Re: [gmx-users] Help for GROMACS best performance system

[Simone Orioli]

Hi,
The answer to this question is very system dependent, so my suggestion is
to run a benchmark simulation. If you're simulating a system in explicit
solvent, the performance will remain pretty much stable in time, so you can
run a very short simulation (i.e. 100ps) and check at the end of the log
file how many nanoseconds per day would you simulate with a given hardware
configuration. You might want to try many different hardware configurations
and see which one provides the highest ns/day ratio for your system.

Best,
Simone

Il sab 20 apr 2019, 21:09 Ali Sufali  ha
scritto:

> Hi
>
> It's been a while I have started using GROMACS for my researches and now I
> want to buy a system with powerful performance.
>
> I want to choose between these two options
> Is it better to have multiple graphics card on a 12-24 core system or it is
> better to have one or two graphics card on multiple systems which have
> 12-24 cores ?
>
>
>
>
> Ali Sufali
> M.Sc. Student
> University of Tehran
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Cannot select termini with AMBER99sb-ildn

[Neena Susan Eappen]

Hello gromacs users,

I was wondering why with AMBER99sb-ildn force field, peptide termini cannot be 
user defined say like neutral N terminus. Is this because this forcefield is 
mostly for proteins for which N-terminus is always protonated at physiological 
pH?

Many thanks,
Neena
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] No constraints, default potential?

[Neena Susan Eappen]

Hello gromacs users,

When no bond constraints are applied during simulation, what is the default 
potential used to describe bond stretching? Harmonic or Morse?

Many thanks,
Neena
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Help for GROMACS best performance system

[Ali Sufali]

Hi

It's been a while I have started using GROMACS for my researches and now I
want to buy a system with powerful performance.

I want to choose between these two options
Is it better to have multiple graphics card on a 12-24 core system or it is
better to have one or two graphics card on multiple systems which have
12-24 cores ?




Ali Sufali
M.Sc. Student
University of Tehran
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] 2019.2 build warnings

[Alex]

Hi Mark,

Here you are:

 :-) GROMACS - gmx, 2019.2 (-:

    GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. 
Berendsen

    Par Bjelkmar  Christian Blau   Viacheslav Bolnykh Kevin Boyd
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Alan Gray
  Gerrit Groenhof Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
  Aleksei Iupinov   Christoph Junghans Joe Jordan Dimitrios Karkoulis
    Peter Kasson    Jiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg Erik Marklund
    Pascal Merz Pieter Meulenhoff    Teemu Murtola Szilard Pall
    Sander Pronk  Roland Schulz  Michael Shirts    Alexey Shvetsov
   Alfons Sijbers Peter Tieleman  Jon Vincent  Teemu 
Virolainen

 Christian Wennberg    Maarten Wolf
   and the project leaders:
    Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx, version 2019.2
Executable: redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin/./gmx
Data prefix:  redacted/gmx2019.2_gpu/gromacs-2019.2 (source tree)
Working dir:  redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin
Command line:
  gmx -version

GROMACS version:    2019.2
Precision:  single
Memory model:   64 bit
MPI library:    thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:    CUDA
SIMD instructions:  AVX2_256
FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:    enabled
Hwloc support:  hwloc-1.11.0
Tracing support:    disabled
C compiler: /usr/bin/cc GNU 5.4.0
C compiler flags:    -mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast

C++ compiler:   /usr/bin/c++ GNU 5.4.0
C++ compiler flags:  -mavx2 -mfma    -std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast
CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda 
compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on 
Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105
CUDA compiler 
flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; 
;-mavx2;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;

CUDA driver:    10.10
CUDA runtime:   10.10


On 4/20/2019 12:38 PM, Mark Abraham wrote:

Hi,

Your experience looks unusual. What does gmx -version report?

Mark

On Fri., 19 Apr. 2019, 03:02 Alex,  wrote:


Can someone please confirm that my emails indeed reach this board? :)
Thank you.

On 4/16/2019 6:31 PM, Alex wrote:

Okay, more interesting things are happening.
At the end of 'make' I get a bunch of things like

.. nbnxn_cuda.cu (373): warning:
variable "dim_grid" was declared but never referenced
-bash: syntax error near unexpected token `373'

More errors during 'make check' right after " Building NVCC (Device)
object


src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"

then continues as if nothing happened.

Finally, fails test #42 with what appears to be sarcasm:
"...
Thanx for Using GROMACS - Have a Nice Day

Mdrun cannot use the requested (or automatic) number of ranks,
retrying with 8.

Abnormal return value for ' gmx mdrun-nb cpu  -notunepme

mdrun.out 2>&1' was 1

Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 1   -notunepme >mdrun.out
2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
distance_restraints

Abnormal return value for ' gmx mdrun -ntmpi 6   -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun  -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
Re-running orientation-restraints using CPU-based PME

Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu-notunepme

mdrun.out 2>&1' was -1

FAILED. Check mdrun.out, md.log file(s) in
orientation-restraints/pme-cpu for 

Re: [gmx-users] query about different number of solvent molecules added

[neelam wafa]

Thanks sir Mark
It means the results are not faulty and I can continue for further work.
 Thanks for your valuable suggestions.
Regards

On Sat, 20 Apr 2019, 11:37 pm Mark Abraham, 
wrote:

> Hi,
>
> Naturally such differences in system preparation are inevitable, and can be
> seen before any expensive simulation runs. So the absolute energies are
> different for different systems, but fortunately there was little to no
> value in comparing them even when they are formally comparable. However
> estimates of quantities based on energy differences, such as relative free
> energies of binding can be usefully made.
>
> Mark
>
> On Sat., 20 Apr. 2019, 14:17 neelam wafa,  wrote:
>
> > Hi!
> > Dear Sir Justin.
> > I have run 5 ns simulations of two different enzymes in unbound form and
> in
> > complex with 4 different inhibitors each. Now when I compare the data I
> see
> > different number of solvent molecules added in each case( solvent being
> > water) enzyme 1 has +1 charge and neutrallized with one chloride ion
> while
> > enzyme 2 has -7 charge and neutralized with 7 sodium ions. the number
> > solvent molecules added are followings.
> >   Enzyme 1enzyme 2
> > free enzyme   21082 20169
> > ligand1   2107320184
> > ligand 2 21070  20151
> > ligand3  20916  20150
> > ligand 4 20901 20150
> > please tell me does it show any fault in the simulation or how can i
> > interpret it? similarly there are slight diffrences in the total energy
> and
> > density of the system while all my ligands have similar structures
> > differing only in one or two atoms.
> > I have done all my work with your guidance as i have no other expert here
> > to guide me and now need little more guidance. can you suggest me some
> > literature regarding interpretation of such matters.Thanks in advance.
> > Regards
> > Neelam Wafa
> > Ph. D scholar
> > University of the Punjab Lahore, Pakistan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] 2019.2 build warnings

[Mark Abraham]

Hi,

Your experience looks unusual. What does gmx -version report?

Mark

On Fri., 19 Apr. 2019, 03:02 Alex,  wrote:

> Can someone please confirm that my emails indeed reach this board? :)
> Thank you.
>
> On 4/16/2019 6:31 PM, Alex wrote:
> > Okay, more interesting things are happening.
> > At the end of 'make' I get a bunch of things like
> >
> > .. nbnxn_cuda.cu (373): warning:
> > variable "dim_grid" was declared but never referenced
> > -bash: syntax error near unexpected token `373'
> >
> > More errors during 'make check' right after " Building NVCC (Device)
> > object
> >
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"
> > then continues as if nothing happened.
> >
> > Finally, fails test #42 with what appears to be sarcasm:
> > "...
> > Thanx for Using GROMACS - Have a Nice Day
> >
> > Mdrun cannot use the requested (or automatic) number of ranks,
> > retrying with 8.
> >
> > Abnormal return value for ' gmx mdrun-nb cpu  -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> >
> > Abnormal return value for ' gmx mdrun -ntmpi 1   -notunepme >mdrun.out
> > 2>&1' was -1
> > FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
> > distance_restraints
> >
> > Abnormal return value for ' gmx mdrun -ntmpi 6   -notunepme >mdrun.out
> > 2>&1' was 1
> > Retrying mdrun with better settings...
> >
> > Abnormal return value for ' gmx mdrun  -notunepme >mdrun.out 2>&1' was -1
> > FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
> > Re-running orientation-restraints using CPU-based PME
> >
> > Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu-notunepme
> > >mdrun.out 2>&1' was -1
> > FAILED. Check mdrun.out, md.log file(s) in
> > orientation-restraints/pme-cpu for orientation-restraints-pme-cpu
> > Re-running pull_geometry_angle using CPU-based PME
> > Re-running pull_geometry_angle-axis using CPU-based PME
> > Re-running pull_geometry_dihedral using CPU-based PME
> > 3 out of 55 complex tests FAILED"
> >
> > Then finally quits for good. Your suggestions will be highly appreciated.
> >
> > Thank you,
> >
> > Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] query about different number of solvent molecules added

[Mark Abraham]

Hi,

Naturally such differences in system preparation are inevitable, and can be
seen before any expensive simulation runs. So the absolute energies are
different for different systems, but fortunately there was little to no
value in comparing them even when they are formally comparable. However
estimates of quantities based on energy differences, such as relative free
energies of binding can be usefully made.

Mark

On Sat., 20 Apr. 2019, 14:17 neelam wafa,  wrote:

> Hi!
> Dear Sir Justin.
> I have run 5 ns simulations of two different enzymes in unbound form and in
> complex with 4 different inhibitors each. Now when I compare the data I see
> different number of solvent molecules added in each case( solvent being
> water) enzyme 1 has +1 charge and neutrallized with one chloride ion while
> enzyme 2 has -7 charge and neutralized with 7 sodium ions. the number
> solvent molecules added are followings.
>   Enzyme 1enzyme 2
> free enzyme   21082 20169
> ligand1   2107320184
> ligand 2 21070  20151
> ligand3  20916  20150
> ligand 4 20901 20150
> please tell me does it show any fault in the simulation or how can i
> interpret it? similarly there are slight diffrences in the total energy and
> density of the system while all my ligands have similar structures
> differing only in one or two atoms.
> I have done all my work with your guidance as i have no other expert here
> to guide me and now need little more guidance. can you suggest me some
> literature regarding interpretation of such matters.Thanks in advance.
> Regards
> Neelam Wafa
> Ph. D scholar
> University of the Punjab Lahore, Pakistan
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] query about different number of solvent molecules added

[neelam wafa]

Hi!
Dear Sir Justin.
I have run 5 ns simulations of two different enzymes in unbound form and in
complex with 4 different inhibitors each. Now when I compare the data I see
different number of solvent molecules added in each case( solvent being
water) enzyme 1 has +1 charge and neutrallized with one chloride ion while
enzyme 2 has -7 charge and neutralized with 7 sodium ions. the number
solvent molecules added are followings.
  Enzyme 1enzyme 2
free enzyme   21082 20169
ligand1   2107320184
ligand 2 21070  20151
ligand3  20916  20150
ligand 4 20901 20150
please tell me does it show any fault in the simulation or how can i
interpret it? similarly there are slight diffrences in the total energy and
density of the system while all my ligands have similar structures
differing only in one or two atoms.
I have done all my work with your guidance as i have no other expert here
to guide me and now need little more guidance. can you suggest me some
literature regarding interpretation of such matters.Thanks in advance.
Regards
Neelam Wafa
Ph. D scholar
University of the Punjab Lahore, Pakistan
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] concatenate tpr files for PCA analysis

[Mark Abraham]

Hi,

What does gmx dump say about the contents of your xtc file?

Mark

On Fri., 19 Apr. 2019, 08:29 Prasanth G, Research Scholar, <
prasanthgha...@sssihl.edu.in> wrote:

> Dear all,
>
> I am interested in carrying out pca analysis of protein with ligand
> (complex). I had carried out a simulation for 20 ns and extended it by 10
> ns (making it a 30ns simulation).
> I had extracted protein trajectories from both the simulations and joined
> them together using -cat flag.
>
> I observed that in some cases, people perform the analysis with a pdb or a
> gro file (snapshot dumped at 0ns) of the protein. But gmx gives a warning
> stating that the part of protein that has moved out of the box cannot be
> recovered. This made me choose tpr file as a reference.
> When i try to run the gmx covar with 20ns tpr file as reference using the
> below command,
>
> $ gmx_mpi covar -s protein_center_0_20.tpr -f protein_center_0_30.xtc -xpma
> covar.xpm
>
> I get a note like this,
>
> Note: the fit and analysis group are identical,
>   while the fit is mass weighted and the analysis is not.
>   Making the fit non mass weighted.
>
> Calculating the average structure ...
> Reading frame2000 time 2.000
> Constructing covariance matrix (1314x1314) ...
> Reading frame2000 time 2.000
> Read 3002 frames
>
> Trace of the covariance matrix: 27.4516 (nm^2)
> 100%
> Diagonalizing ...
>
> Sum of the eigenvalues: 27.4516 (nm^2)
>
> Writing eigenvalues to eigenval.xvg
>
> Writing reference, average structure & eigenvectors 1--1314 to eigenvec.trr
> Wrote the log to covar.log
>
> It looks like, gmx only considers the 2000 frames (20ns) for analysis. I
> would be grateful if someone can help me in this regard.
>
> --
> Regards,
> Prasanth.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.