
   10.00  270.657562
   11.00  -432.105682
   12.00  -578.059326
   13.00  -397.159760
   14.00  180.598190
   15.00  -159.344788
   16.00  -122.911415
   17.00  470.059418
   18.00  -375.501251
   19.00  -310.881561
   20.00   68.639618
   21.00  157.454422
   22.00  -619.447388
   23.00  -130.864059
   24.00   58.016773
   25.00  -132.054276
   26.00  114.288574
   27.00  -108.022186
   28.00  -235.894424
   29.00  -398.703217
   30.00  252.965332
   31.00  -269.996368
   32.00  -58.096252
   33.00  -291.578918
   34.00   15.896652
   35.00   53.429890
   36.00   43.522858
   37.00  -442.695190
   38.00  111.608665
   39.00  -12.626378
   40.00  -136.936111
   41.00  182.577164
   42.00  -68.747620
   43.00  121.546547
   44.00  127.403526
   45.00  -248.055176
   46.00  184.869797
   47.00  162.962906
   48.00  -387.420013
   49.00  228.167648
   50.00  348.351471
   51.00  -462.909180
   52.00  -234.574936
   53.00  -224.565689
   54.00  311.879456
   55.00  -404.242920
   56.00  -740.461182
   57.00   38.036850
   58.00  -677.158447
   59.00  -117.842407
   60.00  -20.302151
   61.00  -558.201233
   62.00  218.174881
   63.00  -269.575531
   64.00  -153.398697
   65.00  178.027954
   66.00  -193.050797
   67.00  -590.598694
   68.00  -487.503754
   69.00  171.980606
   70.00   84.821785
   71.00  -219.844803
   72.00  -228.680954
   73.00  -145.632614
   74.00   47.675121
   75.00  -310.033478
   76.00  -705.341248
   77.00  212.275406
   78.00   24.035654
   79.00  -221.810410
   80.00  -189.725708
   81.00  217.696289
   82.00  427.632660
   83.00  249.210770
   84.00  -405.385956
   85.00   78.898247
   86.00  -19.268747
   87.00   85.342247
   88.00  155.808731
   89.002.646250
   90.00  -284.466888
   91.00  152.030930
   92.00  280.804352
   93.00  -182.475830
   94.00  -268.784149
   95.00  -470.018829
   96.00  -163.642685
   97.00  291.026855
   98.00  -982.940430
   99.00  155.447800
  100.00   77.415077
-- 
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] control parameter on the Lennard-Jones interactions

[Dallas Warren]

Possibly 
http://manual.gromacs.org/documentation/current/reference-manual/special/tabulated-interaction-functions.html
?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 21 May 2019 at 05:06,  wrote:
>
> maybe I can add  the following section in the itp file (only for the A and B 
> atom) and then vary the W(c12) factor
>
> [ nonbond_params ]
> ; i   j func  V(c6) W(c12)
>
> A  B  1  0.22617E-02  0.74158E-06
>
>
> if this is ok, it is very simple!
>
> Can I define the func 1 for the atom A and B if for the system I used the 
> func 2 (sigma and eps rather then C6 and C12)? I suppose I can, right?
>
> Thank you very much!
>
> Anna
>
>
> > Il 20 maggio 2019 alle 18.15 battis...@libero.it ha scritto:
> >
> >
> > Dear all,
> >
> >
> > by considering there is no response to my post, I suppose in gromacs 
> > there is no way to solve exactly my problem.
> >
> > Also if no exactly, has anyone a kind of suggestion to go in the 
> > direction of my calcultation?
> >
> > Many thanks in advance,
> >
> > Anna
> >
> >
> >
> > > > Il 16 maggio 2019 alle 7.17 battis...@libero.it ha scritto:
> > >
> > >
> > >
> > > Dear gromacs members,
> > >
> > > I would ask you if in gromacs is possible to add a control 
> > > parameter on the Lennard-Jones interactions.
> > > For example we have two atoms A and B and the corresponding 
> > > parameters;  sigma(A), eps(A),  sigma(B), esp(B); then for the A-B 
> > > interactions we have the parameters obtained with the Lorentz-Berthelot 
> > > or with the geometrical average.
> > >
> > > I would like to have a standard interaction between A or B with 
> > > the other atoms of the system.  In the same time I would like to add a 
> > > control parameter C on the interaction between A and B to have the 
> > > following potential:
> > > 
> > > V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)]
> > >
> > > Is it possible? How can I manage this calculation?
> > >
> > >
> > > Many thanks,
> > >
> > >
> > > Anna
> > >
> > >
> > >
> > >
> > >
> > > >
> >
> >
> >
>
>
>
> --
> 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] Differences between Parrinello-Rahman, Nose-Hoover and MTTK - between LINCS and SHAKE

[Mark Abraham]

Hi,

On Mon, 20 May 2019 at 19:55, Anh Vo  wrote:

> Hi All,
>
> I’m currently running GROMACS to simulate a simple phospholipid bilayer
> membrane (POPC) under deformation.
>
> 1. For production step, GROMACS does not allow me to use Nose-Hoover
> barostat for pressure coupling, I can only choose among Berendsen,
> Parrinello-Rahman, Isotropic or MTTK options.
>
> What are the differences between *Parrinello-Rahman, Nose-Hoover and MTTK?*
>

There's some good background information at
http://manual.gromacs.org/current/reference-manual/algorithms/molecular-dynamics.html#pressure-coupling.
Berendsen does not sample a relevant distribution. N-H has doubtful ability
to sample ergodically, but probably is the best practical choice. MTTK
perhaps has some theoretical advantages, but cannot be used with
constraints, so the loss in sampling / increased cost is probably
ineffective overall.

Nose-Hoover can be used for temperature coupling, but not for pressure
> coupling. Why is that?
>

P-R barostat has never been implemented.


> 2. I'm not very clear what is constraints?


Constrained bonds cannot oscillate. The fastest oscillations in the system
restrict the size of the timestep that can be taken, those are the bond
vibrations involving H atoms. It has been found that rigid bonds are
roughly good a model as simple Hookes springs, and permit a larger
timestep. The larger timestep permits better sampling.

And what are the differences
> between LINCS and SHAKE constraint algorithm?
>

Very little, but LINCS is the algorithm of choice in GROMACS because it can
be parallelised well.
http://manual.gromacs.org/current/reference-manual/algorithms/constraint-algorithms.html

3. What does "refcoord_scaling" do in pressure coupling?
>

Scales the reference coordinates for position restraints - do check out the
mdp option documentation :-)

Mark

Thank you very much for sharing your time.
>
> Best regards,
> Anh Vo
> --
> 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] control parameter on the Lennard-Jones interactions

[battistia]

maybe I can add  the following section in the itp file (only for the A and B 
atom) and then vary the W(c12) factor

[ nonbond_params ]
; i   j func  V(c6) W(c12)

A  B  1  0.22617E-02  0.74158E-06


if this is ok, it is very simple!

Can I define the func 1 for the atom A and B if for the system I used the func 
2 (sigma and eps rather then C6 and C12)? I suppose I can, right?

Thank you very much!

Anna


> Il 20 maggio 2019 alle 18.15 battis...@libero.it ha scritto:
> 
> 
> Dear all,
> 
> 
> by considering there is no response to my post, I suppose in gromacs 
> there is no way to solve exactly my problem.
> 
> Also if no exactly, has anyone a kind of suggestion to go in the 
> direction of my calcultation?
> 
> Many thanks in advance,
> 
> Anna
> 
> 
> 
> > > Il 16 maggio 2019 alle 7.17 battis...@libero.it ha scritto:
> > 
> > 
> > 
> > Dear gromacs members,
> > 
> > I would ask you if in gromacs is possible to add a control 
> > parameter on the Lennard-Jones interactions.
> > For example we have two atoms A and B and the corresponding 
> > parameters;  sigma(A), eps(A),  sigma(B), esp(B); then for the A-B 
> > interactions we have the parameters obtained with the Lorentz-Berthelot or 
> > with the geometrical average.
> > 
> > I would like to have a standard interaction between A or B with the 
> > other atoms of the system.  In the same time I would like to add a control 
> > parameter C on the interaction between A and B to have the following 
> > potential:
> > V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)]
> > 
> > Is it possible? How can I manage this calculation?
> > 
> > 
> > Many thanks,
> > 
> > 
> > Anna
> > 
> > 
> > 
> > 
> > 
> > > 
> 
>  
> 


 
-- 
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] Differences between Parrinello-Rahman, Nose-Hoover and MTTK - between LINCS and SHAKE

[Anh Vo]

Hi All,

I’m currently running GROMACS to simulate a simple phospholipid bilayer
membrane (POPC) under deformation.

1. For production step, GROMACS does not allow me to use Nose-Hoover
barostat for pressure coupling, I can only choose among Berendsen,
Parrinello-Rahman, Isotropic or MTTK options.

What are the differences between *Parrinello-Rahman, Nose-Hoover and MTTK?*
Nose-Hoover can be used for temperature coupling, but not for pressure
coupling. Why is that?

2. I'm not very clear what is constraints? And what are the differences
between LINCS and SHAKE constraint algorithm?

3. What does "refcoord_scaling" do in pressure coupling?

Thank you very much for sharing your time.

Best regards,
Anh Vo
-- 
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] gmx_clustsize

[Bratin Kumar Das]

Thanks for your reply

On Mon 20 May, 2019, 9:24 PM David van der Spoel, 
wrote:

> Den 2019-05-20 kl. 11:24, skrev Bratin Kumar Das:
> > Hi,
> >  I wan to calculate the size of oligomers formed during the course of
> > simulation. Therefore I used gmx clustsize. The command I used is given
> > below
> >   > gmx clustsize -f md-cntr.xtc -s extend9.tpr -n protein_index.ndx -nc
> > no_of_clust.xvg -ac avg_cluster_size -hc hist_clust.xvg -dt 100 -cut 0.6
> > -pbc -mol -b 0 -e 5
> > The calculation is ended up with an error which is given below
>
> I think it means you have one cluster during the whole simulation. Note
> that periodic boundary conditions are taken into account.
>
> Try reducing the cut-off distance.
>
> > Back Off! I just backed up no_of_clust.xvg to ./#no_of_clust.xvg.2#
> >
> > Back Off! I just backed up avg_cluster_size.xvg to
> > ./#avg_cluster_size.xvg.2#
> >
> > Back Off! I just backed up maxclust.xvg to ./#maxclust.xvg.3#
> >
> > Back Off! I just backed up temp.xvg to ./#temp.xvg.3#
> > Reading frame   0 time0.000   Reading file extend9.tpr, VERSION
> > 2016.5 (single precision)
> > Reading file extend9.tpr, VERSION 2016.5 (single precision)
> > Using molecules rather than atoms. Not reading index file
> protein_index.ndx
> > Last frame   5000 time 5.000
> >
> > Back Off! I just backed up maxclust.ndx to ./#maxclust.ndx.1#
> > Total number of atoms in clusters =  13284
> > cmid: 1, cmax: 1, max_size: 13284
> >
> > Back Off! I just backed up csize.xpm to ./#csize.xpm.1#
> >
> > ---
> > Program: gmx clustsize, version 2016.5
> > Source file: src/gromacs/fileio/matio.cpp (line 690)
> >
> > Fatal error:
> > Lo: 0.00, Mid: 1.00, Hi: 1.00
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > Can any one help me out..what kind of error it is.
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> 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] EXTERNAL: Re: gromacs make check failure

[Paul bauer]

Hello,

if it takes this long then something is going wrong, so you don't need 
to wait that long.

What happens when you build without MPI?

Cheers

Paul

On 20/05/2019 18:14, Nelson Chris AWE wrote:

Thanks Paul,
I have run the binary manually, and it's been going for over an hour now so I 
guess there is something wrong with it - I'll leave it running overnight and 
see if it completes.
Cheers,
Chris

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Paul bauer
Sent: 20 May 2019 15:34
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: EXTERNAL: Re: [gmx-users] gromacs make check failure

Hello,

from looking at the output from make check it looks like this is harmless. The 
tests simply took longer than the internally set cut-off of 30 seconds.
If you are unsure about the build, you can run the test binary manually from 
the build directory with (./gmxpreprocess-test in the same directory where you 
can find the gmx binary).
Then it won't use the cut-off and will take as much time as it will need.

Cheers

Paul

On 20/05/2019 16:26, Nelson Chris AWE wrote:

Hi All,
I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and
OpenMPI

When I run make check, I get a failure on test 29:

29 - GmxPreprocessTests (Timeout)

Any advice would be much appreciated.

Links to output files:

1.  Build environment 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ksdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=vq67KLEfO8%2FOvDEx80mS22FpO4B4WogQbKHS5UKEO%2Bk%3Dreserved=0
 )
2.  Build output 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1PQFllv49M-Op6HLtdKsRJfwHbFeEsintdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=kvDO4%2FnuLOUAz2SemHqGQ2XuN%2Fdzbwz%2B9S4bk%2BAFsfs%3Dreserved=0
 )
3.  Dependency list 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7Tdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=ckVLYxFG0XpM797geks%2Fpmd75B5SSDt8EZt8J0Aro5w%3Dreserved=0
 )
4.  Make checkout output 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1data=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=ylFHabQdXHeSBIQ4TNhujWeRin5jTkKFv7VAhuCmzR8%3Dreserved=0
 )
5.  mdrun - version output
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdri
ve.google.com%2Fopen%3Fid%3D1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6Ddata
=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9
%7C72654b74be024361a62716b132e3fdd0%7C0sdata=UIVAn%2BTTdZx6ljvGQl
%2FQA4jJM1A%2Bbz3dvK8YmGAoBd8%3Dreserved=0 )

Kind regards,
Chris.


Christopher J. Nelson
High Performance Computing
Direct: +44(0)118 98 55021
F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK

The information in this email and in any attachment(s) is commercial
in confidence. If you are not the named addressee(s) or if you receive
this email in error then any distribution, copying or use of this
communication or the information in it is strictly prohibited. Please
notify us immediately by email at admin.internet(at)awe.co.uk, and
then delete this message from your computer. While attachments are
virus checked, AWE plc does not accept any liability in respect of any
virus which is not detected. AWE Plc Registered in England and Wales
Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR


--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

--
Gromacs Users mailing list

* Please search the archive at 
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=KY80wFoIdiVSSGMT%2BTzCwUATufKAFWEqKcmU%2Fm11zzQ%3Dreserved=0
 before posting!

* Can't post? Read 
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=3aLnTCJD%2FWtFronNOkYCl0jXr%2BQegYzYm%2BODizL7QdU%3Dreserved=0

* For (un)subscribe requests visit
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=GVmhgOVcj9QeuLhkZ%2FcNSxW6NfTTcoD9HQ4n2W0mpig%3Dreserved=0
 or send a mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] control parameter on the Lennard-Jones interactions

[battistia]

Dear all,


by considering there is no response to my post, I suppose in gromacs there is 
no way to solve exactly my problem.

Also if no exactly, has anyone a kind of suggestion to go in the direction of 
my calcultation?

Many thanks in advance,

Anna



> Il 16 maggio 2019 alle 7.17 battis...@libero.it ha scritto:
> 
> 
> 
> Dear gromacs members,
> 
> I would ask you if in gromacs is possible to add a control parameter on 
> the Lennard-Jones interactions.
> For example we have two atoms A and B and the corresponding parameters;  
> sigma(A), eps(A),  sigma(B), esp(B); then for the A-B interactions we have 
> the parameters obtained with the Lorentz-Berthelot or with the geometrical 
> average.
> 
> I would like to have a standard interaction between A or B with the other 
> atoms of the system.  In the same time I would like to add a control 
> parameter C on the interaction between A and B to have the following 
> potential:
> V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)]
> 
> Is it possible? How can I manage this calculation?
> 
> 
> Many thanks,
> 
> 
> Anna
> 
> 
> 
> 
> 


 
-- 
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] EXTERNAL: Re: gromacs make check failure

[Nelson Chris AWE]

Thanks Paul,
I have run the binary manually, and it's been going for over an hour now so I 
guess there is something wrong with it - I'll leave it running overnight and 
see if it completes.
Cheers,
Chris

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Paul bauer
Sent: 20 May 2019 15:34
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: EXTERNAL: Re: [gmx-users] gromacs make check failure

Hello,

from looking at the output from make check it looks like this is harmless. The 
tests simply took longer than the internally set cut-off of 30 seconds.
If you are unsure about the build, you can run the test binary manually from 
the build directory with (./gmxpreprocess-test in the same directory where you 
can find the gmx binary).
Then it won't use the cut-off and will take as much time as it will need.

Cheers

Paul

On 20/05/2019 16:26, Nelson Chris AWE wrote:
> Hi All,
> I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and
> OpenMPI
>
> When I run make check, I get a failure on test 29:
>
> 29 - GmxPreprocessTests (Timeout)
>
> Any advice would be much appreciated.
>
> Links to output files:
>
>1.  Build environment 
> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ksdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=vq67KLEfO8%2FOvDEx80mS22FpO4B4WogQbKHS5UKEO%2Bk%3Dreserved=0
>  )
>2.  Build output 
> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1PQFllv49M-Op6HLtdKsRJfwHbFeEsintdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=kvDO4%2FnuLOUAz2SemHqGQ2XuN%2Fdzbwz%2B9S4bk%2BAFsfs%3Dreserved=0
>  )
>3.  Dependency list 
> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7Tdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=ckVLYxFG0XpM797geks%2Fpmd75B5SSDt8EZt8J0Aro5w%3Dreserved=0
>  )
>4.  Make checkout output 
> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1data=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=ylFHabQdXHeSBIQ4TNhujWeRin5jTkKFv7VAhuCmzR8%3Dreserved=0
>  )
>5.  mdrun - version output
> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdri
> ve.google.com%2Fopen%3Fid%3D1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6Ddata
> =01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9
> %7C72654b74be024361a62716b132e3fdd0%7C0sdata=UIVAn%2BTTdZx6ljvGQl
> %2FQA4jJM1A%2Bbz3dvK8YmGAoBd8%3Dreserved=0 )
>
> Kind regards,
> Chris.
>
>
> Christopher J. Nelson
> High Performance Computing
> Direct: +44(0)118 98 55021
> F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK
>
> The information in this email and in any attachment(s) is commercial
> in confidence. If you are not the named addressee(s) or if you receive
> this email in error then any distribution, copying or use of this
> communication or the information in it is strictly prohibited. Please
> notify us immediately by email at admin.internet(at)awe.co.uk, and
> then delete this message from your computer. While attachments are
> virus checked, AWE plc does not accept any liability in respect of any
> virus which is not detected. AWE Plc Registered in England and Wales
> Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR


--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

--
Gromacs Users mailing list

* Please search the archive at 
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=KY80wFoIdiVSSGMT%2BTzCwUATufKAFWEqKcmU%2Fm11zzQ%3Dreserved=0
 before posting!

* Can't post? Read 
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=3aLnTCJD%2FWtFronNOkYCl0jXr%2BQegYzYm%2BODizL7QdU%3Dreserved=0

* For (un)subscribe requests visit
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=GVmhgOVcj9QeuLhkZ%2FcNSxW6NfTTcoD9HQ4n2W0mpig%3Dreserved=0
 or send a mail to gmx-users-requ...@gromacs.org.
The information in this email and in any attachment(s) is commercial in 
confidence. If you are not the named 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 45

[Nidhin Thomas]

Dear Justin,

Thanks a lot for the prompt reply.

I ran another simulation with a larger box size with and without external 
electric field (field direction is Y-axis). I used anisotropic pressure 
coupling for both simulations. Water box without external electric field had 
fluctuation in the beginning but stabilized soon. The simulation continued 
without fail. However, the system with external electric field deformed 
continuously. System with EF fails once the dimension of the box vector 
(Y-axis) along the direction of electric field reduces below the minimum box 
dimension. The error message is copied below.

Fatal error:
The Y-size of the box (2.641246) times the triclinic skew factor (1.00) is
smaller than the number of DD cells (2) times the smallest allowed cell size
(1.322000)

I feel that box is shrinking in the direction of applied electric field 
(Y-axis) like there is an external compressive stress applied in that 
direction. I do not understand how this type of a stress is generated in the 
system.

I have also shared link to an image that shows how the box vectors are changing 
with simulation time. When EF is applied, simulation fails in few picoseconds. 
But water box without EF did not fail.

Could you please help me understand why system with external electric field 
would behave different from water box without EF?

https://www.dropbox.com/s/zu7vl2wr99sube2/Box%20vectors%20with%20and%20without%20EF.png?dl=0

Thanks,

Nidhin Thomas



> On 5/19/19 11:32 PM, Nidhin Thomas wrote:
>> Hello GROMACS users,
>> 
>> I tried to apply a static electric field across a water box. I used  
>> anisotropic pressure coupling. Details of the pressure coupling is given 
>> below.
>> 
>> pcoupl  = Parrinello-Rahman
>> pcoupltype  = anisotropic
>> tau_p   = 5.0
>> compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
>> ref_p   = 1.0 1.0 1.0 0 0 0
>> ;
>> constraints = h-bonds
>> constraint_algorithm= LINCS
>> continuation= yes
>> ;
>> electric-field-y = 0.1 0 0 0
>> 
>> I see that water box size reduced in the direction of application of 
>> electric field (Y) and increased in X and Z direction.
>> 
>> Original Size = (3.90 x 3.90 x 3.90) nm
>> Final Size = (4.39 x 2.66 x 5.16) nm
>> 
>> Could someone please help me understand why the water box is shrinking in 
>> the direction of electric field ? can someone please let me know how 
>> external electric field is actually implemented in GROMACS ?
> 
> Anisotropic pressure coupling intrinsically leads to the distortion of 
> the box shape. Run a control simulation of water with no electric field 
> and you will see the same thing.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> 
> Virginia Tech Department of Biochemistry
> 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] gmx_clustsize

[David van der Spoel]

Den 2019-05-20 kl. 11:24, skrev Bratin Kumar Das:

Hi,
 I wan to calculate the size of oligomers formed during the course of
simulation. Therefore I used gmx clustsize. The command I used is given
below
  > gmx clustsize -f md-cntr.xtc -s extend9.tpr -n protein_index.ndx -nc
no_of_clust.xvg -ac avg_cluster_size -hc hist_clust.xvg -dt 100 -cut 0.6
-pbc -mol -b 0 -e 5
The calculation is ended up with an error which is given below


I think it means you have one cluster during the whole simulation. Note 
that periodic boundary conditions are taken into account.


Try reducing the cut-off distance.


Back Off! I just backed up no_of_clust.xvg to ./#no_of_clust.xvg.2#

Back Off! I just backed up avg_cluster_size.xvg to
./#avg_cluster_size.xvg.2#

Back Off! I just backed up maxclust.xvg to ./#maxclust.xvg.3#

Back Off! I just backed up temp.xvg to ./#temp.xvg.3#
Reading frame   0 time0.000   Reading file extend9.tpr, VERSION
2016.5 (single precision)
Reading file extend9.tpr, VERSION 2016.5 (single precision)
Using molecules rather than atoms. Not reading index file protein_index.ndx
Last frame   5000 time 5.000

Back Off! I just backed up maxclust.ndx to ./#maxclust.ndx.1#
Total number of atoms in clusters =  13284
cmid: 1, cmax: 1, max_size: 13284

Back Off! I just backed up csize.xpm to ./#csize.xpm.1#

---
Program: gmx clustsize, version 2016.5
Source file: src/gromacs/fileio/matio.cpp (line 690)

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Can any one help me out..what kind of error it is.




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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] gromacs make check failure

[Paul bauer]

Hello,

from looking at the output from make check it looks like this is 
harmless. The tests simply took longer than the internally set cut-off 
of 30 seconds.
If you are unsure about the build, you can run the test binary manually 
from the build directory with (./gmxpreprocess-test in the same 
directory where you can find the gmx binary).

Then it won't use the cut-off and will take as much time as it will need.

Cheers

Paul

On 20/05/2019 16:26, Nelson Chris AWE wrote:

Hi All,
I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and OpenMPI

When I run make check, I get a failure on test 29:

29 - GmxPreprocessTests (Timeout)

Any advice would be much appreciated.

Links to output files:

   1.  Build environment 
(https://drive.google.com/open?id=1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ks )
   2.  Build output 
(https://drive.google.com/open?id=1PQFllv49M-Op6HLtdKsRJfwHbFeEsint )
   3.  Dependency list 
(https://drive.google.com/open?id=13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7T )
   4.  Make checkout output 
(https://drive.google.com/open?id=1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1 )
   5.  mdrun - version output 
(https://drive.google.com/open?id=1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6D )

Kind regards,
Chris.


Christopher J. Nelson
High Performance Computing
Direct: +44(0)118 98 55021
F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK

The information in this email and in any attachment(s) is commercial in 
confidence. If you are not the named addressee(s) or if you receive this email 
in error then any distribution, copying or use of this communication or the 
information in it is strictly prohibited. Please notify us immediately by email 
at admin.internet(at)awe.co.uk, and then delete this message from your 
computer. While attachments are virus checked, AWE plc does not accept any 
liability in respect of any virus which is not detected. AWE Plc Registered in 
England and Wales Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR



--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

--
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] gromacs make check failure

[Nelson Chris AWE]

Hi All,
I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and OpenMPI

When I run make check, I get a failure on test 29:

29 - GmxPreprocessTests (Timeout)

Any advice would be much appreciated.

Links to output files:

  1.  Build environment 
(https://drive.google.com/open?id=1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ks )
  2.  Build output 
(https://drive.google.com/open?id=1PQFllv49M-Op6HLtdKsRJfwHbFeEsint )
  3.  Dependency list 
(https://drive.google.com/open?id=13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7T )
  4.  Make checkout output 
(https://drive.google.com/open?id=1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1 )
  5.  mdrun - version output 
(https://drive.google.com/open?id=1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6D )

Kind regards,
Chris.


Christopher J. Nelson
High Performance Computing
Direct: +44(0)118 98 55021
F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK

The information in this email and in any attachment(s) is commercial in 
confidence. If you are not the named addressee(s) or if you receive this email 
in error then any distribution, copying or use of this communication or the 
information in it is strictly prohibited. Please notify us immediately by email 
at admin.internet(at)awe.co.uk, and then delete this message from your 
computer. While attachments are virus checked, AWE plc does not accept any 
liability in respect of any virus which is not detected. AWE Plc Registered in 
England and Wales Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR
-- 
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] Rupture force definition

[Justin Lemkul]

On 5/17/19 6:15 AM, Rakesh Mishra wrote:

Dear Justin

After long time again I want to ask one question.
If suppose I want to repeat the same production
simulation ( final md simulation) for different seeds,
then how to do. Because as from the knowledge of
gromacs there is no manual way to put different seeds
in the .mdp files.


gen-seed gives you different starting velocities. If you want to perform 
independent simulations they need to either start from (1) different 
velocities, (2) different conformations, or (3) different pull vectors.


-Justin



On Mon, Jun 25, 2018 at 7:27 PM Justin Lemkul  wrote:



On 6/25/18 8:48 AM, Rakesh Mishra wrote:

Dear Justin.

I have observed one thing that during pulling (Constant velocity pulling

)

of dsDNA/dsRNA ( globally say Nucleic acid ) along helical direction, we
observe that in the force/time .xvg file, some time force value  is +ve

and

some time force value is -ve. So why it happens. In my thinking it should
always be +ve.

Free energy surfaces are rugged. Some intermediate conformations may
result in local free energy wells.

-Justin


On Mon, Jun 11, 2018 at 5:37 PM, Justin Lemkul  wrote:


On 6/8/18 2:52 AM, Rakesh Mishra wrote:


Dear Justin .
I have  two query

1-What can be the optimized value of rate can be taken
for pulling of  dsDNA/dsRNA using gromacs format where solvent is

aqua.

   From your umbrella sampling manual,  rate is very high like (0.01

nm/ps),

which is equal to 0.0001Angstrom/fs.


You'll note in the SI we tested lower values and achieved the same
outcome, so you need to test a few to be sure that whatever pull rate

you

impose does not introduce artifacts. There is no way, a priori, to know
what an "optimized" rate would be. That term also has multiple
interpretations.

2- In pulling mdp file no random seed is discussed. But if we want to

obtain 2 or 3 different trajectory during
pulling ( of the same system ) for  different seed, then how to

give

different seed in pulling  mdp file.

Note -  In my thinking in gromacs, gen_seed  = -1 is default value.

And

it
comes , when NVT is applied ( where
velocity generation is allowed, to achieve required
temperature through maxwell distribution ). But in case of pulling,

where

no velocity
generation is allowed . Then how to calculate different
pulling simulation of the same system for different seeds.


One does not supply a new random seed when doing a continuation of a

run.

If you want to start new simulations in each window or in multiple
replicates of a run, then use "gen_seed = -1" to get a completely random
seed based on the process ID.


-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.





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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] protein water rdf with coordination number

[Justin Lemkul]

On 5/19/19 7:11 PM, Dallas Warren wrote:

RDF ->
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html

Coordination number ->
https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions
Will need to integrate the g(r) with radius, using the particle
average density across the box.


Also note that gmx rdf makes no attempt to account for excluded volume 
of solute molecules like proteins, so I don't think you can even get a 
quantitatively correct coordination number from it in a case like this. 
For a homogeneous system, it works fine, but not when there's some 
large, irregularly shaped object in the way.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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] External electric field applied to water box

[Justin Lemkul]

On 5/19/19 11:32 PM, Nidhin Thomas wrote:

Hello GROMACS users,

I tried to apply a static electric field across a water box. I used  
anisotropic pressure coupling. Details of the pressure coupling is given below.

pcoupl  = Parrinello-Rahman
pcoupltype  = anisotropic
tau_p   = 5.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p   = 1.0 1.0 1.0 0 0 0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
electric-field-y = 0.1 0 0 0

I see that water box size reduced in the direction of application of electric 
field (Y) and increased in X and Z direction.

Original Size = (3.90 x 3.90 x 3.90) nm
Final Size = (4.39 x 2.66 x 5.16) nm

Could someone please help me understand why the water box is shrinking in the 
direction of electric field ? can someone please let me know how external 
electric field is actually implemented in GROMACS ?


Anisotropic pressure coupling intrinsically leads to the distortion of 
the box shape. Run a control simulation of water with no electric field 
and you will see the same thing.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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] Pressure coupling in expanded ensemble simulations

[Gregory Man Kai Poon]

Hi Michael,

Our system of interest here is a set of small proteins with disordered regions. 
 The literature suggests that RE methods are not well-suited to sampling such 
systems with dynamically "hot/cold" regions (and requiring more specialized 
techniques such as the link below) on the one hand, while approaches such as 
simulated tempering may be more efficient on the other.  We also wanted lower 
requirements on CPU cores given the level of hardware we have access to.

https://www.ncbi.nlm.nih.gov/pubmed/25136274

We have been working with toy systems such as the Ala10 peptide in TIP3P to 
define the workflow with Metropolis MC moves and the WL histogram.  As you 
suggested previously, we ran an NVT ensemble from 280 to 330 K, with 11 
linearly spaced intervals (with a v-rescale tcoupl), starting with a 
NPT-equilibrated system.  The usual diagnostics look okay (e.g., acceptance 
ratio).  The pressure of the system after several hundred ns runs did not seem 
very different, given the typical RMSD on the order of 100's of bar even when 
pressure coupling is on.  Obviously, if we could move the sampling back to NPT 
would be very helpful.  Kindly let me know what specific info you would like to 
see.

Thanks again for your help,

Gregory


On 5/19/2019 11:05 PM, Michael Shirts wrote:

Ah, sorry, I thought there was more information coming.

Have you considered just using temperature replica exchange?  It's not that
much less efficient, and is easier to deal with.  Replica exchange should
be working with NPT (as long as you use Parrinello-Rahman and a reasonable
temperature control algorithm).  The size scaling is about the same; i.e.
if you need a lot of replicas, you will also need a lot of expanded
ensemble intermediates.




On Fri, May 17, 2019 at 8:06 AM Gregory Man Kai Poon 
 wrote:



Hi Michael,

I am just following up on your thoughts on how carrying out expanded
ensemble at NVT and converting back to NPT on the mailing list.  Again I
appreciate your advice in this area.

Best wishes,

Gregory


On 5/8/2019 12:01 PM, Michael Shirts wrote:

Yeah, this is an unfortunately place in the code where not all combinations
work - very long story.  Hopefully this will be working better in 2020.

What I would recommend is, if possible, performing the expanded ensemble
simulation at NVT.  Everything should work fine there (paper coming out
hopefully soon comparing a bunch of free energy methods).  Once can always
correct the free energy at lambda=1 from NVT to NPT.  I Can fill in the
details.

You do NOT want to do Berendsen for NPT when running expanded ensemble.
The results will be incorrect (as I have learned by sad experience_

On Wed, May 8, 2019 at 8:14 AM Gregory Man Kai Poon 
mailto:gp...@gsu.edu>


 wrote:





Hi all:

We are interested to do expanded ensemble simulations (such as simulated
tempering) on GROMACS.  Extensive fiddling with the settings and
googling on other people's experience suggests that these simulations
must use the md-vv integrator, which in turn is compatible with
Berendsen or MTTK coupling for pressure.  However, MTTK does not work
with constraints, which are needed for the forcefields.  Berendsen can
handle constraints but is not recommended for preserving thermodynamic
ensembles.  Any ideas on how one should proceed?

Many thanks for your thoughts.

Gregory


--
Gromacs Users mailing list

* Please search the archive at

https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Cgpoon%40gsu.edu%7Cf2483cf7c772405c9fab08d6dcd01fa6%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636939183786870008sdata=8FzpvoKLUx0xmXnPCrBOIoSvj%2FOR%2Bwf2VnllHv6Nr0k%3Dreserved=0
before
posting!

* Can't post? Read
https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Cgpoon%40gsu.edu%7Cf2483cf7c772405c9fab08d6dcd01fa6%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636939183786870008sdata=E45aW%2BrtTKV5pmA6LF%2F6qSa68VnEJKVV2%2F0jt%2BIRfBk%3Dreserved=0

* For (un)subscribe requests visit

https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Cgpoon%40gsu.edu%7Cf2483cf7c772405c9fab08d6dcd01fa6%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636939183786870008sdata=oD2hr2VuQoxYWl3FzS8tqrXa8v3eqgKZnOccYWjFT9Y%3Dreserved=0
or
send a mail to 
gmx-users-requ...@gromacs.org.


--

Gregory M. K. Poon, PhD, RPh
Associate Professor
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
Ph (404) 413-5491 | 
gp...@gsu.edu
--
Gromacs Users mailing list

* Please search the 

[gmx-users] gmx_clustsize

[Bratin Kumar Das]

Hi,
I wan to calculate the size of oligomers formed during the course of
simulation. Therefore I used gmx clustsize. The command I used is given
below
 > gmx clustsize -f md-cntr.xtc -s extend9.tpr -n protein_index.ndx -nc
no_of_clust.xvg -ac avg_cluster_size -hc hist_clust.xvg -dt 100 -cut 0.6
-pbc -mol -b 0 -e 5
The calculation is ended up with an error which is given below
Back Off! I just backed up no_of_clust.xvg to ./#no_of_clust.xvg.2#

Back Off! I just backed up avg_cluster_size.xvg to
./#avg_cluster_size.xvg.2#

Back Off! I just backed up maxclust.xvg to ./#maxclust.xvg.3#

Back Off! I just backed up temp.xvg to ./#temp.xvg.3#
Reading frame   0 time0.000   Reading file extend9.tpr, VERSION
2016.5 (single precision)
Reading file extend9.tpr, VERSION 2016.5 (single precision)
Using molecules rather than atoms. Not reading index file protein_index.ndx
Last frame   5000 time 5.000

Back Off! I just backed up maxclust.ndx to ./#maxclust.ndx.1#
Total number of atoms in clusters =  13284
cmid: 1, cmax: 1, max_size: 13284

Back Off! I just backed up csize.xpm to ./#csize.xpm.1#

---
Program: gmx clustsize, version 2016.5
Source file: src/gromacs/fileio/matio.cpp (line 690)

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Can any one help me out..what kind of error it is.
-- 
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.