Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

[Shlomit Afgin]

How can I make GROMACS use devtoolset-6?





[shlomit@cn gromacs-2019.5]$ type gcc

gcc is /bin/gcc

[shlomit@cn gromacs-2019.5]$ scl enable devtoolset-6 bash

[shlomit@cn gromacs-2019.5]$ type gcc

gcc is /bin/gcc



Shlomit





On 15/01/2020, 12:07, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on 
behalf of Tru Huynh"  wrote:



On Wed, Jan 15, 2020 at 08:50:46AM +, Shlomit Afgin wrote:

>

> Hi,

> I tried to install GROMACS 2019.5 on CentOS7,

> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

>

> I have already installed devtoolset-6 and still get this error:

installed, but not using it?



[tru@elitebook840g3 ~]$ type gcc

gcc is /usr/bin/gcc

[tru@elitebook840g3 ~]$ scl enable devtoolset-6 bash

[tru@elitebook840g3 ~]$ type gcc

gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc



Tru



--

Tru Huynh (PhD) | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37

https://research.pasteur.fr/en/team/structural-bioinformatics/

Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

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Re: [gmx-users] Lambda Weights from Expanded Ensemble Code

[Michael Shirts]

The simulated tempering options haven't been as well tested as the
hamiltonian expanded ensemble version.  The weights SHOULD be showing up in
the column that says -nan, but clearly they aren't.  If you file a redmine
issue, I may be able to take a look, but it might take a while to address.

On Wed, Jan 15, 2020 at 8:52 PM Daniel Kozuch  wrote:

> Hello,
>
> I am interested in using simulated tempering in GROMACS (2019.5) under the
> expanded ensemble options. Is there a way to monitor the ensemble weights
> as the simulation progresses? I think in theory they are supposed to be
> printed out in the log file, but it is only printing 0, -nan, and inf:
>
> MC-lambda information
>   N  Temp.(K)Count   G(in kT)  dG(in kT)
> ...
>  36  359.105  118   -nan   -nan <<
>  37  366.880   96   -nan   -nan
>  38  374.852  107   -nan   -nan
>  39  383.026  129   -nan   -nan
>  40  391.407  166   -nan   -nan
>  41  400.000  199   -nan0.0
>
> Here are my relevant mdp settings:
> simulated-tempering = yes
> nstexpanded = 500
> simulated-tempering-scaling = exponential
> lmc-stats   = metropolis-transition
> lmc-move= metropolis
>
> Any suggestions?
>
> Best,
> Dan Kozuch
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[gmx-users] Lambda Weights from Expanded Ensemble Code

[Daniel Kozuch]

Hello,

I am interested in using simulated tempering in GROMACS (2019.5) under the
expanded ensemble options. Is there a way to monitor the ensemble weights
as the simulation progresses? I think in theory they are supposed to be
printed out in the log file, but it is only printing 0, -nan, and inf:

MC-lambda information
  N  Temp.(K)Count   G(in kT)  dG(in kT)
...
 36  359.105  118   -nan   -nan <<
 37  366.880   96   -nan   -nan
 38  374.852  107   -nan   -nan
 39  383.026  129   -nan   -nan
 40  391.407  166   -nan   -nan
 41  400.000  199   -nan0.0

Here are my relevant mdp settings:
simulated-tempering = yes
nstexpanded = 500
simulated-tempering-scaling = exponential
lmc-stats   = metropolis-transition
lmc-move= metropolis

Any suggestions?

Best,
Dan Kozuch
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Re: [gmx-users] Hydrogen bonding criteria in Gromacs

[Myunggi Yi]

Dear Dr. Justin Lemkul,

Can you explain why the D-H-A is 150?

If H-D-A is 30, then D-H-A should be smaller than 150 degrees.
Since the sum of interior angles of a triangle should be 180 degrees...
See the following triangle.

 H

D   A


Am I missing something?


On Thu, Jan 16, 2020 at 2:30 AM Justin Lemkul  wrote:

>
>
> On 1/15/20 11:57 AM, Pandya, Akash wrote:
> > Hi all,
> >
> > I  wanted to ask a couple of questions about the hydrogen bonding
> calculation in Gromacs.
> >
> >
> >1.   Why is the default angle cutoff 30 degrees? The reason I ask
> this is because I’ve seen in other packages with higher angle cutoffs.
>
> It depends on how the software defines the angle. The GROMACS convention
> is the angle corresponds to H-D-A rather than D-H-A like some other
> programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional"
> 150-degree D-H-A cutoff.
>
> >2.  What’s the best way to define cutoffs for my system? I know this
> is ambiguous, but is there a procedure I can use to decide?
>
> The default criteria are widely used and usually don't require any tuning.
>
> -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] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[Justin Lemkul]

On 1/15/20 6:58 PM, ZHANG Cheng wrote:

Hi Justin, what kind of information should I look at in the log files? They are too big 
to paste here. Would it be possible if you can see them 
athttps://github.com/lanselibai/gromacs-20200115;?


It doesn't look like either of those runs actually finished, and you 
have very frequent restarts from checkpoint files, so I don't see 
performance statistics. Relevant information will be printed in an 
obvious summary at the end of the output.


Try running a very short simulation with each version that runs to 
completion and look at the end of the .log file.


Also note that at least in version 5.1, you are not compiling GROMACS 
for maximum performance.


-Justin



Thank you!


--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Thu, Jan 16, 2020 03:38 AM
To:"gromacs.org_gmx-users"http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce 
-inter -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL 
-nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append


--
==

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] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[ZHANG Cheng]

Hi Justin, what kind of information should I look at in the log files? They are 
too big to paste here. Would it be possible if you can see them 
athttps://github.com/lanselibai/gromacs-20200115;?


Thank you!


--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Thu, Jan 16, 2020 03:38 AM
To:"gromacs.org_gmx-users"http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce 
-inter -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL 
-nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append
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Re: [gmx-users] cmaptypes format

[Justin Lemkul]

On 1/15/20 2:38 PM, Marcelo Depólo wrote:

Hi everyone!

I was wondering about the cmaptypes format within cmap.itp file.

[ cmaptypes ]
C N CT C N 1 24 24\

I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid
size. What does this '1' mean?


Probably a useless/dummy function type.

-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] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[Justin Lemkul]

On 1/15/20 2:38 PM, ZHANG Cheng wrote:

I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the 
preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" 
and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.


Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", 
while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can 
do in the "VERSION 2019.3" so as to accelerate the MD?


I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce 
-inter -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL 
-nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append


Performance metrics are reported in the .log file from the run. Check 
there to see what is happening.


-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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[gmx-users] cmaptypes format

[Marcelo Depólo]

Hi everyone!

I was wondering about the cmaptypes format within cmap.itp file.

[ cmaptypes ]
C N CT C N 1 24 24\

I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid
size. What does this '1' mean?

Thanks in advance!
--
Marcelo Depólo Polêto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464
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[gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[ZHANG Cheng]

I have a nearly identical run using the "VERSION 2019.3" compared to my 
previous "VERSION 5.1.1". Everything during the preparation is the same except 
"-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" 
and "-r npt.gro" are added in the grompp commands for NVT, NPT and production 
run, respectively.


Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in 
the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can 
I ask is this normal? Is there some configuration I can do in the "VERSION 
2019.3" so as to accelerate the MD?


I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce 
-inter -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL 
-nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append
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[gmx-users] gmx genconf

[Alex]

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

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

Regards,
Alex
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Re: [gmx-users] Hydrogen bonding criteria in Gromacs

[Justin Lemkul]

On 1/15/20 11:57 AM, Pandya, Akash wrote:

Hi all,

I  wanted to ask a couple of questions about the hydrogen bonding calculation 
in Gromacs.


   1.   Why is the default angle cutoff 30 degrees? The reason I ask this is 
because I’ve seen in other packages with higher angle cutoffs.


It depends on how the software defines the angle. The GROMACS convention 
is the angle corresponds to H-D-A rather than D-H-A like some other 
programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional" 
150-degree D-H-A cutoff.



   2.  What’s the best way to define cutoffs for my system? I know this is 
ambiguous, but is there a procedure I can use to decide?


The default criteria are widely used and usually don't require any tuning.

-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] Umbrella sampling with restraint on the center of mass of ligand

[Justin Lemkul]

On 1/15/20 6:32 AM, gmx user1 wrote:

Dear GMX users

I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols used by Subramanian et al (
https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00624 ;
https://www.sciencedirect.com/science/article/pii/S0005273615004319?via%3Dihub
)

Yet, I am not certain of which .mdp settings I should use to accomplish my
goal, the documentation is not clear and most infomation I find
refers to the application of harmonic potentials when the reaction
coordinate is a distance between two groups.


If you're not clear what the published method is or how to reproduce it, 
I suggest you contact the corresponding author and ask for sample input 
files.



Here are my .mdp settings:

pull= yes
pull_print_com  = yes
pull_print_ref_value= yes
pull_nstxout= 500
pull_nstfout= 0
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 1
pull_coord1_geometry= direction-periodic
pull_coord1_vec = 0 0 1
pull-coord1-origin  = 0 0 0
pull_group1_name= LIG
pull_coord1_groups  = 0 1
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_start   = yes   ; define initial COM distance > 0
pull_coord1_rate= 0.0   ; restrain in place
pull_coord1_k   = 500  ; kJ mol^-1 nm^-2

Essentially, I created a vector between the center-of-mass of the ligand
and an absolute reference (0,0,0) and I had to use pull_coord1_geometry =
direction-periodic ( instead of direction) ,because the simulation crashed.
This also forces me to perform an NVE simulation.

Is this the right way of applying a an harmonic restraint on the
center-of-mass of a ligand for umbrella sampling? Are these settings
correct?


If you're looking at ligand translocation across a membrane, you should 
not be using (0,0,0) as a reference. The conventional reaction 
coordinate is the normal to the bilayer, so the reaction coordinate 
connects the COM of the bilayer with the COM of the ligand along the z-axis.


-Justin

--
==

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

Virginia Tech Department of Biochemistry
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Re: [gmx-users] Query regarding do_dssp program

[Justin Lemkul]

On 1/15/20 12:27 AM, Sundari wrote:

I tried all the options.. I load gro file instead of xtc. At zero frame I
gave representations new cartoon + secondary structure.. then I calculate
sec str details by going on vmd timeline.
I don't know what I am missing.. I am doing the same which I used all the
time.
Because these are two totally different secondary structures that's why I
was worrying.. because these are major structures one reports so Very
important to resolve this issue.


Without access to the coordinate file, there's nothing I can tell you. 
If you want to send me that snapshot off-list, I can probably take a 
quick look and see if I can get to the bottom of it.


-Justin


On Wednesday, January 15, 2020, Justin Lemkul  wrote:



On 1/13/20 9:15 AM, Sundari wrote:


Yes, Sir,  I  made the gro file for a particular time by using "gmx
trjconv" command ( also checked with -pbc mol, whole, no_jump options )
but every time the 2ndary structure visualization in vmd is different from
dssp sequence of residues in gromacs. Fox example in my protein dssp shows
8 residues making beta-sheets but when I load that particular time frame
in
vmd for visualizing the structure,  these 8 residues showing 5-helix
structure.

Please suggest something.


I'm afraid I can't. Those are two completely different hydrogen bonding
patterns and I can't imagine how the algorithms would differ so
dramatically. I have seen VMD render coils for helices and sheets but never
a totally different secondary structure. Be sure you're telling VMD to
re-compute structures and re-color the secondary structure elements at
every snapshot for trajectory visualization, otherwise it will render
everything the same as the initial frame, which will obviously be wrong in
the case of large structural changes.

-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

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http://www.thelemkullab.com

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Lab: 303 Engel Hall

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Re: [gmx-users] Hydrogen bonding criteria in Gromacs

[Quyen V. Vu]

Hydrogen bonding is approximated by charge-dipole interaction, which is
very orientation-sensitive, the energy of this kind interactions
are proportional to the cosine of the angle.
https://en.wikibooks.org/wiki/Molecular_Simulation/Charge-Dipole_Interactions



On Wed, Jan 15, 2020 at 5:59 PM Pandya, Akash 
wrote:

> Hi all,
>
> I  wanted to ask a couple of questions about the hydrogen bonding
> calculation in Gromacs.
>
>
>   1.   Why is the default angle cutoff 30 degrees? The reason I ask this
> is because I’ve seen in other packages with higher angle cutoffs.
>   2.  What’s the best way to define cutoffs for my system? I know this is
> ambiguous, but is there a procedure I can use to decide?
>
> Any guidance will be much appreciated.
>
> Thank you,
>
> Akash
>
> Get Outlook for iOS
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[gmx-users] Hydrogen bonding criteria in Gromacs

[Pandya, Akash]

Hi all,

I  wanted to ask a couple of questions about the hydrogen bonding calculation 
in Gromacs.


  1.   Why is the default angle cutoff 30 degrees? The reason I ask this is 
because I’ve seen in other packages with higher angle cutoffs.
  2.  What’s the best way to define cutoffs for my system? I know this is 
ambiguous, but is there a procedure I can use to decide?

Any guidance will be much appreciated.

Thank you,

Akash

Get Outlook for iOS
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[gmx-users] Umbrella sampling with restraint on the center of mass of ligand

[gmx user1]

Dear GMX users

I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols used by Subramanian et al (
https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00624 ;
https://www.sciencedirect.com/science/article/pii/S0005273615004319?via%3Dihub
)

Yet, I am not certain of which .mdp settings I should use to accomplish my
goal, the documentation is not clear and most infomation I find
refers to the application of harmonic potentials when the reaction
coordinate is a distance between two groups.

Here are my .mdp settings:

pull= yes
pull_print_com  = yes
pull_print_ref_value= yes
pull_nstxout= 500
pull_nstfout= 0
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 1
pull_coord1_geometry= direction-periodic
pull_coord1_vec = 0 0 1
pull-coord1-origin  = 0 0 0
pull_group1_name= LIG
pull_coord1_groups  = 0 1
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_start   = yes   ; define initial COM distance > 0
pull_coord1_rate= 0.0   ; restrain in place
pull_coord1_k   = 500  ; kJ mol^-1 nm^-2

Essentially, I created a vector between the center-of-mass of the ligand
and an absolute reference (0,0,0) and I had to use pull_coord1_geometry =
direction-periodic ( instead of direction) ,because the simulation crashed.
This also forces me to perform an NVE simulation.

Is this the right way of applying a an harmonic restraint on the
center-of-mass of a ligand for umbrella sampling? Are these settings
correct?

Any help is appreaciated.

Thanks in advance
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[gmx-users] Fwd: A list of missing interactions

[Sadaf Rani]

Dear Gromacs users
I am facing this error during free energy calculation of protein-ligand for
which I have applied restrained to some atoms of protein residue and
ligand.
A list of missing interactions:
  Restraint Pot. of  1 missing  1

Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
  Restraint Pot. atoms 3437 7908   global  3437  7908

---
Program: gmx mdrun, version 2018.1
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:0 (out of 2)

Fatal error:
1 of the 64584 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (4.47682
nm)
or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck

Could anybody please suggest how should I fix this error? I would be really
thankful.

Regards

Sadaf
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[gmx-users] Regarding high RMSD

[Ashma Khan]

Dear all,
I have calculated the c-alpha RMSD of dimer having 7 residues peptide each
by using command gmx rms. But the calculated RMSD 14 Angstorm is very high,
although I have applied all pbc conditions. Anybody can suggest me why so
much high RMSD is coming or is it possible.

-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh
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Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

[Mark Abraham]

On Wed, 15 Jan 2020 at 11:07, Tru Huynh  wrote:

>
> gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc
>

Good, so is Cmake using it? (e.g. remove the build dir and run cmake again
to see what it first reports, or inspect $builddir/CMakeCache.txt for the
compiler setting)

Mark
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Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

[Tru Huynh]

On Wed, Jan 15, 2020 at 08:50:46AM +, Shlomit Afgin wrote:
> 
> Hi,
> I tried to install GROMACS 2019.5 on CentOS7,
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> 
> I have already installed devtoolset-6 and still get this error:
installed, but not using it?

[tru@elitebook840g3 ~]$ type gcc
gcc is /usr/bin/gcc
[tru@elitebook840g3 ~]$ scl enable devtoolset-6 bash
[tru@elitebook840g3 ~]$ type gcc
gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc

Tru

-- 
Tru Huynh (PhD) | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  
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Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

[Shlomit Afgin]

I ran:

cat /proc/cpuinfo | grep -i avx512



and got:

avx512f avx512dq avx512cd avx512bw avx512vl



So I thought I can use it. Am I wrong?



Shlomit



On 15/01/2020, 11:14, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on 
behalf of Szilárd Páll"  wrote:



Hi,



What hardware are you targeting? Unless you need AVX512 support, you could

just manually specify the appropriate setting in GMX_SIMD, e.g.

-DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 is not

supported.



Cheers,

--

Szilárd





On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin 

wrote:



>

> Hi,

> I tried to install GROMACS 2019.5 on CentOS7,

> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

>

> I have already installed devtoolset-6 and still get this error:

>

> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS

> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed

> -- Could not find any flag to build test source (this could be due to

> either the compiler or binutils)

> -- Could not identify number of AVX-512 units - detection program missing

> compilation prerequisites

> -- Could not run code to detect number of AVX-512 FMA units - assuming 2.

> -- Detected best SIMD instructions for this CPU - AVX_512

> CMake Error at cmake/gmxManageSimd.cmake:51 (message):

>   Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a

>   lower level of SIMD (slower).

> Call Stack (most recent call first):

>   cmake/gmxManageSimd.cmake:186

> (gmx_give_fatal_error_when_simd_support_not_found)

>   CMakeLists.txt:719 (gmx_manage_simd)

>

>

> Thanks,

> Shlomit

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Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

[Schulz, Roland]

Are you actually using the GCC from the devtoolset or the default one? Cmake 
tells you at the very beginning which compiler it is using.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se  users-boun...@maillist.sys.kth.se> On Behalf Of Shlomit Afgin
> Sent: Wednesday, January 15, 2020 12:51 AM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag
> 
> 
> Hi,
> I tried to install GROMACS 2019.5 on CentOS7, cmake .. -
> DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> 
> I have already installed devtoolset-6 and still get this error:
> 
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
> -- Could not find any flag to build test source (this could be due to either 
> the
> compiler or binutils)
> -- Could not identify number of AVX-512 units - detection program missing
> compilation prerequisites
> -- Could not run code to detect number of AVX-512 FMA units - assuming 2.
> -- Detected best SIMD instructions for this CPU - AVX_512 CMake Error at
> cmake/gmxManageSimd.cmake:51 (message):
>   Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
>   lower level of SIMD (slower).
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:186
> (gmx_give_fatal_error_when_simd_support_not_found)
>   CMakeLists.txt:719 (gmx_manage_simd)
> 
> 
> Thanks,
> Shlomit
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Re: [gmx-users] Loading topology into vmd

[Miro Astore]

This is very helpful thank you. I think I can use this. I will also ask the
vmd mail list.

Best, Miro

Le mer. 15 janv. 2020 à 19:35, Alessandra Villa <
alessandra.villa.bio...@gmail.com> a écrit :

> Hi,
> One of the criteria that VMD uses to define bond is distance criteria. When
> you source your gro file, this criteria is applied.
> One way one, I have used is to not visualize  undesired bonds, is the
> following:
> delete the undesired bonds, save the vmd setting (*.vmd file),  load the
> setting before any of the following visualizations.
> That is not the most elegant way, but it works in my case.
> For more elegant ways, you could ask to VMD maillist.
> Best regards
> Alessandra
>
>
> On Tue, Jan 14, 2020 at 8:59 PM Miro Astore  wrote:
>
> > Hi kenny, thanks for getting back to me.
> >
> > I use something similar to what you've suggested to deal with periodic
> > boundary conditions. My current issue is that vmd will place a bond
> between
> > two atoms that are close together in the first frame of the visualization
> > even if those atoms aren't linked in the topology. The fake bonds are
> then
> > kept throughout the visualization . That is, when I load just a gro and a
> > trr.
> >
> > A psf file would fix this situation but my efforts to recreate a whole
> one
> > from my complex system using top2psf.pl hasn't borne much fruit.
> >
> > Just wondering what other people have tried.
> >
> > Best, Miro
> >
> > Le mer. 15 janv. 2020 à 02:20, Kenny Goossens <
> goossens_ke...@hotmail.com>
> > a écrit :
> >
> > > Hi,
> > >
> > > I'm not sure what you mean by "bonds that aren't in the simulation",
> but
> > > from my experience, converting your .gro file with gmx trjconv using
> the
> > > -pbc mol and -ur compact options usually gives a clean visualisation.
> If
> > > necessary, you can also use the -center option to center a specific
> > > structure/residue in the box. You can have the output written in the
> .gro
> > > file format, or convert to anything more convenient.
> > >
> > > With kind regards,
> > > __
> > > Kenneth Goossens, PhD student
> > > Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> > > University of Antwerp - Campus Drie Eiken
> > > Universiteitsplein 1
> > > B-2610 Wilrijk
> > > Belgium
> > >
> > >
> > >
> > > 
> > > Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens Miro Astore
> <
> > > miro.ast...@gmail.com>
> > > Verzonden: dinsdag 14 januari 2020 3:48
> > > Aan: gromacs.org_gmx-users@maillist.sys.kth.se <
> > > gromacs.org_gmx-users@maillist.sys.kth.se>
> > > Onderwerp: [gmx-users] Loading topology into vmd
> > >
> > > Hello all,
> > >
> > > I'm just wondering how people load topologies for systems simulated in
> > > gromacs into vmd. It is very annoying to have bonds that aren't in the
> > > simulation placed in the visualisation. I'm wondering if anyone has a
> > > solution that is easier than simply creating a psf file of the .gro
> > system
> > > as this can be time consuming for systems with strange geometries.
> > >
> > > Best, Miro
> > > --
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> > > posting!
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Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

[Szilárd Páll]

Hi,

What hardware are you targeting? Unless you need AVX512 support, you could
just manually specify the appropriate setting in GMX_SIMD, e.g.
-DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 is not
supported.

Cheers,
--
Szilárd


On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin 
wrote:

>
> Hi,
> I tried to install GROMACS 2019.5 on CentOS7,
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
> I have already installed devtoolset-6 and still get this error:
>
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
> -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
> -- Could not find any flag to build test source (this could be due to
> either the compiler or binutils)
> -- Could not identify number of AVX-512 units - detection program missing
> compilation prerequisites
> -- Could not run code to detect number of AVX-512 FMA units - assuming 2.
> -- Detected best SIMD instructions for this CPU - AVX_512
> CMake Error at cmake/gmxManageSimd.cmake:51 (message):
>   Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
>   lower level of SIMD (slower).
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:186
> (gmx_give_fatal_error_when_simd_support_not_found)
>   CMakeLists.txt:719 (gmx_manage_simd)
>
>
> Thanks,
> Shlomit
> --
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[gmx-users] Error: Cannot find AVX 512F compiler flag

[Shlomit Afgin]

Hi,
I tried to install GROMACS 2019.5 on CentOS7,
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

I have already installed devtoolset-6 and still get this error:

-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to either 
the compiler or binutils)
-- Could not identify number of AVX-512 units - detection program missing 
compilation prerequisites
-- Could not run code to detect number of AVX-512 FMA units - assuming 2.
-- Detected best SIMD instructions for this CPU - AVX_512
CMake Error at cmake/gmxManageSimd.cmake:51 (message):
  Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
  lower level of SIMD (slower).
Call Stack (most recent call first):
  cmake/gmxManageSimd.cmake:186 
(gmx_give_fatal_error_when_simd_support_not_found)
  CMakeLists.txt:719 (gmx_manage_simd)


Thanks,
Shlomit
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Re: [gmx-users] Loading topology into vmd

[Alessandra Villa]

Hi,
One of the criteria that VMD uses to define bond is distance criteria. When
you source your gro file, this criteria is applied.
One way one, I have used is to not visualize  undesired bonds, is the
following:
delete the undesired bonds, save the vmd setting (*.vmd file),  load the
setting before any of the following visualizations.
That is not the most elegant way, but it works in my case.
For more elegant ways, you could ask to VMD maillist.
Best regards
Alessandra


On Tue, Jan 14, 2020 at 8:59 PM Miro Astore  wrote:

> Hi kenny, thanks for getting back to me.
>
> I use something similar to what you've suggested to deal with periodic
> boundary conditions. My current issue is that vmd will place a bond between
> two atoms that are close together in the first frame of the visualization
> even if those atoms aren't linked in the topology. The fake bonds are then
> kept throughout the visualization . That is, when I load just a gro and a
> trr.
>
> A psf file would fix this situation but my efforts to recreate a whole one
> from my complex system using top2psf.pl hasn't borne much fruit.
>
> Just wondering what other people have tried.
>
> Best, Miro
>
> Le mer. 15 janv. 2020 à 02:20, Kenny Goossens 
> a écrit :
>
> > Hi,
> >
> > I'm not sure what you mean by "bonds that aren't in the simulation", but
> > from my experience, converting your .gro file with gmx trjconv using the
> > -pbc mol and -ur compact options usually gives a clean visualisation. If
> > necessary, you can also use the -center option to center a specific
> > structure/residue in the box. You can have the output written in the .gro
> > file format, or convert to anything more convenient.
> >
> > With kind regards,
> > __
> > Kenneth Goossens, PhD student
> > Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> > University of Antwerp - Campus Drie Eiken
> > Universiteitsplein 1
> > B-2610 Wilrijk
> > Belgium
> >
> >
> >
> > 
> > Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens Miro Astore <
> > miro.ast...@gmail.com>
> > Verzonden: dinsdag 14 januari 2020 3:48
> > Aan: gromacs.org_gmx-users@maillist.sys.kth.se <
> > gromacs.org_gmx-users@maillist.sys.kth.se>
> > Onderwerp: [gmx-users] Loading topology into vmd
> >
> > Hello all,
> >
> > I'm just wondering how people load topologies for systems simulated in
> > gromacs into vmd. It is very annoying to have bonds that aren't in the
> > simulation placed in the visualisation. I'm wondering if anyone has a
> > solution that is easier than simply creating a psf file of the .gro
> system
> > as this can be time consuming for systems with strange geometries.
> >
> > Best, Miro
> > --
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> > posting!
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