[gmx-users] Mailing list for Postdoctoral opportunities in Simulations

[Peter Mawanga]

Hello everyone

Can someone please send me mailing list addresses where I could get updates
on Postdoctoral positions available in the field of simulations.

-- 
Cheers
Peter
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Re: [gmx-users] question on ffG43a1p force field

[Lei Qian]

Thank you Dr. Lemkul,
Could I ask one more question? Thank you!

When I did the step for adding ions and minimization and equilibration
steps, one warning always showed up.
So I had to add -maxwarn 2 after the command gmx grompp.
This warning is as follows:

WARNING 1 [file topol.top, line 48]:
  The GROMOS force fields have been parametrized with a physically
  incorrect multiple-time-stepping scheme for a twin-range cut-off. When
  used with a single-range cut-off (or a correct Trotter
  multiple-time-stepping scheme), physical properties, such as the density,
  might differ from the intended values. Check if molecules in your system
  are affected by such issues before proceeding. Further information may be
  available at https://redmine.gromacs.org/issues/2884.

It seems this warning is related to the GROMOS force field (for
phosphorylation) you sent to me last week.
Could I disregard this warning?
Thanks!

Lei









On Sun, Aug 18, 2019 at 10:54 AM Justin Lemkul  wrote:

>
>
> On 8/18/19 3:24 AM, Lei Qian wrote:
> > Could I ask one more question about your *gromos43a1p.ff* force filed ?
> > Thanks!
> > I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce
> >
> > It shows a fatal error:
> > "Fatal error:
> > The residues in the chain xxx--xxx do not have a consistent type. The
> first
> > residue has type 'Protein', while residue *SEP is of type 'Other'*.
> > Either there is a mistake in your chain, or it includes nonstandard
> residue
> > names that have not yet been added to the *residuetypes.dat file* in the
> > GROMACS library directory."
> >
> > Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add
> > "SEP   protein" to the list.
> > However, the fatal error still shows up after this change.
> > Could I ask how to solve this problem?
>
> You need to change the installed residuetypes.dat file, not the one in
> the source.
>
> -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] Topology for phosphorylated protein in gromacs using Amber Forcefield

[Seketoulie Keretsu]

Dear Expert,

I know this issue has been raised earlier  by others but I'm still having
trouble with generating topology files for a phosphorylated protein,
phosphorylated at Tyrosine 1034 residue. I am using gromacs2018 and
Amber99SB protein as FF. The residue in the PDB file is shown below.

ATOM   1294  N   PTR A1034  -2.670 -10.279 -15.822  1.00 16.60   N
ATOM   1295  CA  PTR A1034  -2.446  -9.183 -16.725  1.00 16.94   C
ATOM   1296  C   PTR A1034  -3.533  -8.144 -16.622  1.00 18.89   C
ATOM   1297  O   PTR A1034  -4.612  -8.406 -16.068  1.00 19.06   O
ATOM   1298  CB  PTR A1034  -2.291  -9.698 -18.159  1.00 18.90   C
ATOM   1299  CG  PTR A1034  -3.542 -10.337 -18.686  1.00 24.64   C
ATOM   1300  CD1 PTR A1034  -3.802 -11.695 -18.501  1.00 22.99   C
ATOM   1301  CD2 PTR A1034  -4.492  -9.556 -19.348  1.00 23.91   C
ATOM   1302  CE1 PTR A1034  -4.980 -12.268 -18.990  1.00 23.96   C
ATOM   1303  CE2 PTR A1034  -5.639 -10.107 -19.829  1.00 26.74   C
ATOM   1304  CZ  PTR A1034  -5.884 -11.455 -19.654  1.00 32.04   C
ATOM   1305  OH  PTR A1034  -6.953 -11.808 -20.159  1.00 41.31   O
ATOM   1306  P   PTR A1034  -7.810 -13.106 -19.896  1.00 46.59   P
ATOM   1307  O1P PTR A1034  -9.076 -12.851 -20.613  1.00 45.47   O
ATOM   1308  O2P PTR A1034  -8.107 -13.257 -18.394  1.00 55.84   O1-
ATOM   1309  O3P PTR A1034  -6.994 -14.285 -20.476  1.00 42.59   O

As advised in some previous letters, I copied residuetypes.dat and
added "PTR" to it.
I have also tried
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue

Some experts mentioned modern amber FF can handle phosphorylated
residues. But, I can't seem to find the right way to do it.

query 1: Please advise how to go about this. I have never worked on
Phosphorylated

residues and have no like minded people to discuss with. A brief step
wise instruction would really help me and others

doing this for the first time (this problem has been asked frequently
on Research gate and here too).

query 2: should atom be treated at ATOM or HETATM ?

Thanks.

Sincerely,

Keretsu
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Re: [gmx-users] Gromacs FEP tutorial

[Mark Abraham]

Hi,

To which tutorial are you referring?

Mark

On Mon., 19 Aug. 2019, 19:09 Alex Mathew,  wrote:

> Can anyone tell me which thermodynamics cycle was used in the tutorial? for
> FEP.
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[gmx-users] Gromacs FEP tutorial

[Alex Mathew]

Can anyone tell me which thermodynamics cycle was used in the tutorial? for
FEP.
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Re: [gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

[Justin Lemkul]

On 8/19/19 9:17 AM, sunyeping wrote:

Hi, Justin:

This is my circumstance: I have a crystal structure of a DNA-binding 
protein (I call it as "A"), but I cannot get the crystal structure of 
the A-DNA complex and I have to give a prediction of what the cystal 
structure of A-DNA complex might be like. So I docked a DNA structure 
to the crystal structure of A and used the resulting complex as the 
initial structure for MD simulation and got a trajectory. Now I want 
to exact the one frame from the trajectory which is most possibly 
close to the the cystal structure of the A-DNA complex from the 
trajectory.


Now I have a crystal structure of DNA in complex with a protein (I 
call it as "B") belonging to the same family as the protein I am 
studying. So I want to use this available crystal structure of B-DNA 
complex as a reference structure and find a frame which has the 
smallest rmsd against B-DNA complex. The problem is, A-DNA and B-DNA 
have different number of atoms, so gmx rmsd doesn't work. What could I 
do in such a circumstance?




Save a subset of atoms (trajectory and matching .tpr) that are common to 
both and compute the RMSD. That's the only way to do it.


-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] How to calculate interaction energy between two groups for every frame in a trajectory?

[sunyeping]

Hi, Justin:

This is my circumstance: I have a crystal structure of a DNA-binding protein (I 
call it as "A"), but I cannot get the crystal structure of the A-DNA complex 
and I have to give a prediction of what the cystal structure of A-DNA complex 
might be like. So I docked a DNA structure to the crystal structure of A and 
used the resulting complex as the initial structure for MD simulation and got a 
trajectory. Now I want to exact the one frame from the trajectory which is most 
possibly close to the the cystal structure of the A-DNA complex from the 
trajectory. 

Now I have a crystal structure of DNA in complex with a protein (I call it as 
"B") belonging to the same family as the protein I am studying. So I want to 
use this available crystal structure of B-DNA complex as a reference structure 
and find a frame which has the smallest rmsd against   B-DNA complex. The 
problem is, A-DNA and B-DNA have different number of atoms, so gmx rmsd doesn't 
work. What could I do in such a circumstance?

Best regards,
Yeping
--
From:Justin Lemkul 
Sent At:2019 Aug. 19 (Mon.) 20:54
To:gromacs 
Subject:Re: [gmx-users] How to calculate interaction energy between two groups 
for every frame in a trajectory?



On 8/19/19 7:44 AM, Sun Yeping wrote:
> Hello Justin,
>
> Thank you for your answer. I agree that the physical meaning of 
> interaction energy is questionable. Actually, the structure with the 
> lowest interaction energy between two groups in the trajectory is very 
> different from what I expect.
>
>  Then, how should I find a structure from a MD trajectory which is 
> most possibly close to the real structure?  I

Agreement with reality depends on the availability of data regarding the 
biomolecule(s) in solution.

> think maybe I can select a real crystal structure related to the 
> structure upon which the MD simulation was done, and use it as the 
> reference structure, and calculate rmsd of each frame in the 
> trajectory against the reference structure, and find the one with the 
> smallest rmsd. But how to calculate the rmsd? The simulated structure 
> has different atom number with the reference structure, so gmx rmsd 
> wouldn't work. Do you know which method can work in this case?

RMSD to a crystal structure does not tell you anything about how 
realistic your results are. Crystal environments are very different from 
solution so RMSD doesn't tell you anything conclusive. I don't 
understand why you don't have a matching reference structure - you had 
to start your simulation from some known coordinates, no?

-Justin

>
> Best wishes.
>
> Yeping Sun
>
> On Mon, Aug 19, 2019 at 6:59 PM Justin Lemkul  > wrote:
>
>
>
> On 8/18/19 11:28 PM, sunyeping wrote:
> > Hello Bratin Kumar Das，
> >
> > Your answer is correst but irrelevent to my question. By adding
> energygrps option in the mdp and rerun the trajectory and generate
> the edr file containing the interation energy information which
> can be extracted by enemat. However enemat only gives the range of
> the interaction energy. My question is how to  calculate
> interaction energy between two groups for every frame in the
> trajectory.
>
> That is precisely what Bratin is telling you to do, and his answer is
> exactly correct.
>
> You need to use gmx energy, not gmx enemat, to get the interaction
> energy values in every frame. Then find the lowest and extract the
> corresponding frame with trjconv. Whether or not this quantity has
> any
> physical meaning is, however, questionable for most force fields.
>
> -Justin
>
> > --
> > From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in
> >
> > Sent At:2019 Aug. 19 (Mon.) 11:11
> > To:gromacs  >; 孙业平  >
> > Subject:Re: [gmx-users] How to calculate interaction energy
> between two groups for every frame in a trajectory?
> >
> > You need to prepare one .mdp file where the energygrps = DNA
> Protein ( as example). Generate the .tpr file and rerun using
> mdrun module.
> > gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc
> > On Mon 19 Aug, 2019, 8:09 AM sunyeping,  > wrote:
> > Dear all,
> >
> >   I am doing protein-DNA complex simulations with gromacs and I
> have gotten a trajectory. Now I want to calculate interaction
> energy between the protein and the DNA in every frame of the
> trajectory so that I can pick out a frame in which the 
> interaction energy between them is the largest, but I don't know
> how. I have used "enemat" , but it only gives a range of the
> energy, not every frame. The output read:
> >
> >   Last energy frame read 5000 tim

Re: [gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

[Justin Lemkul]

On 8/19/19 7:44 AM, Sun Yeping wrote:

Hello Justin,

Thank you for your answer. I agree that the physical meaning of 
interaction energy is questionable. Actually, the structure with the 
lowest interaction energy between two groups in the trajectory is very 
different from what I expect.


 Then, how should I find a structure from a MD trajectory which is 
most possibly close to the real structure?  I


Agreement with reality depends on the availability of data regarding the 
biomolecule(s) in solution.


think maybe I can select a real crystal structure related to the 
structure upon which the MD simulation was done, and use it as the 
reference structure, and calculate rmsd of each frame in the 
trajectory against the reference structure, and find the one with the 
smallest rmsd. But how to calculate the rmsd? The simulated structure 
has different atom number with the reference structure, so gmx rmsd 
wouldn't work. Do you know which method can work in this case?


RMSD to a crystal structure does not tell you anything about how 
realistic your results are. Crystal environments are very different from 
solution so RMSD doesn't tell you anything conclusive. I don't 
understand why you don't have a matching reference structure - you had 
to start your simulation from some known coordinates, no?


-Justin



Best wishes.

Yeping Sun

On Mon, Aug 19, 2019 at 6:59 PM Justin Lemkul > wrote:




On 8/18/19 11:28 PM, sunyeping wrote:
> Hello Bratin Kumar Das，
>
> Your answer is correst but irrelevent to my question. By adding
energygrps option in the mdp and rerun the trajectory and generate
the edr file containing the interation energy information which
can be extracted by enemat. However enemat only gives the range of
the interaction energy. My question is how to  calculate
interaction energy between two groups for every frame in the
trajectory.

That is precisely what Bratin is telling you to do, and his answer is
exactly correct.

You need to use gmx energy, not gmx enemat, to get the interaction
energy values in every frame. Then find the lowest and extract the
corresponding frame with trjconv. Whether or not this quantity has
any
physical meaning is, however, questionable for most force fields.

-Justin

> --
> From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in
>
> Sent At:2019 Aug. 19 (Mon.) 11:11
> To:gromacs mailto:gmx-us...@gromacs.org>>; 孙业平 mailto:sunyep...@aliyun.com>>
> Subject:Re: [gmx-users] How to calculate interaction energy
between two groups for every frame in a trajectory?
>
> You need to prepare one .mdp file where the energygrps = DNA
Protein ( as example). Generate the .tpr file and rerun using
mdrun module.
> gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc
> On Mon 19 Aug, 2019, 8:09 AM sunyeping, mailto:sunyep...@aliyun.com>> wrote:
> Dear all,
>
>   I am doing protein-DNA complex simulations with gromacs and I
have gotten a trajectory. Now I want to calculate interaction
energy between the protein and the DNA in every frame of the
trajectory so that I can pick out a frame in which the 
interaction energy between them is the largest, but I don't know
how. I have used "enemat" , but it only gives a range of the
energy, not every frame. The output read:
>
>   Last energy frame read 5000 time 50.000
>   Will build energy half-matrix of 2 groups, 6 elements, over
5001 frames
>   Matrix of Coul-SR energy ranges from -18999.681641 to -1608.268188
>   Matrix of LJ-SR energy ranges from -2540.941650 to -675.151306
>   Matrix of total energy ranges from -21540.623047 to -2283.419434
>
>   So could you tell me how to calculate interaction energy
between two groups for every frame in a trajectory?
>
>   Best regards.
>   --
>   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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.

-- 
==


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

Re: [gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

[Sun Yeping]

Hello Justin,

Thank you for your answer. I agree that the physical meaning of interaction
energy is questionable. Actually, the structure with the lowest interaction
energy between two groups in the trajectory is very different from what I
expect.

 Then, how should I find a structure from a MD trajectory which is most
possibly close to the real structure?  I think maybe I can select a real
crystal structure related to the structure upon which the MD simulation was
done, and use it as the reference structure, and calculate rmsd of each
frame in the trajectory against the reference structure, and find the one
with the smallest rmsd. But how to calculate the rmsd? The simulated
structure has different atom number with the reference structure, so gmx
rmsd wouldn't work. Do you know which method can work in this case?

Best wishes.

Yeping Sun

On Mon, Aug 19, 2019 at 6:59 PM Justin Lemkul  wrote:

>
>
> On 8/18/19 11:28 PM, sunyeping wrote:
> > Hello Bratin Kumar Das，
> >
> > Your answer is correst but irrelevent to my question. By adding
> energygrps option in the mdp and rerun the trajectory and generate the edr
> file containing the interation energy information which can be extracted by
> enemat. However enemat only gives the range of the interaction energy. My
> question is how to  calculate interaction energy between two groups for
> every frame in the trajectory.
>
> That is precisely what Bratin is telling you to do, and his answer is
> exactly correct.
>
> You need to use gmx energy, not gmx enemat, to get the interaction
> energy values in every frame. Then find the lowest and extract the
> corresponding frame with trjconv. Whether or not this quantity has any
> physical meaning is, however, questionable for most force fields.
>
> -Justin
>
> > --
> > From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> > Sent At:2019 Aug. 19 (Mon.) 11:11
> > To:gromacs ; 孙业平 
> > Subject:Re: [gmx-users] How to calculate interaction energy between two
> groups for every frame in a trajectory?
> >
> > You need to prepare one .mdp file where the energygrps = DNA Protein (
> as example). Generate the .tpr file and rerun using mdrun module.
> > gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc
> > On Mon 19 Aug, 2019, 8:09 AM sunyeping,  wrote:
> > Dear all,
> >
> >   I am doing protein-DNA complex simulations with gromacs and I have
> gotten a trajectory. Now I want to calculate interaction energy between the
> protein and the DNA in every frame of the trajectory so that I can pick out
> a frame in which the  interaction energy between them is the largest, but I
> don't know how. I have used "enemat" , but it only gives a range of the
> energy, not every frame. The output read:
> >
> >   Last energy frame read 5000 time 50.000
> >   Will build energy half-matrix of 2 groups, 6 elements, over 5001 frames
> >   Matrix of Coul-SR energy ranges from -18999.681641 to -1608.268188
> >   Matrix of LJ-SR energy ranges from -2540.941650 to -675.151306
> >   Matrix of total energy ranges from -21540.623047 to -2283.419434
> >
> >   So could you tell me how to calculate interaction energy between two
> groups for every frame in a trajectory?
> >
> >   Best regards.
> >   --
> >   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
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/19/19 2:00 AM, Priyanka Singh wrote:

Hii
I am new to simulations. I want to ask is it ok to use ligand topology
build using PRODRG server if using amber force field for RNA-ligand
simulation. what precautions one should take ends of the RNA molecule.
PRODRG is for GROMOS and produces very low-quality topologies. You 
cannot combine GROMOS topologies with AMBER (nor can you mix and match 
any force fields). Do everything with one force field. AMBER + GAFF is a 
much better option.


-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] "comm-mode = Angular" gives error

[Justin Lemkul]

On 8/19/19 12:39 AM, Jorden Cabal wrote:

Dear Users,
I am trying to perform simulation of a very large and complex system and
which requires me to make the simulation box rectangular cube instead (box
dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to
minimize the number of atoms present in the system.

I am facing the problem of interaction between periodic images due to
rotational movement of the macro molecule. I have tried lowering the
*nstcomm* (frequency of removal of center of mass velocity) to 10 and it
seems it might work but the speed become very slow because it also requires
*nstcalcenergy* to 10.

When I use *comm-mode="Angular"* with *comm-grps="system" *it says "*too
many warnings*" and the warning is
*"Removing the rotation around the center of mass in a periodic system,
this can lead to artifacts. Only use this on a single (cluster of)
molecules. This cluster should not cross periodic boundaries*"

*"Although this problem can be ignored using -maxwarn option in the grompp
command. I want to know that if that is the correct thing to do?" *

*Instead, *I have also tried to work this out by changing the* comm-grps=
"Protein" *but then it throws two warnings first being the same as
mentioned above and the second warning says "*Some atoms are not part of
any center of mass motion removal group. This may lead to artifacts. In
most cases one should use one group for the whole system*"

Again this can be ignored using -maxwarn option but is that right to do?
Please suggest me regarding this.


This is not the purpose of comm-mode/comm-grps, which account for net 
COM motion as a function of other errors in the simulation (Google the 
"flying ice cube effect"). You can't prevent your molecules from 
rotating in any physically realistic way. The simulation box needs to be 
larger to avoid these interactions, and comm-mode/comm-grps is not the 
way to get around it.


-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] How to calculate interaction energy between two groups for every frame in a trajectory?

[Justin Lemkul]

On 8/18/19 11:28 PM, sunyeping wrote:

Hello Bratin Kumar Das，

Your answer is correst but irrelevent to my question. By adding energygrps 
option in the mdp and rerun the trajectory and generate the edr file containing 
the interation energy information which can be extracted by enemat. However 
enemat only gives the range of the interaction energy. My question is how to  
calculate interaction energy between two groups for every frame in the 
trajectory.


That is precisely what Bratin is telling you to do, and his answer is 
exactly correct.


You need to use gmx energy, not gmx enemat, to get the interaction 
energy values in every frame. Then find the lowest and extract the 
corresponding frame with trjconv. Whether or not this quantity has any 
physical meaning is, however, questionable for most force fields.


-Justin


--
From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Sent At:2019 Aug. 19 (Mon.) 11:11
To:gromacs ; 孙业平 
Subject:Re: [gmx-users] How to calculate interaction energy between two groups 
for every frame in a trajectory?

You need to prepare one .mdp file where the energygrps = DNA Protein ( as 
example). Generate the .tpr file and rerun using mdrun module.
gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc
On Mon 19 Aug, 2019, 8:09 AM sunyeping,  wrote:
Dear all,

  I am doing protein-DNA complex simulations with gromacs and I have gotten a trajectory. 
Now I want to calculate interaction energy between the protein and the DNA in every frame 
of the trajectory so that I can pick out a frame in which the  interaction energy between 
them is the largest, but I don't know how. I have used "enemat" , but it only 
gives a range of the energy, not every frame. The output read:

  Last energy frame read 5000 time 50.000
  Will build energy half-matrix of 2 groups, 6 elements, over 5001 frames
  Matrix of Coul-SR energy ranges from -18999.681641 to -1608.268188
  Matrix of LJ-SR energy ranges from -2540.941650 to -675.151306
  Matrix of total energy ranges from -21540.623047 to -2283.419434

  So could you tell me how to calculate interaction energy between two groups 
for every frame in a trajectory?

  Best regards.
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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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[gmx-users] AVX_512 and GROMACS

[tarzan p]

Hi all.I have a dual socket Xeon GOLD 6148 which has the capabilities for 

 Instruction Set Extensions   Intel® SSE4.2, Intel® AVX, Intel® AVX2, Intel® 
AVX-512
but hen why si gromacs giving the error for AVX_512 but takes AVX2_256???
Adding the out put 


/Downloads/gromacs-2019/build-gromacs$ cmake .. -DGMX_SIMD=AVX_512-- Enabling 
RDTSCP support
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_FLAG_ACCEPTED
-- Performing Test C_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test C_arch_AVX_FLAG_ACCEPTED
-- Performing Test C_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test C_hgnu_FLAG_ACCEPTED
-- Performing Test C_hgnu_FLAG_ACCEPTED - Failed
-- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test C_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)
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test CXX_hgnu_FLAG_ACCEPTED
-- Performing Test CXX_hgnu_FLAG_ACCEPTED - Failed
-- 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)
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)


-- Configuring incomplete, errors occurred!
See also 
"/home/gdd/Downloads/gromacs-2019/build-gromacs/CMakeFiles/CMakeOutput.log".
See also 
"/home/gdd/Downloads/gromacs-2019/build-gromacs/CMakeFiles/CMakeError.log".


~/Downloads/gromacs-2019/build-gromacs$ cmake .. -DGMX_SIMD=AVX2_256-- 
Performing Test C_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx2_mfma_COMPILE_WORKS
-- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags:  -mavx2 -mfma
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
-- The GROMACS-managed build of FFTW 3 will configure with the following 
optimizations: --enable-sse2;--enable-avx;--enable-avx2
-- Configuring done
-- Generating done
-- Build files have been written to: 
/home/gdd/Downloads/gromacs-2019/build-gromacs


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