[gmx-users] How to install gromacs on cpu cluster

[sunyeping]

Dear everyone,

I would like to install gromacs on a cpu cluster of 12 nodes, with each node 
containing 32 cores. The gcc version on the cluster is 4.4.7. Which version of 
gromacs can be properly compiled with this gcc version?

The cluster support PBS job submission system, then what is the correct options 
for cmake (or maybe configure) when compiling gromacs?

Thank you in advance.

Best regards.
Yeping
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Re: [gmx-users] How to install gromacs on cpu cluster

[Benson Muite]

Hi Yeping,

It may be easier to install a newer version of GCC. Are there any GPUs 
on your cluster?


Benson

On 6/29/19 11:27 AM, sunyeping wrote:


Dear everyone,

I would like to install gromacs on a cpu cluster of 12 nodes, with each node 
containing 32 cores. The gcc version on the cluster is 4.4.7. Which version of 
gromacs can be properly compiled with this gcc version?

The cluster support PBS job submission system, then what is the correct options 
for cmake (or maybe configure) when compiling gromacs?

Thank you in advance.

Best regards.
Yeping

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Re: [gmx-users] How to install gromacs on cpu cluster

[sunyeping]

Hello Benson,

Thank you for respond to my question. There is no GPU on my cluster.

Best regards,

Yeping
--
From:Benson Muite 
Sent At:2019 Jun. 29 (Sat.) 16:56
To:gromacs ; 孙业平 
Subject:Re: [gmx-users] How to install gromacs on cpu cluster

Hi Yeping,

It may be easier to install a newer version of GCC. Are there any GPUs 
on your cluster?

Benson

On 6/29/19 11:27 AM, sunyeping wrote:
>
> Dear everyone,
>
> I would like to install gromacs on a cpu cluster of 12 nodes, with each node 
> containing 32 cores. The gcc version on the cluster is 4.4.7. Which version 
> of gromacs can be properly compiled with this gcc version?
>
> The cluster support PBS job submission system, then what is the correct 
> options for cmake (or maybe configure) when compiling gromacs?
>
> Thank you in advance.
>
> Best regards.
> Yeping
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Re: [gmx-users] How to install gromacs on cpu cluster

[Benson Muite]

Hi Yeping,

Minimum required compiler version for the latest release is GCC 4.8.1 :

http://manual.gromacs.org/documentation/current/install-guide/index.html

GROMACS 4.5 seems to indicate support for GCC 4.5 
(http://www.gromacs.org/Documentation/Installation_Instructions_4.5)


Is CMAKE on your cluster? If so what version?

Regards,

Benson

On 6/29/19 12:08 PM, sunyeping wrote:

Hello Benson,

Thank you for respond to my question. There is no GPU on my cluster.

Best regards,

Yeping

--
From:Benson Muite 
Sent At:2019 Jun. 29 (Sat.) 16:56
To:gromacs ; 孙业平 
Subject:Re: [gmx-users] How to install gromacs on cpu cluster

Hi Yeping,

It may be easier to install a newer version of GCC. Are there any GPUs

on your cluster?

Benson

On 6/29/19 11:27 AM, sunyeping wrote:
>
> Dear everyone,
>
> I would like to install gromacs on a cpu cluster of 12 nodes, with each 
node containing 32 cores. The gcc version on the cluster is 4.4.7. Which version 
of gromacs can be properly compiled with this gcc version?
>
> The cluster support PBS job submission system, then what is the correct 
options for cmake (or maybe configure) when compiling gromacs?
>
> Thank you in advance.
>
> Best regards.
> Yeping



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[gmx-users] interrupt of gmx mdrun

[Andrew Bostick]

Hi gromacs users,

I am doing MD simulation of a protein (from pdb ). After equilibration
phases, I used following commands:

gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt p topol.top -o md.tpr -n
index.ndx

gmx_mpi mdrun -v -nb gpu -deffnm  md >& md.job &

But, mdrun was interrupted in step 8237500. I repeated last command. This
happened again but in step 6837500.

The last lines of md.log file is as follows:


   Step   Time Lambda
683750013675.00.0

   Energies (kJ/mol)
  AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
5.30550e+036.71343e+032.61548e+022.78159e+033.61962e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
4.03766e+04   -3.33403e+03   -4.03105e+052.26409e+03   -3.12540e+05
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
5.98029e+04   -2.52737e+052.95155e+02   -2.28999e+025.62166e+00
   Constr. rmsd
2.50195e-05

What is the reason of this interruption. How to resolve that?

Best,
Andrew
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[gmx-users] Transference of dihedral potentials between united atom and all-atom force fields

[Pragati Sharma]

Hello gromacs users,

I have a query regarding transference of dihedral potentials between united
atom and all-atom force fields. Suppose, for a dihedral of four carbon
atoms in polybutadine (united atoms: CH2-CH=CH-CH2). Can I use the same
dihedral potentials or force constants for the same set of atoms in an
all-atom force field where carbon and hydrogens are treated separately
while keeping the potential functions same.

Thanks, Pragati
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[gmx-users] appropriate forcefield

[starlight]

Hi, I want to perform some simulations to study the interaction of 2 very
small peptides with each other in the water. I want to put these peptides
separately in water to give a structure and then do a simulation of them
with each other in water to study the peptide-peptide interaction. I need
to know the position of the hydrogen bonds that form between these peptides
in water.
So I want to know about the true force field and water molecule model for
these simulations. I find few articles that try some force fields to such
simulations but they don't say which ff is more appropriate than the
others. Would you please help me to know about it and recommend some
articles. Thank you
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Re: [gmx-users] Transference of dihedral potentials between united atom and all-atom force fields

[Peter Stern]

No, of course not.  United atom potentials are optimized taking into account 
that the hydrogens are not included.  Think about it.  If you use the United 
atom dihedral potential in an all-atom force field you will also be adding to 
that all the dihedral potentials which include the hydrogen atoms.  Clearly 
this is not going to be the same for a particular C-C bond.

And in general, you cannot transfer parameters from one force field to another. 
 I think that has been emphasized repeatedly in this forum.

Regards,
Peter


Sent from my iPhone

On Jun 29, 2019, at 2:10 PM, Pragati Sharma 
mailto:pragati2...@gmail.com>> wrote:

Hello gromacs users,

I have a query regarding transference of dihedral potentials between united
atom and all-atom force fields. Suppose, for a dihedral of four carbon
atoms in polybutadine (united atoms: CH2-CH=CH-CH2). Can I use the same
dihedral potentials or force constants for the same set of atoms in an
all-atom force field where carbon and hydrogens are treated separately
while keeping the potential functions same.

Thanks, Pragati
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Re: [gmx-users] Transference of dihedral potentials between united atom and all-atom force fields

[Justin Lemkul]

On 6/29/19 12:39 PM, Peter Stern wrote:

No, of course not.  United atom potentials are optimized taking into account 
that the hydrogens are not included.  Think about it.  If you use the United 
atom dihedral potential in an all-atom force field you will also be adding to 
that all the dihedral potentials which include the hydrogen atoms.  Clearly 
this is not going to be the same for a particular C-C bond.

And in general, you cannot transfer parameters from one force field to another. 
 I think that has been emphasized repeatedly in this forum.


100% agree with everything Peter has said above and I will add this (I 
have said it before but will say it again): dihedrals do not correspond 
to any real physical force. They are mathematical Band-Aids that account 
for inaccuracies in our treatment of nonbonded terms in 1-4 
interactions. Some force fields apply scaling factors to these 
interactions, others do not. In any case, a dihedral term is absolutely 
connected to a force field parameter set (like other force field terms, 
but perhaps even more obviously so) because it is inextricably linked to 
the (1) atomic charges, (2) LJ terms, and (3) 1-4 scaling factor, if 
applicable.


-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] Constraints Error; In Using Tetrahedral Zinc Dummy Model

[Mahdi Bagherpoor]

Dear Gromacs users,

I am trying to simulate a zinc-finger protein in explicit water, *with
CHARMM36 FF*. Unfortunately, I did not find any *tetrahedral zinc force*
field in Gromacs and therefore I converted the tetrahedral dummy zinc model
used in CHARMM27 FF to the format of Gromacs. The minimization of the
system goes perfect but unfortunately when I start *NVT simulation*, I get
this error:


WARNING 1 [file topol.top, line 57]:
  The bond in molecule-type Dummy_chain_X between atoms 2 DZ1 and 3 DZ2 has
  an estimated oscillational period of 6.1e-03 ps, which is less than 5
  times the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.
...
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

---
Here, DZ1 and DZ2 are dummy atoms related to tetrahedral zinc model. *in
mdp file*, I have used *h-bonds* *Lincs* constraint. When I use the
*all-bond* in the mdp file again I get another error that is:
---

WARNING 1 [file topol.top, line 57]:
  There are atoms at both ends of an angle, connected by constraints and
  with masses that differ by more than a factor of 13. This means that
  there are likely dynamic modes that are only very weakly coupled. To
  ensure good equipartitioning, you need to either not use constraints on
  all bonds (but, if possible, only on bonds involving hydrogens) or use
  integrator = sd or decrease one or more tolerances:
  verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
  4 or SHAKE tolerance <= 1e-05

Number of degrees of freedom in T-Coupling group Protein_DNA_ZNT is 6936.89
Number of degrees of freedom in T-Coupling group Water_and_ions is 179547.11



Does this error mean that I need to constraint zinc bonds beside h-bonds?
If so, how should I do it? *I will appreciate* if you let me know any idea
to fix this problem.

Cheers,
Mahdi
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Re: [gmx-users] How to install gromacs on cpu cluster

[sunyeping]

Hi,  Benson,

I can install gcc-4.9 for compiling the latest version of gromacs 
(gromacs_2019.3) in my own account directory (/data/home/sunyp/software/GCC. 
For proper submission of task with PBS system, which options of cmake should I 
use?
According to the "Quick and dirty cluster installation" section of the gromacs 
installation guide, it seems that a quick and dirty installation should be 
done, and then another installation with MPI should be done to the same 
location with the non-MPI installation. I am not very clear how these should be 
done exactly. Could you give the exact commands?
Best regards
Yeping

Q; gromacs 
Subject:Re: [gmx-users] How to install gromacs on cpu cluster

Hi Yeping,
Minimum required compiler version for the latest release is GCC 4.8.1 :
http://manual.gromacs.org/documentation/current/install-guide/index.html
GROMACS 4.5 seems to indicate support for GCC 4.5 
(http://www.gromacs.org/Documentation/Installation_Instructions_4.5)
Is CMAKE on your cluster? If so what version?
Regards,
Benson
On 6/29/19 12:08 PM, sunyeping wrote:
Hello Benson,

Thank you for respond to my question. There is no GPU on my cluster.

Best regards,

Yeping
--
From:Benson Muite 
Sent At:2019 Jun. 29 (Sat.) 16:56
To:gromacs ; 孙业平 
Subject:Re: [gmx-users] How to install gromacs on cpu cluster

 Hi Yeping,

 It may be easier to install a newer version of GCC. Are there any GPUs 
 on your cluster?

 Benson

 On 6/29/19 11:27 AM, sunyeping wrote:
 >
 > Dear everyone,
 >
 > I would like to install gromacs on a cpu cluster of 12 nodes, with each node 
 > containing 32 cores. The gcc version on the cluster is 4.4.7. Which version 
 > of gromacs can be properly compiled with this gcc version?
 >
 > The cluster support PBS job submission system, then what is the correct 
 > options for cmake (or maybe configure) when compiling gromacs?
 >
 > Thank you in advance.
 >
 > Best regards.
 > Yeping 

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Re: [gmx-users] How to install gromacs on cpu cluster

[Benson Muite]

Hi Yeping,

May want to use GCC 7 or GCC 8

https://gcc.gnu.org/

Follow instructions for how to get GCC working, see

https://gcc.gnu.org/install/

Once have a new version of GCC in your own directory, you will probably 
want to then compile an MPI library (eg. OpenMPI - 
https://www.open-mpi.org/or MPICH - https://www.mpich.org) in your home 
directory as well, the MPI library should be compiled with the GCC 
version that you use. I have not used PBS in a while, but the MPI 
library should pick this up. For programs on a single node, PBS should 
be able to just run the compiled executable.


What version of cmake do you have on your system?

Will try to write a short script later today. You may also want to look 
at Spack which  offers an automated GROMACS installation (but it can be 
helpful to set it up yourself for good performance):


https://github.com/spack/spack

Regards,

Benson

On 6/30/19 3:36 AM, sunyeping wrote:

Hi,  Benson,

I can install gcc-4.9 for compiling the latest version of gromacs 
(gromacs_2019.3) in my own account directory 
(/data/home/sunyp/software/GCC. For proper submission of task with PBS 
system, which options of cmake should I use?
According to the "Quick and dirty cluster installation" section of the 
gromacs installation guide, it seems that a quick and dirty 
installation should be done, and then another installation with MPI 
should be done to the same location with the non-MPI installation. I 
am not very clear how these should be done exactly. Could you give the 
exact commands?

Best regards
Yeping


  Q


  ; gromacs 

Subject:Re: [gmx-users] How to install gromacs on cpu cluster

Hi Yeping,

Minimum required compiler version for the latest release is GCC
4.8.1 :

http://manual.gromacs.org/documentation/current/install-guide/index.html

GROMACS 4.5 seems to indicate support for GCC 4.5
(http://www.gromacs.org/Documentation/Installation_Instructions_4.5)

Is CMAKE on your cluster? If so what version?

Regards,

Benson

On 6/29/19 12:08 PM, sunyeping wrote:
Hello Benson,

Thank you for respond to my question. There is no GPU on my cluster.

Best regards,

Yeping
--
From:Benson Muite 
Sent At:2019 Jun. 29 (Sat.) 16:56
To:gromacs ; 孙业平 
Subject:Re: [gmx-users] How to install gromacs on cpu cluster

Hi Yeping,

It may be easier to install a newer version of GCC. Are there any GPUs

on your cluster?

Benson

On 6/29/19 11:27 AM, sunyeping wrote:
>
> Dear everyone,
>
> I would like to install gromacs on a cpu cluster of 12 nodes, with each 
node containing 32 cores. The gcc version on the cluster is 4.4.7. Which version 
of gromacs can be properly compiled with this gcc version?
>
> The cluster support PBS job submission system, then what is the correct 
options for cmake (or maybe configure) when compiling gromacs?
>
> Thank you in advance.
>
> Best regards.
> Yeping



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Re: [gmx-users] clustering of ions during NPT simulation

[Netaly Khazanov]

H Justin,
I used  amber99sb-ildn FF for the simulation.
Which parameters do you suggest to use?
Thanks in advance

On Fri, Jun 28, 2019 at 8:15 PM Justin Lemkul  wrote:

>
>
> On 6/27/19 8:44 AM, Netaly Khazanov wrote:
> > Hi All,
> > I perform simulation of a transmembrane protein in a membrane in 1M
> > concentration of NaCl.
> > During the simulation, I noticed that ions began to cluster and they are
> > not evenly spread after 10 ns. Is it a problem or I can proceed further?
>
> Some ion parameters are known to aggregate but this issue is long since
> solved. You don't state which parameters you used, but if they are
> outdated (which is likely the case with most/all of the AMBER force
> fields provided with GROMACS), you need to use better parameters.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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>


-- 
Netaly
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