Re: [gmx-users] 2019.2 build warnings

2019-05-08 Thread Alex 
Just to update: we rolled back to 2018.1 due to a new simulation, which 
is running perfectly fine on the older version.


The only difference between this simulation and everything we've tried 
so far is that each charge value in the topology (for about 3000 atoms) 
has something like five digits -- directly copied from a DFT output. On 
all machines running 2018.1 the initial dynamic relaxation initially 
hiccuped at 400% CPU load (instead of normal 2000%) doing something for 
a few minutes, but then always recovered and continued to run normally. 
2019.2 ended up throwing errors about pressure scaling on one try and 
quietly segfaulted on another. On the same machine, rolling back to 
2018.1 resulted in normal operation.


I can provide the input if needed (including the batch sh file), but I 
don't think we'll be using 2019.2 in the near future, though I kept a 
backup of the build.


Alex


On 5/2/2019 12:42 AM, Alex wrote:

Hi Szilárd,

Thanks a bunch. I have upgraded to 2019.2 and a fairly large 
"production" test seems to be running without any issues.


Alex

On 5/1/2019 5:07 AM, Szilárd Páll wrote:

Hi,

You can safely ignore the errors as these are caused by properties of 
your

hardware that the test scripts are not dealing well enough -- though
admittedly, two of the three errors should be avoided along a message
similar to this
"Mdrun cannot use the requested (or automatic) number of OpenMP threads,
retrying with 8."
(which is what I get when I run the tests on a similar machine).

If you need the tests to pass on the node in question, let me know, I 
can

suggest workarounds.

Cheers,
--
Szilárd


On Mon, Apr 29, 2019 at 6:47 PM Alex  wrote:


Hi Szilárd,

Since I don't know which directory inside /complex corresponds to which
tests (at least one of the tests that failed was #42), here's a tarball
of the entire /complex directory per location you specified below:


https://www.dropbox.com/s/44uluopkdan2417/regression_complex_2019.2.tar.gz?dl=0 



If you can help us figure this out, it will be great!

Thanks,

Alex

On 4/29/2019 4:25 AM, Szilárd Páll wrote:

Hi,

I assume you used -DREGRESSIONTEST_DOWNLOAD=ON case in which the tests

are

downloaded and unpacked under
BUILD_TREE/tests/regressiontests-release-2019-[SUFFIX]/

In that directory you find the usual regressiontests tree, from there

under

complex/ you'll find the tests in question.

Cheers,
--
Szilárd


On Fri, Apr 26, 2019 at 7:00 PM Alex  wrote:


Hi Szilárd,

I am at a conference right now, but will do my best to upload the
requested data first thing on Monday. In the meantime, could you 
please

tell me where the stuff of interest would be located within the local
gromacs build directory? I mean, I could make the entire directory a
tarball, but not sure it's all that necessary. I don't remember which

tests

failed, unfortunately...

Thank you!

Alex

On 4/25/2019 2:54 AM, Szilárd Páll wrote:

Hi Alex,

On Wed, Apr 24, 2019 at 9:59 PM Alex  wrote:


Hi Szilárd,

We are using neither Ubuntu 18.04, nor glibc 2.27, but the 
problem is

most certainly there.

OK.

Can you please post the content of the directories of tests that

failed?

It
would be useful to know the exact software configuration 
(reported in

the

log) and the details of the errors (reported in the mdrun.out).

Thanks,
--
Szilárd




Until the issue is solved one way or another, we
will be staying with 2018.1, i guess.

$ lsb_release -a

No LSB modules are available.

Distributor ID: Ubuntu

Description:    Ubuntu 16.04.6 LTS

Release:    16.04

Codename:   xenial

Ubuntu GLIBC 2.23-0ubuntu11


On 4/24/2019 4:57 AM, Szilárd Páll wrote:

What OS are you using? There are some known issues with the Ubuntu

18.04

+

glibc 2.27 which could explain the errors.
--
Szilárd





--
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.

--
Gromacs Users mailing list

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

[gmx-users] Energy conservation problem in NVE simulation for a system with frozen atoms

2019-05-08 Thread Yi Ren 


Hi all,

I am simulating a system with two slabs and water molecules in between.
The slabs were frozen during simulations and I've exclude the interactions
between slab atoms. After energy minimization, I run nvt at 300 K for 10
ns, followed by annealing the system to 250 K in 1 ns. Then another nvt
was run at 250 K for 6 ns. So far, everything was normal. Then I switched
to nve simulation by turning off the thermostat. However, the energy of
the system kept decreasing (temperature was reaching 0 K). I was using
Group cut-off for all the simulations. I've checked the energy between
different groups. The energies between slab and slab, both coulombic and
LJ are 0, which make sense because I've exclude the interactions. The
energies between water and water, on the other hand, decreased to a huge
extend. I am not sure why this happened. If I remove the slabs, only
simulate water molecules, then it works just fine.

Please let me know if you have ever encountered such problem. Any
suggestions would be greatly appreciated.

I am using Gromacs/5.1.4 and the parameters in .mdp file are listed as
follows:
Input Parameters:
   integrator = md
   tinit  = 0
   dt = 0.002
   nsteps = 2500
   init-step  = 0
   simulation-part= 1
   comm-mode  = Linear
   nstcomm= 100
   bd-fric= 0
   ld-seed= 603782470
   emtol  = 10
   emstep = 0.01
   niter  = 20
   fcstep = 0
   nstcgsteep = 1000
   nbfgscorr  = 10
   rtpi   = 0.05
   nstxout= 25
   nstvout= 25
   nstfout= 0
   nstlog = 25
   nstcalcenergy  = 100
   nstenergy  = 25
   nstxout-compressed = 0
   compressed-x-precision = 1000
   cutoff-scheme  = Group
   nstlist= 10
   ns-type= Grid
   pbc= xyz
   periodic-molecules = FALSE
   verlet-buffer-tolerance= 0.005
   rlist  = 1
   rlistlong  = 1
   nstcalclr  = 0
   coulombtype= PME
   coulomb-modifier   = None
   rcoulomb-switch= 0
   rcoulomb   = 1
   epsilon-r  = 1
   epsilon-rf = inf
   vdw-type   = Cut-off
   vdw-modifier   = None
   rvdw-switch= 0
   rvdw   = 1
   DispCorr   = EnerPres
   table-extension= 1
   fourierspacing = 0.16
   fourier-nx = 36
   fourier-ny = 36
   fourier-nz = 48
   pme-order  = 4
   ewald-rtol = 1e-05
   ewald-rtol-lj  = 0.001
   lj-pme-comb-rule   = Geometric
   ewald-geometry = 0
   epsilon-surface= 0
   implicit-solvent   = No
   gb-algorithm   = Still
   nstgbradii = 1
   rgbradii   = 1
   gb-epsilon-solvent = 80
   gb-saltconc= 0
   gb-obc-alpha   = 1
   gb-obc-beta= 0.8
   gb-obc-gamma   = 4.85
   gb-dielectric-offset   = 0.009
   sa-algorithm   = Ace-approximation
   sa-surface-tension = 2.05016
   tcoupl = No
   nsttcouple = -1
   nh-chain-length= 0
   print-nose-hoover-chain-variables = FALSE
   pcoupl = No
   pcoupltype = Isotropic
   nstpcouple = -1
   tau-p  = 1
   compressibility (3x3):
  compressibility[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compressibility[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compressibility[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   ref-p (3x3):
  ref-p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref-p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref-p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord-scaling   = No
   posres-com (3):
  posres-com[0]= 0.0e+00
  posres-com[1]= 0.0e+00
  posres-com[2]= 0.0e+00
   posres-comB (3):
  posres-comB[0]= 0.0e+00
  posres-comB[1]= 0.0e+00
  posres-comB[2]= 0.0e+00
   QMMM   = FALSE
   QMconstraints

[gmx-users] 2019.2 not using all available cores

2019-05-08 Thread Dallas Warren 
gmx 2019.2 compiled using threads only uses a single core mdrun_mpi
compiled using MPI only uses a single core, gmx 2016.3 using threads
uses all 12 cores.

For compiling thread version of 2019.2 used:
cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs-2019.2

For compiling MPI version of 2019.2 used:
cmake .. -DGMX_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_GPU=ON
-DCMAKE_CXX_COMPILER=/usr/lib64/mpi/gcc/openmpi/bin/mpiCC
-DCMAKE_C_COMPILER=/usr/lib64/mpi/gcc/openmpi/bin/mpicc
-DGMX_BUILD_MDRUN_ONLY=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs-2019.2

Between building both to of those, deleted the build directory.


GROMACS:  gmx, version 2019.2
Executable:   /usr/local/gromacs/gromacs-2019.2/bin/gmx
Data prefix:  /usr/local/gromacs/gromacs-2019.2
Working dir:  /home/dallas/experiments/current/19-064/P6DLO
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:  AVX_256
FFT library:fftw-3.3.8-sse2
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
C compiler: /usr/bin/cc GNU 7.4.0
C compiler flags:-mavx -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.4.0
C++ compiler flags:  -mavx-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;;
;-mavx;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver:10.10
CUDA runtime:   10.10


GROMACS:  mdrun_mpi, version 2019.2
Executable:   /usr/local/gromacs/gromacs-2019.2/bin/mdrun_mpi
Data prefix:  /usr/local/gromacs/gromacs-2019.2
Working dir:  /home/dallas/experiments/current/19-064/P6DLO
Command line:
  mdrun_mpi -version

GROMACS version:2019.2
Precision:  single
Memory model:   64 bit
MPI library:MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:CUDA
SIMD instructions:  AVX_256
FFT library:fftw-3.3.8-sse2
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
C compiler: /usr/lib64/mpi/gcc/openmpi/bin/mpicc GNU 7.4.0
C compiler flags:-mavx -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler:   /usr/lib64/mpi/gcc/openmpi/bin/mpiCC GNU 7.4.0
C++ compiler flags:  -mavx-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;;
;-mavx;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver:10.10
CUDA runtime:   10.10


/usr/local/gromacs/gromacs-2016.3/bin/gmx -version

GROMACS:  gmx, version 2016.3
Executable:   /usr/local/gromacs/gromacs-2016.3/bin/gmx
Data prefix:  /usr/local/gromacs/gromacs-2016.3
Working dir:  /home/dallas/experiments/current/19-064/P6DLO
Command line:
  gmx -version

GROMACS version:2016.3
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:CUDA
SIMD instructions:  AVX_256
FFT library:fftw-3.3.8-sse2
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   Tue Mar 21 13:21:15 AEDT 2017
Built by:   dallas@morph [CMAKE]
Build OS/arch:  Linux 4.4.49-16-default x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU

[gmx-users] How to calculate Stress Strain curve in GROMACS

2019-05-08 Thread Anh Vo 
Dear GROMACS users,



I’m currently running GROMACS to simulate a simple phospholipid bilayer
membrane (POPC) under deformation, and plot the von Mises stress-strain
curve to determine yielding point.

Hence, how can I obtain stress strain value to plot the curve for a
deformed membrane in GROMACS?


I have got the membrane deformed and tried to get the stress-strain curve
by extract output pressure from .edr file. The general shape of the curve
is correct, but the yield stress/ yield strain value is wrong. Why did I
get the wrong value and where/ which parameter files should I address to
solve this problem?


Thank you very much.


Regards,

Anh Vo
-- 
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] Error in mdrun

2019-05-08 Thread Hanin Omar 
Hi allI am trying to run md simulation of a 83 residue protein with 
AMBER99SB-ILDN protein forcefield and TIP3P water model, i am adding 
orientation restraint to my protein alone however when i run NVT equlibration i 
get this errorFatal error:
Found 5384 copies of a molecule with orientation restrains while the current
code only supports a single copy. If you want to ensemble average, run
multiple copies of the system using the multi-sim feature of mdrun.


To my understanding this means that gromacs is applying the RDC restraints on 
all water molecule which is weird cause in my topology file i added the 
restraint file before including the water topology like this:; Include RDC 
restraint file
#include "RDC-restraint.itp"

; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp" also in my mdp file i have this 
section:;Options for orientation restraint
orire    = yes
orire-fc = 1   ; Orientation restraints force constant
orire-tau    = 0   ; Turn off time averaging
orire-fitgrp = backbone 

is their something i need to add so that gromacs apply the rdc restraint only 
on the protein.i really appreciate the helpThank you 
Hanin OMar
-- 
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] Pressure coupling in expanded ensemble simulations

2019-05-08 Thread Michael Shirts 
Yeah, this is an unfortunately place in the code where not all combinations
work - very long story.  Hopefully this will be working better in 2020.

What I would recommend is, if possible, performing the expanded ensemble
simulation at NVT.  Everything should work fine there (paper coming out
hopefully soon comparing a bunch of free energy methods).  Once can always
correct the free energy at lambda=1 from NVT to NPT.  I Can fill in the
details.

You do NOT want to do Berendsen for NPT when running expanded ensemble.
The results will be incorrect (as I have learned by sad experience_

On Wed, May 8, 2019 at 8:14 AM Gregory Man Kai Poon  wrote:

> Hi all:
>
> We are interested to do expanded ensemble simulations (such as simulated
> tempering) on GROMACS.  Extensive fiddling with the settings and
> googling on other people's experience suggests that these simulations
> must use the md-vv integrator, which in turn is compatible with
> Berendsen or MTTK coupling for pressure.  However, MTTK does not work
> with constraints, which are needed for the forcefields.  Berendsen can
> handle constraints but is not recommended for preserving thermodynamic
> ensembles.  Any ideas on how one should proceed?
>
> Many thanks for your thoughts.
>
> Gregory
>
>
> --
> 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] Using grace in windows

2019-05-08 Thread Subhomoi Borkotoky 
Hi,

You can use qtGrace in Windows directly.

Regards,

Subhomoi B.


On Wed, May 8, 2019, 7:14 PM DEEPANSHU SINGLA 
wrote:

> I am trying to plot graph from gromacs generated xvg files in windows 10
> using Linux subsystem command line. I installed grace using the same
> command line. When I try to plot the graph using grce in the command line
> by using the following command : xmgrace filename.xvg
>
> I get the following error:
>
> Can't open display
> Failed initializing GUI, exiting
>
> Please, guide me help me in ploting the graph in windows.
>
> Sent from Mail for Windows 10
>
> --
> 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] About densmap tool

2019-05-08 Thread Yasser Almeida Hernández 

Hello,

I am working with a membrane protein inserted in a heterogeneous 
bilayer, with different lipids at different ratios. I used gmx densmap 
to obtain 2D maps of the lipids distribution, based in the PO4 group. I 
use the command as following:


gmx densmap -s  -f  -n  -od 
 -unit nm-2 -bin 0.1


Attached is one example of one of my raw output maps.

According with the command-line reference: "The normalization of the 
output is set with the -unit option. The default produces a true number 
density. Unit nm-2 leaves out the normalization for the averaging or the 
angular direction. Option count produces the count for each grid cell. 
When you do not want the scale in the output to go from zero to the 
maximum density, you can set the maximum with the option -dmax."


I am not sure if I am interpreting the results in a proper way.

1 - If "Unit nm-2 leaves out the normalization for the averaging or the 
angular direction", what do the numbers in the output file actually mean?


2 - Are they the average in each grid point, along the whole simulation 
time?


3 - It may sound as a silly question, but how does this command define 
"density"?


Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

-- 
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] Using grace in windows

2019-05-08 Thread DEEPANSHU SINGLA 
Thank you Mr.  Micholas D. for the reply.  Sir is it possible to use
qtgrace by using linux subsystem command line. If so then can you please
tell me the commands to do so.


Deepanshu

On Wed, 8 May 2019, 19:14 DEEPANSHU SINGLA, 
wrote:

> I am trying to plot graph from gromacs generated xvg files in windows 10
> using Linux subsystem command line. I installed grace using the same
> command line. When I try to plot the graph using grce in the command line
> by using the following command : xmgrace filename.xvg
>
>
>
> I get the following error:
>
>
>
> Can't open display
>
> Failed initializing GUI, exiting
>
>
>
> Please, guide me help me in ploting the graph in windows.
>
>
>
> Sent from Mail  for
> Windows 10
>
>
>
-- 
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] Implicit Solvent with User Defined Potentials

2019-05-08 Thread Akash Banerjee 
Dear Gromacs Developer,

I want to use the implicit solvent (gbsa algorithm) along with User-defined
tabulated potentials. Apparently, the implicit solvent option is not
compatible with the vdw-type=USer option. Can I please get some advice on
this?

Thank you for your help.

Kind regards,
Akash
-- 
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] Pressure coupling in expanded ensemble simulations

2019-05-08 Thread Gregory Man Kai Poon 
Hi all:

We are interested to do expanded ensemble simulations (such as simulated 
tempering) on GROMACS.  Extensive fiddling with the settings and 
googling on other people's experience suggests that these simulations 
must use the md-vv integrator, which in turn is compatible with 
Berendsen or MTTK coupling for pressure.  However, MTTK does not work 
with constraints, which are needed for the forcefields.  Berendsen can 
handle constraints but is not recommended for preserving thermodynamic 
ensembles.  Any ideas on how one should proceed?

Many thanks for your thoughts.

Gregory


-- 
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] Using grace in windows

2019-05-08 Thread Smith, Micholas D. 
This is more of a linux subsystem question than a gromacs question; however, 
you may want to know that there is a native grace for windows: qtGrace (its on 
source-forge). Not exactly the same as grace, but works really well.


-Micholas


===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of DEEPANSHU 
SINGLA 
Sent: Wednesday, May 8, 2019 9:44:36 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Using grace in windows

I am trying to plot graph from gromacs generated xvg files in windows 10 using 
Linux subsystem command line. I installed grace using the same command line. 
When I try to plot the graph using grce in the command line by using the 
following command : xmgrace filename.xvg

I get the following error:

Can't open display
Failed initializing GUI, exiting

Please, guide me help me in ploting the graph in windows.

Sent from Mail for Windows 10

--
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] Using grace in windows

2019-05-08 Thread DEEPANSHU SINGLA 
I am trying to plot graph from gromacs generated xvg files in windows 10 using 
Linux subsystem command line. I installed grace using the same command line. 
When I try to plot the graph using grce in the command line by using the 
following command : xmgrace filename.xvg

I get the following error:

Can't open display
Failed initializing GUI, exiting

Please, guide me help me in ploting the graph in windows.

Sent from Mail for Windows 10

-- 
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] Fwd: atoms are not part of any of the T-Coupling groups

2019-05-08 Thread ISHRAT JAHAN 
Thank you Justin sir for the reply. I have resolved my problem.

On Wed, May 8, 2019, 5:57 PM Justin Lemkul  wrote:

>
>
> On 5/7/19 1:41 AM, ISHRAT JAHAN wrote:
> > -- Forwarded message -
> > From: ISHRAT JAHAN 
> > Date: Tue, May 7, 2019 at 11:05 AM
> > Subject: atoms are not part of any of the T-Coupling groups
> > To: 
> >
> >
> > Dear all,
> > I am trying to calculate the lennard Jones interaction energy between
> > protein and urea in the first solvation shell. I have made the index
> group
> > of urea molecule in the first solvation shell and then tried to generate
> > the .tpr file using that index. After running the command
> > gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
> > prot_u3M_rerun -n water_urea_5ofprot.ndx
> > following error occur-
> > 35099 atoms are not part of any of the T-Coupling groups
> > part of  .mdp file and index file is given below
> > rvdw=  1.2^M
> > fourierspacing = 0.12^M
> > fourier_nx = 0^M
> > fourier_ny = 0^M
> > fourier_nz = 0^M
> > pme_order = 4^M
> > ewald_rtol = 1e-5^M
> > optimize_fft = yes^M
> > ; Berendsen temperature coupling is on in two groups^M
> > Tcoupl  =  V-rescale^M
> > tc-grps =  Protein   Urea_5ofprot^M
> > tau_t   =  0.10.1 ^M
> > ref_t   =  300300   ^M
> > ; Energy monitoring^M
> > energygrps  =  Protein  Urea_5ofprot
> > ; Isotropic pressure coupling is now on^M
> > Pcoupl  =  berendsen^M
> >   and at the end of the Index file i have only added the residue index of
> > urea within 5 of protein and save the index file.
>
> While you can define whatever energygrps you like (note that the
> molecules will change over time and your results may end up being not
> useful), you need to couple all atoms in the system to a thermostat via
> tc-grps. Your urea selection is only a subset of the urea molecules, and
> if you have any other solvent, ions, etc. they are not being accounted
> for. tc-grps = Protein Non-Protein is almost always the way to go.
>
> -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
>
> * 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] Fwd: atoms are not part of any of the T-Coupling groups

2019-05-08 Thread Justin Lemkul 




On 5/7/19 1:41 AM, ISHRAT JAHAN wrote:

-- Forwarded message -
From: ISHRAT JAHAN 
Date: Tue, May 7, 2019 at 11:05 AM
Subject: atoms are not part of any of the T-Coupling groups
To: 


Dear all,
I am trying to calculate the lennard Jones interaction energy between
protein and urea in the first solvation shell. I have made the index group
of urea molecule in the first solvation shell and then tried to generate
the .tpr file using that index. After running the command
gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
prot_u3M_rerun -n water_urea_5ofprot.ndx
following error occur-
35099 atoms are not part of any of the T-Coupling groups
part of  .mdp file and index file is given below
rvdw=  1.2^M
fourierspacing = 0.12^M
fourier_nx = 0^M
fourier_ny = 0^M
fourier_nz = 0^M
pme_order = 4^M
ewald_rtol = 1e-5^M
optimize_fft = yes^M
; Berendsen temperature coupling is on in two groups^M
Tcoupl  =  V-rescale^M
tc-grps =  Protein   Urea_5ofprot^M
tau_t   =  0.10.1 ^M
ref_t   =  300300   ^M
; Energy monitoring^M
energygrps  =  Protein  Urea_5ofprot
; Isotropic pressure coupling is now on^M
Pcoupl  =  berendsen^M
  and at the end of the Index file i have only added the residue index of
urea within 5 of protein and save the index file.


While you can define whatever energygrps you like (note that the 
molecules will change over time and your results may end up being not 
useful), you need to couple all atoms in the system to a thermostat via 
tc-grps. Your urea selection is only a subset of the urea molecules, and 
if you have any other solvent, ions, etc. they are not being accounted 
for. tc-grps = Protein Non-Protein is almost always the way to go.


-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

* 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] Gromacs2018.5 install with gaussian09 for QM/MM

2019-05-08 Thread Justin Lemkul 



On 5/7/19 9:59 PM, 辛志宏 wrote:

Dear Gromacs support,
I want to install Gromacs 2018.5 with gaussian09 software support in Centos 
system, I try to use “--with-qmmm-gaussian” when I compile gromacs, but it does 
not work. I wonder how to compile gromacs with gaussian support, please help me 
?


The detail command is as follows:

cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs \
   -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx \
   -DGMX_OPENMP=ON \
   -DGMX_FFT_LIBRARY=fftw3 \
   -DFFTWF_LIBRARY="/opt/fftw-3.3.8/lib/libfftw3f.a" \
   -DFFTWF_INCLUDE_DIR="/opt/fftw-3.3.8/include/"  \
   -DGMX_MPI=on \
   -DGMX_CPU_ACCELERATION=AVX_256 \
   --with-qmmm-gaussian \
   2>&1 | tee cm.log
Gromacs 2018.5 compile and install successfully without “--with-qmmm-gaussian \”


That's extremely old syntax using the autoconf build system. What you 
want is -DGMX_QMMM_PROGRAM=GAUSSIAN, but be aware that the QM/MM 
interface in GROMACS is unmaintained and may not even currently work.


-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

* 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] How to calculate tetrahedral order parameter in GROMACS

2019-05-08 Thread Soham Sarkar 
Thanks. I am checking.

On Wed, 8 May 2019, 2:30 pm David van der Spoel, 
wrote:

> Den 2019-05-07 kl. 14:34, skrev Soham Sarkar:
> > Hello,
> >I have two systems. One containing only water and the other one
> > contains protein and water. Using g_select I made water in 1st solvation
> > shell but the use of g_hydorder I cannot understand. I read the
> disscussion
> > so far disscussed. For these two systems which index I need to choose,
> > water or OW? What is the use of sgang1 and sgang2? Any suggestion
> > is appreciated.
> > Thanks and regards
> > Soham
> >
> The tool is not made for anything else than water I'm afraid. Please
> check this paper for details.
>
> Bjorn Steen Sæthre, Alex C. Hoffmann and David van der Spoel: Order
> parameters and algorithmic approaches for detection and demarcation of
> interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor.
> Comput. 10 pp. 5606-5616 (2014)
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * 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] How to calculate tetrahedral order parameter in GROMACS

2019-05-08 Thread David van der Spoel 

Den 2019-05-07 kl. 14:34, skrev Soham Sarkar:

Hello,
   I have two systems. One containing only water and the other one
contains protein and water. Using g_select I made water in 1st solvation
shell but the use of g_hydorder I cannot understand. I read the disscussion
so far disscussed. For these two systems which index I need to choose,
water or OW? What is the use of sgang1 and sgang2? Any suggestion
is appreciated.
Thanks and regards
Soham

The tool is not made for anything else than water I'm afraid. Please 
check this paper for details.


Bjorn Steen Sæthre, Alex C. Hoffmann and David van der Spoel: Order 
parameters and algorithmic approaches for detection and demarcation of 
interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor. 
Comput. 10 pp. 5606-5616 (2014)


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

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

* 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.