[gmx-users] Fwd: no atom pairs for dispersion correction

[Sadaf Rani]

Dear Gromacs users
I am running an MD simulation of the protein-ligand complex. At the start
of the production run, I am getting this warning. What does it mean and how
should I fix it?

*WARNING: There are no atom pairs for dispersion correction*

Thanks in advance.

Sadaf
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Re: [gmx-users] Issue with PMF

[Justin Lemkul]

On 4/2/20 4:19 PM, Alex wrote:

Thanks Justin for the response.

On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul  wrote:



On 4/2/20 12:53 PM, Alex wrote:

Dear all,
By using the below setting I am getting a very nice umbrella histogram

and

iact also shows a very good integrated Autocorrelation time. However, the
PMF profile is unexpected. Below I have also provided a gmx wham command

I

am using, part of the pullx.xvg of one of the windows and also
corresponding part in log file.
Would you please help me find out what the problem might be?

What is the problem?


Below link shows the histogram and PMF, actually I was expecting that the
PMF reach a plateau in the region marked by B in the figure as we are fully
inside the bulk area of the thin film. However, there are some region from
15 to 20 kcal/mol different respect to the expected plateau. Here we have
10nm thick thin film.

https://drive.google.com/open?id=1ve50thHG4wORe0-fKdoIsPncQpEyuwcz



Bootstrapping may underestimate the real error. How well converged is 
the PMF with respect to time, e.g. computing the PMF from the first half 
and last half of the simulation time?



One more question: does it make sense to manually shift the plateau of

the

PMF plot to zero (when we plot it), instead of using using the -zprof0

flag?

There is no difference. The -zprof0 just adds a constant so the PMF is
zero at the specified point on the reaction coordinate.


%
pull = yes
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = Mol_A
pull-group2-name = Thin_film

pull-coord1-groups   = 1 2
pull-coord1-type = umbrella
pull-coord1-dim  = N N Y
pull-coord1-start= no   ;--> manually we define the distance for
all windows
pull-coord1-rate = 0.0  ;--> We don't want the roups to move
pull-coord1-geometry = distance
pull-coord1-k= 1   ;;kJ/(mol nm^2)
pull-print-components= Yes
pull-nstxout = 2000
pull-nstfout = 2000
pull-print-com1  = yes
pull-coord1-init = 1.65
%
#Part of the one of the pullx.xvg file
@ legend length 2
@ s0 legend "1"
@ s1 legend "1 dZ"
@ s2 legend "1 g 1 Z"
@ s3 legend "1 g 2 Z"
0.  0.0155171   0.0155171   9.89805 9.91357
2.  0.0103956   0.0103956   9.90227 9.91266
4.  0.0146962   0.0146962   9.89733 9.91202
6.  0.00656533  0.00656533  9.90404 9.91061
8.  0.00228074  0.00228074  9.90945 9.91174
10. 0.00967605  0.00967605  9.90514 9.91482

%
gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist
-bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o
profile.xvg -b 3000 -unit kCal -v

   %
#Similar massage as below I have for all windows (tpr files).
Reading file prd.1.tpr, VERSION 2018.7 (single precision)

File prd.1.tpr, 1 coordinates, with these options:
  Geometry distance   k = 1 position = 0

  dimensions

[N N Y] (1 dimensions). Used: Yes
  Pull group coordinates of 2 groups expected in pullx files.
  Reference value of the coordinate not expected in pullx files.

Reading pull force file prd_pullf.1.xvg, expecting 2 columns:
  Columns for pull coordinate 1
  reaction coordinate: 1
  center-of-mass of groups:0
  reference position column:   No
  Found 2501 times in prd_pullf.1.xvg
%--

Actually, I was suspicious of these "Reference value of the coordinate not
expected in pullx files."  and "reference position column:   No" which
I have in log file of gmx wham for each windows's tpr.


I have no experience with that; the pullx.xvg file format has changed a 
lot over time. I always use pullf.xvg and it's never an issue.



Concerning your PMF tutorial, when the distance between chain_A and chain_B
is calculated by gmx distance, why the -oall is used to get the absolute
distance out of x,y and z, while the -oxyz would be much better as we can
take the Z component of the distance similar (corresponding) to the
considered reaction coordinate in the tutorial?


The two quantities should be essentially equivalent for the purposes of 
the tutorial.


-Justin


Regards,
Alex


Thank you,
Alex

--
==

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

==

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Re: [gmx-users] Issue with PMF

[Alex]

Thanks Justin for the response.

On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul  wrote:

>
>
> On 4/2/20 12:53 PM, Alex wrote:
> > Dear all,
> > By using the below setting I am getting a very nice umbrella histogram
> and
> > iact also shows a very good integrated Autocorrelation time. However, the
> > PMF profile is unexpected. Below I have also provided a gmx wham command
> I
> > am using, part of the pullx.xvg of one of the windows and also
> > corresponding part in log file.
> > Would you please help me find out what the problem might be?
>
> What is the problem?
>
Below link shows the histogram and PMF, actually I was expecting that the
PMF reach a plateau in the region marked by B in the figure as we are fully
inside the bulk area of the thin film. However, there are some region from
15 to 20 kcal/mol different respect to the expected plateau. Here we have
10nm thick thin film.

https://drive.google.com/open?id=1ve50thHG4wORe0-fKdoIsPncQpEyuwcz


> > One more question: does it make sense to manually shift the plateau of
> the
> > PMF plot to zero (when we plot it), instead of using using the -zprof0
> flag?
>
> There is no difference. The -zprof0 just adds a constant so the PMF is
> zero at the specified point on the reaction coordinate.
>
> > %
> > pull = yes
> > pull-ngroups = 2
> > pull-ncoords = 1
> > pull-group1-name = Mol_A
> > pull-group2-name = Thin_film
> >
> > pull-coord1-groups   = 1 2
> > pull-coord1-type = umbrella
> > pull-coord1-dim  = N N Y
> > pull-coord1-start= no   ;--> manually we define the distance for
> > all windows
> > pull-coord1-rate = 0.0  ;--> We don't want the roups to move
> > pull-coord1-geometry = distance
> > pull-coord1-k= 1   ;;kJ/(mol nm^2)
> > pull-print-components= Yes
> > pull-nstxout = 2000
> > pull-nstfout = 2000
> > pull-print-com1  = yes
> > pull-coord1-init = 1.65
> > %
> > #Part of the one of the pullx.xvg file
> > @ legend length 2
> > @ s0 legend "1"
> > @ s1 legend "1 dZ"
> > @ s2 legend "1 g 1 Z"
> > @ s3 legend "1 g 2 Z"
> > 0.  0.0155171   0.0155171   9.89805 9.91357
> > 2.  0.0103956   0.0103956   9.90227 9.91266
> > 4.  0.0146962   0.0146962   9.89733 9.91202
> > 6.  0.00656533  0.00656533  9.90404 9.91061
> > 8.  0.00228074  0.00228074  9.90945 9.91174
> > 10. 0.00967605  0.00967605  9.90514 9.91482
> > 
> > %
> > gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist
> > -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o
> > profile.xvg -b 3000 -unit kCal -v
> >
> >   %
> > #Similar massage as below I have for all windows (tpr files).
> > Reading file prd.1.tpr, VERSION 2018.7 (single precision)
> >
> > File prd.1.tpr, 1 coordinates, with these options:
> >  Geometry distance   k = 1 position = 0
>  dimensions
> > [N N Y] (1 dimensions). Used: Yes
> >  Pull group coordinates of 2 groups expected in pullx files.
> >  Reference value of the coordinate not expected in pullx files.
> >
> > Reading pull force file prd_pullf.1.xvg, expecting 2 columns:
> >  Columns for pull coordinate 1
> >  reaction coordinate: 1
> >  center-of-mass of groups:0
> >  reference position column:   No
> >  Found 2501 times in prd_pullf.1.xvg
> > %--
>
Actually, I was suspicious of these "Reference value of the coordinate not
expected in pullx files."  and "reference position column:   No" which
I have in log file of gmx wham for each windows's tpr.

Concerning your PMF tutorial, when the distance between chain_A and chain_B
is calculated by gmx distance, why the -oall is used to get the absolute
distance out of x,y and z, while the -oxyz would be much better as we can
take the Z component of the distance similar (corresponding) to the
considered reaction coordinate in the tutorial?

Regards,
Alex

> >
> > Thank you,
> > Alex
>
> --
> ==
>
> 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.k

Re: [gmx-users] Simulation of Protein-Protein Complex

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 4/2/20 3:38 PM, Surya Sanjay wrote:

Hello Dr. Lemkul,
You were very helpful (I was pondering this problem for about four 
days before you told me this and it all makes sense now). To complete 
the solvation step, should I combine the topol.top files of both 
protein chains?


You should only ever have one topol.top. pdb2gmx will write each protein 
chain topology to .itp files that are #included within it.


-Justin


Thanks,
Surya

On Thu, Apr 2, 2020 at 3:25 PM Justin Lemkul > wrote:




On 4/2/20 3:19 PM, Surya Sanjay wrote:
> Hello all,
> I am a beginner Gromacs user and I have been using the Gromacs
tutorials on
> mdtutorials.com/gmx/ . I would like
to simulate the binding of the
> infectious and normally-folded prion variants, and I want to
know if the
> protein-protein complex procedure is different from that of
protein-ligand
> systems.

A system containing several proteins is functionally no different
than
simulating one protein. Don't equate protein-protein systems to
protein-ligand systems, which often require external ligand
parametrization. None of that is necessary when dealing with proteins.

-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

==

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.



--
==

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

==

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Re: [gmx-users] Fwd: geometry optimization of metalloenzyme

[Justin Lemkul]

On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:

Hello everyone,

I am trying to minimize the potential energy of a
metalloenzyme containing Ni and Fe atoms.
What is the best way to constrain (fix?) the position of the active site
atoms
during the geometry optimization?
I have tried introducing bonds with relatively high force constants and
alternatively, tried introducing a [constraints] section,
but the atoms are still not staying put.


Bonds or constraints will maintain distances between atoms (relative 
position) but not absolute position.



Or should one use extra position restraints?


If the absolute position matters, yes. I would think the approach of 
adding restraints or constraints between atoms would be more meaningful 
given that preserving coordination geometry is often the defect in MM 
treatment of transition metals.


-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

==

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Re: [gmx-users] Simulation of Protein-Protein Complex

[Justin Lemkul]

On 4/2/20 3:19 PM, Surya Sanjay wrote:

Hello all,
I am a beginner Gromacs user and I have been using the Gromacs tutorials on
mdtutorials.com/gmx/. I would like to simulate the binding of the
infectious and normally-folded prion variants, and I want to know if the
protein-protein complex procedure is different from that of protein-ligand
systems.


A system containing several proteins is functionally no different than 
simulating one protein. Don't equate protein-protein systems to 
protein-ligand systems, which often require external ligand 
parametrization. None of that is necessary when dealing with proteins.


-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

==

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Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] Fwd: geometry optimization of metalloenzyme

[Nadia Elghobashi-Meinhardt]

Hello everyone,

I am trying to minimize the potential energy of a
metalloenzyme containing Ni and Fe atoms.
What is the best way to constrain (fix?) the position of the active site
atoms
during the geometry optimization?
I have tried introducing bonds with relatively high force constants and
alternatively, tried introducing a [constraints] section,
but the atoms are still not staying put.
Or should one use extra position restraints?

Any tips are welcome!
Thank you.
-- 
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Re: [gmx-users] Effect of atomic charge on bonding parameters

[Justin Lemkul]

On 4/2/20 2:45 PM, Neena Susan Eappen wrote:

Hi Justin,

What is the criteria for opls bond types?


I don't understand the question. Nonbonded and bonded atom types can be 
separate (this is uncommon, but something that OPLS does) because bonded 
interactions may be more transferable than nonbonded paramters. I have 
no idea why OPLS has opls_237 and opls_238 when they have the same 
bonded type and same LJ parameters. They're effectively identical so 
this is probably a very poor example when trying to learn how the force 
field works.


If you're trying to generate a topology for some new species, try the 
LigParGen server rather than going about it manually.


-Justin


Thank you,
Neena

From: Neena Susan Eappen
Sent: Wednesday, April 1, 2020 12:05 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Effect of atomic charge on bonding parameters

Hello gromacs users,

Following two atoms (opls_ 237 and 238) have different atomic charges, but same 
bond type and thereby same parameters in the ffbonded.itp file. Is the effect 
of charge on bonding ignored? Is that possible?

; name   bond_type masscharge   ptype  sigma  
epsilon
opls_237 N714.00670 -0.760   A  3.25000e-01  
7.11280e-01
opls_238 N714.00670 -0.500   A  3.25000e-01  
7.11280e-01

(Taken from ffnonbonded.itp file)

Thank you,
Neena


--
==

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

==

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Re: [gmx-users] Issue with PMF

[Justin Lemkul]

On 4/2/20 12:53 PM, Alex wrote:

Dear all,
By using the below setting I am getting a very nice umbrella histogram and
iact also shows a very good integrated Autocorrelation time. However, the
PMF profile is unexpected. Below I have also provided a gmx wham command I
am using, part of the pullx.xvg of one of the windows and also
corresponding part in log file.
Would you please help me find out what the problem might be?


What is the problem?


One more question: does it make sense to manually shift the plateau of the
PMF plot to zero (when we plot it), instead of using using the -zprof0 flag?


There is no difference. The -zprof0 just adds a constant so the PMF is 
zero at the specified point on the reaction coordinate.



%
pull = yes
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = Mol_A
pull-group2-name = Thin_film

pull-coord1-groups   = 1 2
pull-coord1-type = umbrella
pull-coord1-dim  = N N Y
pull-coord1-start= no   ;--> manually we define the distance for
all windows
pull-coord1-rate = 0.0  ;--> We don't want the roups to move
pull-coord1-geometry = distance
pull-coord1-k= 1   ;;kJ/(mol nm^2)
pull-print-components= Yes
pull-nstxout = 2000
pull-nstfout = 2000
pull-print-com1  = yes
pull-coord1-init = 1.65
%
#Part of the one of the pullx.xvg file
@ legend length 2
@ s0 legend "1"
@ s1 legend "1 dZ"
@ s2 legend "1 g 1 Z"
@ s3 legend "1 g 2 Z"
0.  0.0155171   0.0155171   9.89805 9.91357
2.  0.0103956   0.0103956   9.90227 9.91266
4.  0.0146962   0.0146962   9.89733 9.91202
6.  0.00656533  0.00656533  9.90404 9.91061
8.  0.00228074  0.00228074  9.90945 9.91174
10. 0.00967605  0.00967605  9.90514 9.91482

%
gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist
-bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o
profile.xvg -b 3000 -unit kCal -v

  %
#Similar massage as below I have for all windows (tpr files).
Reading file prd.1.tpr, VERSION 2018.7 (single precision)

File prd.1.tpr, 1 coordinates, with these options:
 Geometry distance   k = 1 position = 0 dimensions
[N N Y] (1 dimensions). Used: Yes
 Pull group coordinates of 2 groups expected in pullx files.
 Reference value of the coordinate not expected in pullx files.

Reading pull force file prd_pullf.1.xvg, expecting 2 columns:
 Columns for pull coordinate 1
 reaction coordinate: 1
 center-of-mass of groups:0
 reference position column:   No
 Found 2501 times in prd_pullf.1.xvg
%--

Thank you,
Alex


--
==

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

==

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[gmx-users] Simulation of Protein-Protein Complex

[Surya Sanjay]

Hello all,
I am a beginner Gromacs user and I have been using the Gromacs tutorials on
mdtutorials.com/gmx/. I would like to simulate the binding of the
infectious and normally-folded prion variants, and I want to know if the
protein-protein complex procedure is different from that of protein-ligand
systems.
Thanks,
Surya
-- 
Gromacs Users mailing list

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Re: [gmx-users] (no subject)

[Daniel Burns]

Start here: http://www.mdtutorials.com/gmx/.  An introduction to linux book
might be helpful as well if you are not already familiar with it.

Good luck!

On Thu, Apr 2, 2020 at 2:05 PM Feriel Terbeche  wrote:

> Hello!
> My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im
> preparing my  last study's project (master degrees), wich is about
> hemophila A and factor VIII where I have to use gromacs, but, I don't know
> how to use it even I have it on my computer and unfortunately no one here
> can help me because no one used it before.  I really need help but I don't
> know from where I'll get it, so can I have some advices. Thank you
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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[gmx-users] (no subject)

[Feriel Terbeche]

Hello!
My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im preparing my 
 last study's project (master degrees), wich is about hemophila A and factor 
VIII where I have to use gromacs, but, I don't know how to use it even I have 
it on my computer and unfortunately no one here can help me because no one used 
it before.  I really need help but I don't know from where I'll get it, so can 
I have some advices. Thank you

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Re: [gmx-users] Effect of atomic charge on bonding parameters

[Neena Susan Eappen]

Hi Justin,

What is the criteria for opls bond types?

Thank you,
Neena

From: Neena Susan Eappen
Sent: Wednesday, April 1, 2020 12:05 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] Effect of atomic charge on bonding parameters

Hello gromacs users,

Following two atoms (opls_ 237 and 238) have different atomic charges, but same 
bond type and thereby same parameters in the ffbonded.itp file. Is the effect 
of charge on bonding ignored? Is that possible?

; name   bond_type masscharge   ptype  sigma  
epsilon
opls_237 N714.00670 -0.760   A  3.25000e-01  
7.11280e-01
opls_238 N714.00670 -0.500   A  3.25000e-01  
7.11280e-01

(Taken from ffnonbonded.itp file)

Thank you,
Neena
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[gmx-users] Issue with PMF

[Alex]

Dear all,
By using the below setting I am getting a very nice umbrella histogram and
iact also shows a very good integrated Autocorrelation time. However, the
PMF profile is unexpected. Below I have also provided a gmx wham command I
am using, part of the pullx.xvg of one of the windows and also
corresponding part in log file.
Would you please help me find out what the problem might be?

One more question: does it make sense to manually shift the plateau of the
PMF plot to zero (when we plot it), instead of using using the -zprof0 flag?

%
pull = yes
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = Mol_A
pull-group2-name = Thin_film

pull-coord1-groups   = 1 2
pull-coord1-type = umbrella
pull-coord1-dim  = N N Y
pull-coord1-start= no   ;--> manually we define the distance for
all windows
pull-coord1-rate = 0.0  ;--> We don't want the roups to move
pull-coord1-geometry = distance
pull-coord1-k= 1   ;;kJ/(mol nm^2)
pull-print-components= Yes
pull-nstxout = 2000
pull-nstfout = 2000
pull-print-com1  = yes
pull-coord1-init = 1.65
%
#Part of the one of the pullx.xvg file
@ legend length 2
@ s0 legend "1"
@ s1 legend "1 dZ"
@ s2 legend "1 g 1 Z"
@ s3 legend "1 g 2 Z"
0.  0.0155171   0.0155171   9.89805 9.91357
2.  0.0103956   0.0103956   9.90227 9.91266
4.  0.0146962   0.0146962   9.89733 9.91202
6.  0.00656533  0.00656533  9.90404 9.91061
8.  0.00228074  0.00228074  9.90945 9.91174
10. 0.00967605  0.00967605  9.90514 9.91482

%
gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist
-bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o
profile.xvg -b 3000 -unit kCal -v

 %
#Similar massage as below I have for all windows (tpr files).
Reading file prd.1.tpr, VERSION 2018.7 (single precision)

File prd.1.tpr, 1 coordinates, with these options:
Geometry distance   k = 1 position = 0 dimensions
[N N Y] (1 dimensions). Used: Yes
Pull group coordinates of 2 groups expected in pullx files.
Reference value of the coordinate not expected in pullx files.

Reading pull force file prd_pullf.1.xvg, expecting 2 columns:
Columns for pull coordinate 1
reaction coordinate: 1
center-of-mass of groups:0
reference position column:   No
Found 2501 times in prd_pullf.1.xvg
%--

Thank you,
Alex
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Re: [gmx-users] Optimising mdrun

[Robert Cordina]

Hi Kevin,

I'm working with the HPC cluster administrator and we manged to get much better 
performance with 

mpirun -np 1  gmx_mpi mdrun -ntomp 16

which got it up to 500 ns/day.  Will now be trying with 

-nb gpu -pme gpu 

and also with 

-pin on

to see if that helps even further.

Thanks,

Robert


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Kevin Boyd
Sent: 02 April 2020 04:59
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Optimising mdrun

Hi -

> This setting is using 16 MPI process and using 2 OpenMP thrads per MPI
proces

With ntomp 1 you should only be getting one OpenMP thread, not sure why that's 
not working. Can you post a link to a log file?

For a small system like that and a powerful GPU, you're likely going to have 
some inefficiency. Can you run replicates? You'd want to do something like this 
(though I'm not sure about the mpirun part, I usually do non-MPI gromacs):
mpirun -np 8 gmx_mpi mdrun -nt 8 -ntomp 8 -ntmpi  1 -pin on -pinoffset 0 -nb 
gpu -pme gpu mpirun -np 8 gmx_mpi mdrun -nt 8 -ntomp 8 -ntmpi  1 -pin on 
-pinoffset 8 -nb gpu -pme gpu

where the first job runs on cores 0-7 and the second job runs on cores 8-15, 
sharing the same GPU.

> The log states "Will do PME sum in reciprocal space for electrostatic
interactions"

Reciprocal space does not indicate whether PME was run on the CPU or GPU, it's 
just reporting math.

On Wed, Apr 1, 2020 at 1:03 AM Robert Cordina 
wrote:

> *Message sent from a system outside of UConn.*
>
>
> Hi,
>
> I'm trying to use GROMACS 2019.3 on two different machines, simulating 
> the same system.  The system is made up of 100 identical molecules, 
> consisting of 61 united atoms each, in a non-aqueous system.  I am 
> however getting vastly different performance on the two machines, and 
> I don't really understand why.  The two machines' specs are as follows:
>
> Machine 1 (stand-alone machine)
>
>
>   *   40-core CPU (Intel Xeon Gold 6148 2.4GHz, 3.7GHz, 20C, 10.4GT/s
> 2UPI, 27M Cache, HT (150W) DDR4-2666) - so 20 hyper-threaded cores to 
> give a total of 40, although in my case only 20 cores are being used 
> given the size of the system (see below)
>   *   1 GPU (Nvidia Quadro RTX5000, 16GB, 4DP, VirtualLink (XX20T))
>   *   Memory (512GB (8x64GB) 2666MHz DDR4 LRDIMM ECC) - although in
> reality only about 10 GB are used during my simulation
>   *   CUDA 10.10
>
> When I simulate my system, I've found that the optimal mdrun settings 
> are extremely simple
>
> mdrun -pin on
>
> This setting uses 1 MPI thread and 20 OpenMP threads, while the PP and 
> PME tasks are carried out automatically on the GPU.  With this I'm 
> getting about 800 ns/day.
>
>
> Machine 2 (part of a HPC cluster - of which I can only use 1 node at a 
> time - the below details are for a GPU node)
>
>
>   *   16 core CPU (Intel Xeon E5-2600, 2.2 GHz)
>   *   1 GPU (NVIDIA Tesla V100-PCIE-32GB)
>   *   Memory (64GB RAM)
>   *   CUDA 10.0
>
> I've tried reading the GROMACS documentation, repeatedly, but I really 
> can't understand much about how to go about choosing the right mdrun 
> settings for this machine.  I've tried several, and the best 
> performance I could get is with
>
> mpirun -np 16 gmx_mpi mdrun -ntomp 1
>
> Even then, I get a performance of about 45-50 ns/day, which is way 
> lower than the 800 ns/day I get with the stand-alone machine.  This 
> setting is using 16 MPI process and using 2 OpenMP thrads per MPI 
> process.  Also, only PP tasks are being carried out on the GPU.  The 
> log states "Will do PME sum in reciprocal space for electrostatic 
> interactions".  Also I get a Warning "On rank 0: oversubscribing the 
> available 16 logical CPU cores per node with 32 threads. This will 
> cause considerable performance loss", with Note "Oversubscribing the CPU, 
> will not pin threads".
>
>
> Does anyone have any guidance as to what I should try to get good 
> performance on the GPU node of the cluster please?  Any help will be 
> really appreciated.
>
> Thanks,
>
> Robert
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Re: [gmx-users] Onsager coefficient

[Sina Omrani]

Yes, they are very similar. r with two subscripts means the position of the
center of mass of the lth molecules of component i.

On Thu, 2 Apr 2020 at 13:55, David van der Spoel 
wrote:

> Den 2020-04-01 kl. 23:05, skrev Sina Omrani:
> > Dear Mr Spoel,
> > I have found out that I couldn't attach an image and I am sorry about
> that.
> > here is a link to the picture.
> >
> https://cdn1.imggmi.com/uploads/2020/4/1/1599cd9ac1102e329ff91759d3314725-full.png
>
> Not sure what is meant by r or v with two subscripts. Otherwise it looks
> a bit like Einsteins formula.
> >
> > On Tue, 31 Mar 2020 at 09:59, David van der Spoel 
> > wrote:
> >
> >> Den 2020-03-30 kl. 22:51, skrev Sina Omrani:
> >>> Hi dear Gromacs users,
> >>> Sorry to ask again but I really appreciate the help on this subject.
> >>>
> >>> thanks.
> >>>
> >>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani 
> >> wrote:
> >>>
> Hi, I would like to calculate the Onsager coefficient but after
> >> months of
>  study, I'm not able to do that. if anybody can help me I would really
>  appreciate it. I don't know if there is a specific command to do it or
> >> it
>  needs a series of analyses.
> 
>  P.S. I attached a picture of a formula that calculates the Onsager
>  coefficient from MD.
> 
>  sincerely,
>  Sina Omrani
> 
> >> I see no attachment and google does not help either. What is an Onsager
> >> coefficient?
> >>
> >> --
> >> 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!
> >>
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> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
>
> --
> David van der Spoel, Ph.D.,
> Professor of Biology
> Uppsala University.
> http://virtualchemistry.org
> --
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Re: [gmx-users] Free energy of protonation

[Sotirios Dionysios I. Papadatos]

My advise is a bit general.
Try the same process with a different molecule (one that can support this 
change), try the same molecule with an AA ff, since it is already done (as you 
mentioned) do you get similar results?
These tests might help you find out if there is something wrong with your mdp.
I haven't changed a bead in free energy so I am not 100% sure, but the few mdp 
options that you provided seem reasonable.

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

Sent: Wednesday, April 1, 2020 7:52 PM
To: Discussion list for GROMACS users 
Subject: [gmx-users] Free energy of protonation

Dear list,

I am trying to calculate the free energy for protonating a single monomer
of oleic acid with the martini forcefield. This in preparation for other
work, and I wanted to start by reproducing what is already done.

To do this, I have defined the following in my topology to describe the
change in protonation state going from A (protonated) to state B (charged).
The martini bead type needs to change as well in this process.

[ atoms ]

; idtypeA   resnr   residu  atomcgnrchargeA   massA typeB
chargeB massB

  1 P4  1   OAN COO 1   0   Qa  -1

I also have this very simple mdp file for doing the transformation

free_energy  = yes

init_lambda-state= 1

fep-lambdas  = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0


And I am using fep-lambdas to describe the entire process. With this, I can
run through grompp and mdrun with different values of init-lambda-state,
but the output I get in each case is the same for each different simulation.


I check this by


gmx analyze -f md.xvg -ee


And I always get the same value for the average. Is there something I am
missing or not specifying properly?


Thanks

/PK
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Re: [gmx-users] converting gromacs topology file to namd topology file

[John Whittaker]

Hi,

A quick google search led me to this:

https://www.ks.uiuc.edu/Research/namd/2.10/ug/node14.html

I've never used NAMD before but apparently you can use gromacs topologies
directly in NAMD. Note the caveats at the bottom of the page.

Would this work or does it not accomplish what you are looking for?

- John

> Hello Dear Gromacs users,
>
> I hope this email finds you well. I am sending this email to ask is there
> any way I can convert gromacs topology file (.itp) to namd (top) file?  I
> appreciate any help,
>
> Best regards,
> Hadi
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Re: [gmx-users] Onsager coefficient

[David van der Spoel]

Den 2020-04-01 kl. 23:05, skrev Sina Omrani:

Dear Mr Spoel,
I have found out that I couldn't attach an image and I am sorry about that.
here is a link to the picture.
https://cdn1.imggmi.com/uploads/2020/4/1/1599cd9ac1102e329ff91759d3314725-full.png


Not sure what is meant by r or v with two subscripts. Otherwise it looks 
a bit like Einsteins formula.


On Tue, 31 Mar 2020 at 09:59, David van der Spoel 
wrote:


Den 2020-03-30 kl. 22:51, skrev Sina Omrani:

Hi dear Gromacs users,
Sorry to ask again but I really appreciate the help on this subject.

thanks.

On Fri, 27 Mar 2020 at 02:23, Sina Omrani 

wrote:



   Hi, I would like to calculate the Onsager coefficient but after

months of

study, I'm not able to do that. if anybody can help me I would really
appreciate it. I don't know if there is a specific command to do it or

it

needs a series of analyses.

P.S. I attached a picture of a formula that calculates the Onsager
coefficient from MD.

sincerely,
Sina Omrani


I see no attachment and google does not help either. What is an Onsager
coefficient?

--
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
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--
David van der Spoel, Ph.D.,
Professor of Biology
Uppsala University.
http://virtualchemistry.org
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[gmx-users] Missing gromacs.lib when building Grmoacs 2020.1 in vs 2019

[孙傲然]

Greetings!




I try to build the newest release (2020.1) using cmake 3.16.4 and vs 2019 in 
windows 10 Enterprise. I finish the configuring and generating using cmake 
following the instruction, but when I try to build the sln file with vs 2019, I 
get about fifty errors "LNK1104 cannot open 
file“..\..\..\..\lib\Debug\gromacs.lib".I have no idea where exactly the 
gromacs.lib is supposed to be since vs only tells me ..\ instead of detailed 
path, and I cannot find such a file named gromacs.lib anywhere on my computer 
or via the internet. So what exactly is the problem and how can I solve it?




Best wishes




Aoran Sun
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