[gmx-users] Range of block lengths in gmx energy error estimate only gives one value

[Barnett, James W]

Good morning,

With gmx energy one can specify a range of block lengths to use for the error
estimate using "-nbmin" and "-nbmax". When I specify a range I still only get
one estimate. I would have expected a different estimate for each block length
in the range to be printed to the screen. I'm not understanding what value is
being printed in this case of specifying the range. If someone can give some
insight, that would be helpful.

Thanks,
Wes

-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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] Methanol geometry parameters

[Barnett, James W]

On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote:
> Dear Peter Stern.
> 
> Yes, I need the starting coordination for methanol, but are there specific
> coordinates like for spce water or tip3p water?
> 
> Where can I find the files .gro or .pdb for methanol ?

Creating a methanol pdb file should be quick with a program like Avogadro or
maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for water.

> 
> 
> Dear Chaban
> 
> Similar molecules have already been studied with this methanol.
> 
> This Methanol is implemented in opls force field.
> 
> I appreciate the time and effort you have spent sorting out that problem.
> 
> D.V.
> 
> 
> 2015-12-04 8:41 GMT+01:00 Kalev Takkis :
> 
> > On 3 December 2015 at 20:05, Vitaly V. Chaban  wrote:
> > 
> > > You, perhaps, need to care about *compatibility* of this old methanol and
> > > your solute molecule.
> > > 
> > 
> > 
> > Why? General caution or do you know that there is something wrong with it?
> > Because if I'm not mistaken, it's the same methanol distributed with
> > Gromacs.
> > 
> > All the best,
> > Kalev
> > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern 
> > > wrote:
> > > 
> > > > The force field parameters are defined in ffbonded.itp and
> > > ffnonbonded.itp.
> > > > You still need starting coordinates for your molecule.
> > > > There are plenty of programs which will do this, but you can probably
> > > find
> > > > it in some pdb entry.
> > > > But, it is also trivial to do by hand since there are only two atoms
> > and
> > > > you know the C-O bond distance, e.g.:
> > > > HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
> > > > HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00
> > > > 
> > > > You should use an existing pdb or gro file as a template for the
> > correct
> > > > format.  gmx pdb2gmx will add the H-atoms.
> > > > 
> > > > Peter Stern
> > > > 
> > > > -Original Message-
> > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> > Daniele
> > > > Veclani
> > > > Sent: Thursday, December 03, 2015 3:31 PM
> > > > To: gmx-us...@gromacs.org
> > > > Subject: Re: [gmx-users] Methanol geometry parameters
> > > > 
> > > > Thank you for your reply.
> > > > 
> > > > Yes, The .itp file for methanol comes from gromacs. But but I need the
> > > > .gro file. I need the geometric parameters like distances, angles and
> > > > diedrals.
> > > > these parameters are not in the .itp file or I'm wrong??
> > > > 
> > > > Best regards
> > > > D.V.
> > > > --
> > > > 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
> > 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.
> > 

-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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

Re: [gmx-users] Help with Gromacs-5.1.1 installation in Cluster

[Barnett, James W]

On Fri, 2015-12-04 at 03:32 -0500, Ashalatha Sreshty wrote:
> Dear Gromacs Users,
> 
> I need help with installation of gromacs-5.1.1 which is mpi enabled to run
> it in a cluster. Although, I was able to compile the the source code
> without any errors, I am unable to find the executables in the bin folder.
> Hence, I need your suggestion on how to rectify it. The step-wise commands
> are as below:

I'm guessing you're expecting to see multiple executables like "mdrun",
"grompp", etc.  Anyways, there's one executable now that prefixes every command
(started with 5.0, now required in 5.1). For most installs it is "gmx". For MPI
installs it's probably "gmx_mpi". Do you have one of those? If not, there is a
different issue.

(This question is on the mailing list about once every week or two now, so
perhaps someone with access to the wiki can put this on the FAQ?)

> 
> Compiling fftw library
> 
> tar xvf fftw-3.3.4.tar.gz
> cd fftw-3.3.4
> /configure --enable-threads --with-pic
> --prefix=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4 --enable-sse2
> make
> make install
> 
> Compilation of groamcs-5.1.1
> 
> tar xvf gromacs-5.1.1.tar.gz
> cd gromacs-5.1.1
> mkdir build
> cd build
> 
> CMAKE_PREFIX_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4:/apps/mvapich2-
> cpu/bin/
> 
> CMAKE_INCLUDE_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4/include
> 
> CMAKE_LIBRARY_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4/lib
> 
> /home1/GroupAS/ashalatha/Programs/cmake-3.1.3-Linux-x86_64/bin/cmake ..
> -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX_PREFIX=_mpi_d -DGMX_DOUBLE=ON
> -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/home1/GroupAS/ashalatha/Programs/gromacs-5.1.1
> -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=fftW3
> -DCMAKE_PREFIX_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4
> -DREGRESSIONTEST_PATH=/home1/GroupAS/ashalatha/Programs/regressiontests-5.1.1
> 
> make
> make check
> make install
> make test
> 
> Please advice.
> 
> Thank you in advance.
> 
> Dr. M. Asha Latha Sreshty,
> Post Doctoral Fellow,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> Bangalore



-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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] Multi-node Replica Exchange Segfault

[Barnett, James W]

I added the -debug flag to my two replica test. The end of my mdrun log files
looks like this (right before it segfaults):

Replica exchange at step 11000 time 22.0
Repl 0 <-> 1  dE_term = -6.536e-01 (kT)
  dpV = -3.524e-05  d = -6.537e-01
Repl ex  0 x  1
Repl pr   1.0

Replica Exchange Order
Replica 0:
Replica 1:
Atom distribution over 16 domains: av 1207 stddev 26 min 1165 max 1238

On Fri, 2015-10-30 at 13:08 +, Barnett, James W wrote:
> Hey Mark,
> 
> On Fri, 2015-10-30 at 08:14 +, Mark Abraham wrote:
> > Hi,
> > 
> > I've never heard of such. You could try a multisim without -replex, to help
> > diagnose.
> 
> 
> A multidir simulation runs without issue when -replex is omitted.
> 
> > 
> > On Fri, 30 Oct 2015 03:33 Barnett, James W <jbarn...@tulane.edu> wrote:
> > 
> > > Good evening here,
> > > 
> > > I get a segmentation fault with my GROMACS 5.1 install only for replica
> > > exchange
> > > simulations right at the first successful exchange on a multi-node run.
> > > Normal
> > > simulations across multiple nodes work fine, and replica exchange
> > > simulations on
> > > one node work fine.
> > > 
> > > I've reproduced the problem with just 2 replicas on 2 nodes with GPU's
> > > disabled
> > > (-nb cpu). Each node has 20 CPU's so I'm using 20 MPI ranks on each
> > > (OpenMPI).
> > > 
> > > I get a segfault right when the first exchange is successful.
> > > 
> > > The only other error I get sometimes is that the Infiniband connection
> > > timed out
> > > retrying the communication between nodes at the exact same moment as the
> > > segfault, but I don't get that every time, and it's usually with all
> > > replicas
> > > going (my goal is to do 30 replicas on 120 cpus). No other error logs, and
> > > mdrun's log does not indicate an error.
> > > 
> > > PBS log: http://bit.ly/1P8Vs49
> > > mdrun log: http://bit.ly/1RD0ViQ
> > > 
> > > I'm currently troubleshooting this some with the sysadmin, but I wanted to
> > > check
> > > to see if anyone has had a similar issue or any further steps to
> > > troubleshoot.
> > > I've also searched the mailing list and used my Google-fu, but it has
> > > failed me
> > > so far.
> > > 
> > > Thanks for your help.
> > > 
> 
> -- 
> James "Wes" Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
> 
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarn...@tulane.edu

-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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] Multi-node Replica Exchange Segfault

[Barnett, James W]

Hey Mark,

On Fri, 2015-10-30 at 08:14 +, Mark Abraham wrote:
> Hi,
> 
> I've never heard of such. You could try a multisim without -replex, to help
> diagnose.


A multidir simulation runs without issue when -replex is omitted.

> 
> On Fri, 30 Oct 2015 03:33 Barnett, James W <jbarn...@tulane.edu> wrote:
> 
> > Good evening here,
> > 
> > I get a segmentation fault with my GROMACS 5.1 install only for replica
> > exchange
> > simulations right at the first successful exchange on a multi-node run.
> > Normal
> > simulations across multiple nodes work fine, and replica exchange
> > simulations on
> > one node work fine.
> > 
> > I've reproduced the problem with just 2 replicas on 2 nodes with GPU's
> > disabled
> > (-nb cpu). Each node has 20 CPU's so I'm using 20 MPI ranks on each
> > (OpenMPI).
> > 
> > I get a segfault right when the first exchange is successful.
> > 
> > The only other error I get sometimes is that the Infiniband connection
> > timed out
> > retrying the communication between nodes at the exact same moment as the
> > segfault, but I don't get that every time, and it's usually with all
> > replicas
> > going (my goal is to do 30 replicas on 120 cpus). No other error logs, and
> > mdrun's log does not indicate an error.
> > 
> > PBS log: http://bit.ly/1P8Vs49
> > mdrun log: http://bit.ly/1RD0ViQ
> > 
> > I'm currently troubleshooting this some with the sysadmin, but I wanted to
> > check
> > to see if anyone has had a similar issue or any further steps to
> > troubleshoot.
> > I've also searched the mailing list and used my Google-fu, but it has
> > failed me
> > so far.
> > 
> > Thanks for your help.
> > 

-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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] Multi-node Replica Exchange Segfault

[Barnett, James W]

On Fri, 2015-10-30 at 13:49 +, Mark Abraham wrote:
> Hi,
> 
> That looks like the segfault is coming while re-doing the domain
> decomposition after successful replica exchange. We have a test case for
> that (even NPT REMD), but perhaps nothing in it changes enough to hit the
> problem. Can you please file an issue at http://redmine.gromacs.org and
> attach your .tprs, so we can reproduce where the segfault happens?

Thanks, I'll file a bug report.

> 
> However, I notice you've had a several attempts with ~zero probability, and
> then suddenly 1 because the energy difference between the two replicas has
> changed sign. That's a bit unlikely. Volume doesn't look like it changed
> much. You could try
> a) NVT REMD (to see if that has the problem)

I get the same issue with NVT. Segfault right at the first successful exchange.
Also energy difference between two replicas changed sign here again.

> b) more equilibration before NPT REMD (in case life is just not stable yet,
> but still there'd be a problem for GROMACS to fix)

I will try this and report if it helps on the bug report.

> c) inspecting the energy components near the final step to see what energy
> component has jumped (in case there's a bug somewhere before REMD got
> involved)

Looking through the energy file with gmx energy nothing seems to stand out.

I originally thought that I was having success running on a single node with
replica exchange, but after further testing when it reaches a successful
exchange I still get the segmentation fault.

> 
> 
> On Fri, Oct 30, 2015 at 2:32 PM Barnett, James W <jbarn...@tulane.edu>
> wrote:
> 
> > I added the -debug flag to my two replica test. The end of my mdrun log
> > files
> > looks like this (right before it segfaults):
> > 
> > Replica exchange at step 11000 time 22.0
> > Repl 0 <-> 1  dE_term = -6.536e-01 (kT)
> >   dpV = -3.524e-05  d = -6.537e-01
> > Repl ex  0 x  1
> > Repl pr   1.0
> > 
> > Replica Exchange Order
> > Replica 0:
> > Replica 1:
> > Atom distribution over 16 domains: av 1207 stddev 26 min 1165 max 1238
> > 
> > On Fri, 2015-10-30 at 13:08 +, Barnett, James W wrote:
> > > Hey Mark,
> > > 
> > > On Fri, 2015-10-30 at 08:14 +, Mark Abraham wrote:
> > > > Hi,
> > > > 
> > > > I've never heard of such. You could try a multisim without -replex, to
> > help
> > > > diagnose.
> > > 
> > > 
> > > A multidir simulation runs without issue when -replex is omitted.
> > > 
> > > > 
> > > > On Fri, 30 Oct 2015 03:33 Barnett, James W <jbarn...@tulane.edu>
> > wrote:
> > > > 
> > > > > Good evening here,
> > > > > 
> > > > > I get a segmentation fault with my GROMACS 5.1 install only for
> > replica
> > > > > exchange
> > > > > simulations right at the first successful exchange on a multi-node
> > run.
> > > > > Normal
> > > > > simulations across multiple nodes work fine, and replica exchange
> > > > > simulations on
> > > > > one node work fine.
> > > > > 
> > > > > I've reproduced the problem with just 2 replicas on 2 nodes with
> > GPU's
> > > > > disabled
> > > > > (-nb cpu). Each node has 20 CPU's so I'm using 20 MPI ranks on each
> > > > > (OpenMPI).
> > > > > 
> > > > > I get a segfault right when the first exchange is successful.
> > > > > 
> > > > > The only other error I get sometimes is that the Infiniband
> > connection
> > > > > timed out
> > > > > retrying the communication between nodes at the exact same moment as
> > the
> > > > > segfault, but I don't get that every time, and it's usually with all
> > > > > replicas
> > > > > going (my goal is to do 30 replicas on 120 cpus). No other error
> > logs, and
> > > > > mdrun's log does not indicate an error.
> > > > > 
> > > > > PBS log: http://bit.ly/1P8Vs49
> > > > > mdrun log: http://bit.ly/1RD0ViQ
> > > > > 
> > > > > I'm currently troubleshooting this some with the sysadmin, but I
> > wanted to
> > > > > check
> > > > > to see if anyone has had a similar issue or any further steps to
> > > > > troubleshoot.
> > > > > I've also searched the mailing list and used my Google-fu, but it has
> > > > > failed me
> > > > > so far.
> > > > > 
> > > > > Thanks for your help.
> > > > > 
> > > 

-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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] Multi-node Replica Exchange Segfault

[Barnett, James W]

Good evening here,

I get a segmentation fault with my GROMACS 5.1 install only for replica exchange
simulations right at the first successful exchange on a multi-node run. Normal
simulations across multiple nodes work fine, and replica exchange simulations on
one node work fine.

I've reproduced the problem with just 2 replicas on 2 nodes with GPU's disabled
(-nb cpu). Each node has 20 CPU's so I'm using 20 MPI ranks on each (OpenMPI).

I get a segfault right when the first exchange is successful. 

The only other error I get sometimes is that the Infiniband connection timed out
retrying the communication between nodes at the exact same moment as the
segfault, but I don't get that every time, and it's usually with all replicas
going (my goal is to do 30 replicas on 120 cpus). No other error logs, and
mdrun's log does not indicate an error.

PBS log: http://bit.ly/1P8Vs49
mdrun log: http://bit.ly/1RD0ViQ

I'm currently troubleshooting this some with the sysadmin, but I wanted to check
to see if anyone has had a similar issue or any further steps to troubleshoot.
I've also searched the mailing list and used my Google-fu, but it has failed me
so far.

Thanks for your help.

-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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] gromacs 4.6.7 plumed -Segmentation fault

[Barnett, James W]

On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote:
> Hi,
> 
> I installed gromacs 4.6.7 with plumed like this:
> module swap PrgEnv-cray PrgEnv-gnu
> module load fftw/3.3.4.0
> module load cray-mpich/7.0.5
> module load gsl/1.15
> module load cmake
> #in /lustre/beagle2/ams/new/gromacs make directory lib2
> 
> mkdir lib2
> 
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> 
> tar zxvf plumed-2.2.0.tgz
> cd plumed-2.2.0
> 
> ./configure CC=cc CXX=CC F77=ftn
> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
> --disable-basic-warnings --disable-openmp
> 
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> CC=cc
> FC=gfortran
> LDF90=gfortran
> CFLAGS=-g -O2
> CXX=CC
> CXXFLAGS=-O -fPIC
> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_MOLFILE=1
> -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1
> -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=1
> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
> LDFLAGS=
> DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/groplu/lib2
> LIBS=-ldl
> SOEXT=
> LD=CC
> LDSO=CC -shared
> GCCDEP=CC
> prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1
> ###
> 
> make
> make install
> 
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> 
> #1. Make a directory for modulefiles (e.g.
> /lustre/beagle2/ams/new/modulefiles/)
> #2. Copy file: cp
> /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
> /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
> #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
> #4. type "module load plumed/2.2.0"
> 
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
> module use /lustre/beagle2/ams/new/modulefiles/
> module load plumed/2.2.0
> 
> ### instal gromacs 4.6.7
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
> tar zxvf gromacs-4.6.7.tar.gz
> cd gromacs-4.6.7/
> ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> --static
> 
> 
> PLUMED patching tool
> 
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) qespresso-5.0.2
> 
> Choose the best matching code/version:3
> 
> mkdir build
> cd build
> 
> 
> export BUILD_WITH_INSTALL_RPATH=TRUE
> export INSTALL_RPATH=""
> export SKIP_BUILD_RPATH=TRUE
> export
> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
> 
> #in /lustre/beagle2/ams/new/gromacs make directory lib
> 
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
> 
> 
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-
> gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-
> gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default
> /lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/li
> b64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/defau
> lt/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos
> /lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/de
> fault/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_
> detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7/build
> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
> -DCMAKE_SKIP_RPATH=ON
> 
> 
> make
> make install
> 
> I am getting Segmentation error if I run it like this:
> 
> #!/bin/bash
> #PBS -N test
> #PBS -j oe
> #PBS -l walltime=01:00:00
> #PBS -l mppwidth=96
> 
> source /opt/modules/default/init/bash
> 
> cd $PBS_O_WORKDIR
> module swap PrgEnv-cray PrgEnv-gnu
> export 

Re: [gmx-users] Gromacs and Gcc5.2

[Barnett, James W]

On Fri, 2015-10-02 at 09:57 +0200, Nicolas Cheron wrote:
> Dear all,
> 
> I am wondering if there is an official statement regarding compiling
> Gromacs with gcc5.2.0 (or any gcc from the 5.x branch). Is it recommended
> or not? Should we expect improvements? 

I don't think there is an official statement other than that versions 4.7 and
above are required. I use 5.2.0 on several systems without any problems. I know
that more recent gcc versions have better SIMD support, so if you're upgrading
from 4.8 series you should see improvements.


> I have tried quickly some small
> benchmarks (with Gromacs 4.6.3 and Gromacs 5.1) and found improvement on
> ns/day between 1 and 3% (with respect to gcc4.8.5).
> 
> Also, during compilation I get several warnings such as:
> 
> In file included from /usr/local/openmpi-gnu/include/mpi.h:253:0,
>  from
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/utility/gmxmpi.h:59,
>  from
> /home2/ncheron/Programs/gromacs
> -5.1/src/gromacs/legacyheaders/types/commrec.h:45,
>  from
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/gmx_ga2la.h:40,
>  from
> /home2/ncheron/Programs/gromacs
> -5.1/src/gromacs/domdec/domdec_constraints.cpp:55:
> /usr/local/openmpi-gnu/include/mpi_portable_platform.h:374:34: warning:
> invalid suffix on literal; C++11 requires a space between literal and
> string macro [-Wliteral-suffix]
> 
> _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEV
> EL__)
> 
> I don't think it is relevant and I am not worried about it, but just wanted
> to check with you.

It looks like to me the warning is generated from your OpenMPI library that
GROMACS links to and not GROMACS itself. I suggest updating OpenMPI to the
latest version and compiling with GCC 5.2 as well.

-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.ed
-- 
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] GMXLIB does not induce residuetype.dat

[Barnett, James W]

On Thu, 2015-10-01 at 20:21 +, Ebert Maximilian wrote:
> Dear list,
> 
> I have my own force field working folder so I cloned the entire top folder to
> no mess with the original files. I added residues to the residue type file to
> add my residues to the protein group. My FF is included due to the GMXLIB
> environmental variable but my modified residuestype.dat not. Any idea why?

Can you give an example of how it is not included? Is there a specific GROMACS
command that is not finding it, or is it something else?

-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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] GROMACS OPLS-AA question

[Barnett, James W]

On Thu, 2015-09-10 at 11:32 -0600, Eric Smoll wrote:
> Hello GROMACS users,
> 
> I am interested in using the OPLS-AA as implemented in GROMACS.
> The OPLS-AA forcefield omits all nonbonded (Coulomb and LJ)
> interactions 1
> and 2 bonds away. Nonbonded interactions 3 bonds are away are scaled
> by
> 1/2. Nonbonded interactions are applied without modification for
> atoms 4 or
> more bonds away or between atoms in different molecules.
> 
> In GROMACS, this is accomplished by excluding Coulomb and LJ
> interactions
> 1, 2, and 3 bonds away with the following directive:
> 
> [ moleculetype ]
> ; name nrexcl
> System 3
> 
> The scaled intramolecular interaction at 3 bonds away is added in
> separately as a "pair" interaction. This is either done manually with
> "[
> pairtypes ]" and "[ pairs ]"  directives or automatically by
> including
> "yes" as the third entry under the "[ defaults ]" directive.
> 
> *Is this correct?*

Essentially this is correct. 1-2, 1-3, and 1-4 nonbonded interactions
are excluded when the number of exclusions is 3. With [ pairs ] and [
pairtypes ] 1-4 nonbonded interactions can be explicitly added back
(the point is that you 1-4 nonbonded interactions typically have
different parameters, so the normal non-bonded parameters for 1-4 are
excluded and then different parameters are added back with [pairs]).
OPLS doesn't do that, but instead generates the 1-4 nonbonded
interactions as specified in the [ defaults ] section.

> 
> The manual states that "the use of [Ryckaert-Bellemans potential
> functions]
> implies exclusion between the first and last atom of the dihedral."
> *This
> statement is referring to the use of  nrexcl=3 in the "[ moleculetype
> ]"
> directive as shown above, correct? The use of RB dihedral functions
> in
> GROMACS does not imply that the scaled "pair" interactions are not
> applied,
> correct?*

My understanding is it is saying 1-4 nonbonded interactions should be
excluded by setting nrexcl=3 when using RB dihedral functions. Clearly
OPLS uses the RB form in GROMACS and generates pairs, so pairs (either
generated or set with [ pairs ]), still apply.

That's my understanding - but you could test it out by setting generate
pairs to no in the [ defaults ] section and see if GROMACS complains
that [ pairs ] is missing even with the RB form of the potential. My
guess is that it will.


-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
-- 
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 create a spherocylindrical wall

[Barnett, James W]

On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> Hi
>   I would like to perform a simulation ( without any periodic
> boundary
> condition) where I need to have a wall of spherocylindrical geometry.
> In
> other words the particles will be confined inside a spherocylinder.
> 
>  Is there any good suggestion on how to achieve that in gromacs?
> 
> 1) One option I thought of achieving that is by having a
> spherocylindrical
> wall potential.  Is there a way of putting the wall potential in the
> form
> of a table-potential ? (Not sure cylinder option in gromacs umbrella
> sampling  not going to be helpful).

This might be do-able and would not require a table potential. Check
out flat-bottom restraints in section 4.3.2 in the reference (PDF)
manual.

> 
> 2)  Or,should I put a bunch of hard sphere which constitute the
> spherocylindrical boundary so that the particles inside the
> spherocylinder
> will have a repulsive interaction each time they come towards the
> boundary ?

I'm not sure how you would implement this in a simple way with GROMACS.


-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.ed
-- 
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] Pull parameters to Restrain motion along the Z Axis

[Barnett, James W.]

 suppose distance between center of masses of protein and DPPC is say
 2.5 in
 the z direction and if pull_start =yes and pull_init is 1.0 then
 sampling
 will be at center of mass distance = 3.5 in only Z direction, since I
 have
 selected N N Y.

That's correct.

 
 and if pull_start =No and pull_init is 1.0 then sampling will be done
 at
 center of mass distance = 1 in only Z direction.

That's correct.

 
 Well,I am using that pull in each mdp file ( minimization,
 equilibration
 and Production). Is that a problem ?

That's fine.

 It remains nearly at the similar
 distance as 0th frame throughout the simulations in Z direction.

You may be near an energy barrier if you are sure that you have set the
pull settings correctly, so you might have to increase the spring
constant k in the pull code to get it exactly where you want it.


 I am sorry for the misunderstanding. I want to allow my protein only
 move
 in x, y direction. I am restricting it so It can't move be in Z
 direction.

There might be other ways to do that with restraints, but this may give
you the result you want, too.

 
 On Wed, Aug 26, 2015 at 8:38 PM, Barnett, James W 
 jbarn...@tulane.edu
 wrote:
 
  pull_start = yes means COM distance is added to the pull_init
  value. So
  whatever distance your two pull groups starts out at plus pull_init
  is the
  window where it will sample.
  
  pull_start = no means just the pull_init value is used as the
  reference
  distance. If you have pull_init set to 1.0 then that is the
  reference
  distance for sampling (the window where it will sample).
  
  If you haven't equilibrated at the reference distance it could take
  a
  little bit for your two groups to get to the reference distance. At
  t=0
  nothing has moved yet, unless you have equilibrated with the same
  pull code
  parameters already (and you probably should, depending on what your
  goal is
  here), so you should not expect the distance between the two groups
  to
  already be near the reference distance before the simulation has
  begun.
  
  If you're looking to restrain the protein's movement to the z-axis
  such
  that it can only move along the z-axis, this is not what you'll be
  achieving. Here are you restricting the movement of the protein
  along the
  z-axis but it is free to move in the x and y directions. I may be
  misunderstanding your goal here. There are some flat-bottom
  restraints you
  can add to make it such that the protein only moves in one
  direction if
  that's your goal. Check the relevant sections in the manual.
  
  --
  James “Wes” Barnett, Ph.D. Candidate
  Louisiana Board of Regents Fellow
  Chemical and Biomolecular Engineering
  
  Tulane University
  341-B Lindy Boggs Center for Energy and Biotechnology
  6823 St. Charles Ave
  New Orleans, Louisiana 70118-5674
  jbarn...@tulane.edu
  
  
  
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of
  Live King
  vikasdubey1...@gmail.com
  Sent: Wednesday, August 26, 2015 5:25 AM
  To: gromacs.org_gmx-users@maillist.sys.kth.se
  Subject: [gmx-users] Pull parameters to Restrain motion along the Z
  Axis
  
  Hi,
  
  I use Gromacs 4.5.5. I have these pull parameters which I use to
  restrain
  my Protein motion along the Z axis.I want to make sure these
  parameters are
  fine or not since , I am not getting expected results.
  Also, please suggest any other parameters I can add.
  
  ;Pull to restrain Z position
  pull = umbrella
  pull_geometry= distance
  ; Select components for the pull vector. default: Y Y Y
  pull_dim = N N Y
  pull_start   = No
  pull_nstxout = 1
  pull_nstfout = 1
  pull_ngroups = 1
  pull_group0  = DPPC
  pull_group1  = Protein
  pull_vec1= 0.0 0.0 0.0
  pull_init1   = 1.0
  pull_rate1   = 0
  pull_k1  = 1000
  pull_kB1 = 1000
  
  
  Here I am completely confused in pull_init and pull_start. From my
  understanding, pull_init is the reference distance at t=0. The
  reference
  distance is the distance between COM of the pull group and COM of
  the
  reference group.I have set my reference group as DPPC and pull
  group as
  Protein, which means my Z_distance should be Ideally ~ 1.00 if my
  pull_start is set up as  No and should be ~0.0 if that is set it
  as
  Yes.Since, pull_start means the initial COM distance is the
  reference
  distance for the first frame.
  
   But my values are instead after the production run:-
  
   with pull_init =1.0 and pull_start = Yes
   time  |d| dx
  dy dz
 0.0004.53616050.98503492.36917383.7407854
  
   with pull_init =1.0 and pull_start= No
  
 0.0002.82224150.78675102.5469491   -0.9268878

Re: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

[Barnett, James W]

Look into the pull code. You'll want to choose two groups (one for the ligand, 
one for the binding site), and one coordinate with those groups where the pull 
rate is not zero (negative rate to bring them together, positive rate to pull 
them apart).

--
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow
Chemical and Biomolecular Engineering

Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Victor Ma 
victordsmag...@gmail.com
Sent: Wednesday, August 26, 2015 12:31 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] what's the easiest way to generate a md trajectory for 
ligand flying into/being pulled out of the pocket?

hello all

I got a urgent request to make a MD movie for pulling the ligand out of the
binding site/or the ligand flying into the pocket . I feel like i need to
run something like steered md, which I've never done before. So can anyone
please suggest a quick and dirty way to generate such a movie?

Thank you!!

Victor
--
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] Pull parameters to Restrain motion along the Z Axis

[Barnett, James W]

pull_start = yes means COM distance is added to the pull_init value. So 
whatever distance your two pull groups starts out at plus pull_init is the 
window where it will sample.

pull_start = no means just the pull_init value is used as the reference 
distance. If you have pull_init set to 1.0 then that is the reference distance 
for sampling (the window where it will sample).

If you haven't equilibrated at the reference distance it could take a little 
bit for your two groups to get to the reference distance. At t=0 nothing has 
moved yet, unless you have equilibrated with the same pull code parameters 
already (and you probably should, depending on what your goal is here), so you 
should not expect the distance between the two groups to already be near the 
reference distance before the simulation has begun.

If you're looking to restrain the protein's movement to the z-axis such that it 
can only move along the z-axis, this is not what you'll be achieving. Here are 
you restricting the movement of the protein along the z-axis but it is free to 
move in the x and y directions. I may be misunderstanding your goal here. There 
are some flat-bottom restraints you can add to make it such that the protein 
only moves in one direction if that's your goal. Check the relevant sections in 
the manual.

--
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow
Chemical and Biomolecular Engineering

Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Live King 
vikasdubey1...@gmail.com
Sent: Wednesday, August 26, 2015 5:25 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Pull parameters to Restrain motion along the Z Axis

Hi,

I use Gromacs 4.5.5. I have these pull parameters which I use to restrain
my Protein motion along the Z axis.I want to make sure these parameters are
fine or not since , I am not getting expected results.
Also, please suggest any other parameters I can add.

;Pull to restrain Z position
pull = umbrella
pull_geometry= distance
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
pull_start   = No
pull_nstxout = 1
pull_nstfout = 1
pull_ngroups = 1
pull_group0  = DPPC
pull_group1  = Protein
pull_vec1= 0.0 0.0 0.0
pull_init1   = 1.0
pull_rate1   = 0
pull_k1  = 1000
pull_kB1 = 1000


Here I am completely confused in pull_init and pull_start. From my
understanding, pull_init is the reference distance at t=0. The reference
distance is the distance between COM of the pull group and COM of the
reference group.I have set my reference group as DPPC and pull group as
Protein, which means my Z_distance should be Ideally ~ 1.00 if my
pull_start is set up as  No and should be ~0.0 if that is set it as
Yes.Since, pull_start means the initial COM distance is the reference
distance for the first frame.

 But my values are instead after the production run:-

 with pull_init =1.0 and pull_start = Yes
 time  |d| dx
dy dz
   0.0004.53616050.98503492.36917383.7407854

 with pull_init =1.0 and pull_start= No

   0.0002.82224150.78675102.5469491   -0.9268878


my protein is nearly at the center of membrane of box size

 7.34147   7.34147   7.34147

If somebody can help me I will be grateful.

Thanks,
Vikas
--
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] Free energy calculations (FEP) and soft core potential 1-1-48

[Barnett, James W]

I was experiencing something similar with 1-1-48, and after switching back to 
1-1-6 my system ran fine  There's a discussion on Redmine about it (see the 
last couple of posts): http://redmine.gromacs.org/issues/1770

This doesn't solve your issue, but it indicates that you may be experiencing a 
bug when you use 1-1-48.

--
James “Wes”​ Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian 
Zachmann frankjulian.zachm...@uab.cat
Sent: Wednesday, July 15, 2015 11:51 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Free energy calculations (FEP) and soft core potential 
1-1-48

It just crashes... Without any error message.
I am now re-running the simulations with fewer lambda points and for 5ns.

Let's see what comes up.

2015-07-15 18:12 GMT+02:00 Barnett, James W jbarn...@tulane.edu:

 Do you get any output with the crash? Or is it just a segmentation fault?

 --
 James “Wes”​ Barnett
 Ph.D. Candidate
 Chemical and Biomolecular Engineering

 Tulane University
 Boggs Center for Energy and Biotechnology, Room 341-B
 New Orleans, Louisiana 70118
 jbarn...@tulane.edu​
 LinkedIn​​


 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian
 Zachmann frankjulian.zachm...@uab.cat
 Sent: Wednesday, July 15, 2015 9:20 AM
 To: gromacs.org_gmx-users@maillist.sys.kth.se
 Subject: [gmx-users] Free energy calculations (FEP) and soft core
 potential 1-1-48

 Dear Gromacs Users,

 I am running free energy calculations (FEP) to estimate relative binding
 affinities. So far, my results don't match the experimental results (not
 even close), so I must be doing something wrong.

 My protocol is the following:

 - Energy minimisation
 - Leap frog minimisation
 - 0.1ns  NVT
 - 2nsSimulated Annealing up to 350K
 - 0.1ns  NPT
 - 1ns MD production run

 During the whole equilibration time I am using umbrella pulling to maintain
 an interaction between one residue and the ligand (especially important
 during SA) but I remove it for MD because I am afraid it would influence my
 results (even though I don't know it for sure).

 The simulation time for 1ns is quite short of course but I have 'nstdhdl'
 put to 10 to get a lot of output.

 The other settings are pasted below. So far I was using 1-1-6 for the soft
 core potential but because the results were not good, I was thinking to try
 1-1-48. However in this case the simulations always crash. Has anybody run
 successfully 1-1-48 soft core potentials in Gromacs and how did you chose
 your settings? Like me pasted below?

 Any other suggestions about what I am doing wrong?
 Could I maintain the pull distance constraint during the MD simulation?

 Best regards,
 Julian

 free_energy  = yes
 init_lambda_state= $i
 ;   0  1  2  3  4  5  6
  7  8  9 10 11 12 13 14 15 16 17
   18 19 20 21 22 23 24 25 26 27 28
 29 30 31 32 33 34 35 36 37 38
 39 40 41 42 43 44 45 46 47 48 49
   50 51 52 53 54 55 56 57 58 59 60
 61 62 63 64 65 66 67 68 69 70
 71 72 73 74 75 76 77 78 79 80 81
   82 83 84 85 86 87 88 89 90 91 92
 93 94 95 96 97 98 99
 fep_lambdas = 0. 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800
 0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800
 0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800
 0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1. 1. 1. 1.
 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
 1. 1. 1.
 vdw_lambdas = 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0.0500 0.1000 0.1500
 0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500
 0.7000 0.7500 0.8000 0.8200 0.8500

Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48

[Barnett, James W]

Do you get any output with the crash? Or is it just a segmentation fault?

--
James “Wes”​ Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian 
Zachmann frankjulian.zachm...@uab.cat
Sent: Wednesday, July 15, 2015 9:20 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Free energy calculations (FEP) and soft core potential 
1-1-48

Dear Gromacs Users,

I am running free energy calculations (FEP) to estimate relative binding
affinities. So far, my results don't match the experimental results (not
even close), so I must be doing something wrong.

My protocol is the following:

- Energy minimisation
- Leap frog minimisation
- 0.1ns  NVT
- 2nsSimulated Annealing up to 350K
- 0.1ns  NPT
- 1ns MD production run

During the whole equilibration time I am using umbrella pulling to maintain
an interaction between one residue and the ligand (especially important
during SA) but I remove it for MD because I am afraid it would influence my
results (even though I don't know it for sure).

The simulation time for 1ns is quite short of course but I have 'nstdhdl'
put to 10 to get a lot of output.

The other settings are pasted below. So far I was using 1-1-6 for the soft
core potential but because the results were not good, I was thinking to try
1-1-48. However in this case the simulations always crash. Has anybody run
successfully 1-1-48 soft core potentials in Gromacs and how did you chose
your settings? Like me pasted below?

Any other suggestions about what I am doing wrong?
Could I maintain the pull distance constraint during the MD simulation?

Best regards,
Julian

free_energy  = yes
init_lambda_state= $i
;   0  1  2  3  4  5  6
 7  8  9 10 11 12 13 14 15 16 17
  18 19 20 21 22 23 24 25 26 27 28
29 30 31 32 33 34 35 36 37 38
39 40 41 42 43 44 45 46 47 48 49
  50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66 67 68 69 70
71 72 73 74 75 76 77 78 79 80 81
  82 83 84 85 86 87 88 89 90 91 92
93 94 95 96 97 98 99
fep_lambdas = 0. 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800
0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800
0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800
0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1. 1. 1. 1.
1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
1. 1. 1. 1. 1. 1. 1. 1. 1. 1.
1. 1. 1.
vdw_lambdas = 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0. 0. 0. 0. 0.0500 0.1000 0.1500
0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500
0.7000 0.7500 0.8000 0.8200 0.8500 0.8700 0.8800 0.8900 0.9000 0.9100
0.9200 0.9300 0.9350 0.9400 0.9450 0.9500 0.9530 0.9570 0.9600 0.9630
0.9670 0.9700 0.9730 0.9770 0.9800 0.9820 0.9840 0.9860 0.9880 0.9900
0.9910 0.9920 0.9930 0.9940 0.9950 0.9955 0.9960 0.9965 0.9970 0.9975
0.9980 0.9983 0.9987 0.9990 0.9992 0.9993 0.9994 0.9995 0.9996 0.9997
0.9998 0. 1.
; 1-1-6
sc-coul= no
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
sc-r-power   = 6
; 1-1-48
;sc-coul   = no   ;
;sc-alpha = 0.0025   ; either 0.5 (sc-r-power = 6) or
0.0025 (sc-r-power = 48)
;sc-power= 1; 1 or 2
;sc-sigma= 0.3  ; default 0.3
;sc-r-power  = 48   ; possible 6, 48
calc-lambda-neighbors= -1
nstdhdl  = 10
dhdl-derivatives = yes
separate-dhdl-file   = yes
--
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

Re: [gmx-users] solvation by ethanol

[Barnett, James W]

This was a different force field, but the idea remains the same:
http://statthermo.blogspot.com/2015/06/using-another-solvent-besides-water-in.html

--
James “Wes”​ Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kumar Meena, 
Santosh kumar...@uni-mainz.de
Sent: Monday, June 29, 2015 5:13 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] solvation by ethanol

Dear all,


I would like to use ethanol as solvent. could you please suggest me the easy 
way to solvate  with ethanol using gromos forcefiled.


Regards,

Santosh Kumar
Institute of Physics, Johannes Gutenberg University Mainz,
Staudinger Weg 7
55099 Mainz
Germany.
?
--
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] Atomtype OW not found

[Barnett, James W]

What does your topology (.top) file look like? And what's the exact command you 
are using for grompp?

--
James “Wes”​ Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Rasha Alqus 
rasha.al...@manchester.ac.uk
Sent: Wednesday, June 3, 2015 8:39 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Atomtype OW not found

Dear Gromacs users,
I am trying to run an md of carbohydrate systems in water, the pdb of 
carbohydrate produced in glycame builder, files were loaded in amber to produce 
topolgy file and coordinate using glycame force file.
I have run glycam2gmx.pl script to convert files into gromacs ones. I would 
like to solavte the sytem using tip5p, but when i run the grompp i get an error

program grompp_d, VERSION 4.5.4
Source code file: toppush.c, line: 1166
Fatal error:
Atomtype OW not found
For more information and tips for troubleshooting, please check the GROMACS

I also tried to do that with other water model and it give me the same issue, 
can you please help me to solve that issue.

Thank for the help
Regards
rasha





--
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] User directive for non-bonded interactions

[Barnett, James W]

Just to weigh in, I think the unclear part is that the section itself is in the 
printed manual (pdf file). The online manual is copied verbatim into the 
printed manual as section 7, so statements like that remain.

--
James “Wes”​ Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul 
jalem...@vt.edu
Sent: Friday, May 29, 2015 7:14 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] User directive for non-bonded interactions

On 5/29/15 8:12 AM, Peter Kroon wrote:
 Hi João,

 That's where it states More information is in the printed manual.


Section 6.10 of the printed manual should cover the details.  Is something there
unclear?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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 assign options of the same type?

[Barnett, James W]

If you use -deffnm it gives the same prefix to all files that are output (and 
requires the same prefix on the .tpr file that is input).

For example, if your tpr file is md.ttr you could do

gmx mdrun -deffnm md

Your checkpoint files will be named md.cpt and your trr files will be named 
md.trr, as well as anything else that is being output as specified in the mdp 
file you used with grompp (energy files, gro files, xtc files, etc).

--
James “Wes”​ Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul 
jalem...@vt.edu
Sent: Sunday, May 24, 2015 7:55 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] how to assign options of the same type?

On 5/24/15 8:29 AM, Zhang, Cheng wrote:
 Dear GROMACS,

 Can I ask how to assign options of the same type?


 For example, on the website of

 http://manual.gromacs.org/current/programs/gmx-mdrun.html


 It is said in the Synopsis:


 [-o [.trr/.cpt/...]


 I want to name the output files as md.trr and md.cpt. However, the followings 
 do not work:


 -o md.trr md.cpt

 -o md.trr/md.cpt

 -o md.trr -o md.cpt


 So do you know what is the syntax?


You can't specify multiple files to any option that is not labeled Mult.  In
the case of mdrun -o, that is the output trajectory format.  The general help
info in the synopsis indicates that this file type may be interchangeable in a
general sense, but here it is somewhat misleading.  You shouldn't try to output
a checkpoint file in lieu of your trajectory.  The .cpt is produced
(automatically) with -cpo.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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] Generate the water box

[Barnett, James W]

Use gmx editconf first to create the box then gmx solvate to fill it with 
water (omitting -box directive this time).

--
James Wes Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Vy Phan 
phanvy120...@gmail.com
Sent: Thursday, May 21, 2015 8:36 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Generate the water box

Dear all,
I can generate the cubic box or the rectangular box  with gmx solvate -cs
water.gro -box
 but I would like to have the octahedron box.I try many way but I can not.
How I can do it?

Thank a lot
Tuong Vy

2015-05-21 1:49 GMT+09:00 Justin Lemkul jalem...@vt.edu:



 On 5/20/15 11:55 AM, 姚懿 wrote:

 genbox without adding a protein.


 More specifically (and for 5.0):

 gmx solvate -cs water.gro -box (whatever size is needed)

 -Justin

  On Wed, May 20, 2015 at 9:56 AM, Vy Phan phanvy120...@gmail.com wrote:

  Dear Gromacs Users,

 Can I generate only water on the Gromacs? I need water box only.

 Thank you
 Tuong Vy
 --
 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.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==

 --
 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] Editconf error

[Barnett, James W]

It'd be more helpful for troubleshooting your problem if you post the entire 
file in each case, not just parts of them. If it's a large file use 
Pastebin.com or something similar.

--
James Wes Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarn...@tulane.edu​
LinkedIn​​



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Jorge Dagnino 
jdagn...@gmail.com
Sent: Friday, May 22, 2015 11:06 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Editconf error

Here are the coordinates from my pdb file:

ATOM  1  N   MET G  27  69.331  43.147  76.443  1.00  0.00
  N
ATOM  2  CA  MET G  27  68.996  44.047  75.331  1.00  0.00
  C
ATOM  3  C   MET G  27  67.818  43.550  74.510  1.00  0.00
  C
ATOM  4  O   MET G  27  66.981  44.264  73.969  1.00  0.00
  O
ATOM  5  CB  MET G  27  70.152  44.201  74.325  1.00  0.00
  C
ATOM  6  CG  MET G  27  70.024  45.547  73.614  1.00  0.00
  C
ATOM  7  SD  MET G  27  70.710  46.841  74.678  1.00  0.00
  S
ATOM  8  CE  MET G  27  70.252  48.118  73.481  1.00  0.00
  C
ATOM  9  N   ALA G  28  67.504  42.250  74.523  1.00  0.00
  N
ATOM 10  CA  ALA G  28  66.247  41.666  74.095  1.00  0.00
  C
ATOM 11  C   ALA G  28  64.968  42.391  74.469  1.00  0.00
  C
ATOM 12  O   ALA G  28  64.064  42.543  73.651  1.00  0.00
  O
ATOM 13  CB  ALA G  28  66.323  40.167  74.396  1.00  0.00
  C
ATOM 14  N   GLU G  29  64.839  42.732  75.756  1.00  0.00
  N
ATOM 15  CA  GLU G  29  63.656  43.315  76.334  1.00  0.00
  C
ATOM 16  C   GLU G  29  63.567  44.789  75.955  1.00  0.00
  C
ATOM 17  O   GLU G  29  62.480  45.354  75.850  1.00  0.00
  O
ATOM 18  CB  GLU G  29  63.662  43.143  77.854  1.00  0.00
  C
ATOM 19  CG  GLU G  29  64.822  43.835  78.553  1.00  0.00
  C
ATOM 20  CD  GLU G  29  64.794  43.644  80.055  1.00  0.00
  C
ATOM 21  OE1 GLU G  29  63.801  44.058  80.689  1.00  0.00
  O
ATOM 22  OE2 GLU G  29  65.765  43.078  80.601  1.00  0.00
  O1-

And here are the coordinates from the .gro file

Giant Rising Ordinary Mutants for A Clerical Setup
16231
   27MET  N1   6.933   4.315   7.644
   27MET H12   7.011   4.352   7.695
   27MET H23   6.854   4.307   7.705
   27MET H34   6.957   4.224   7.608
   27MET CA5   6.900   4.405   7.533
   27MET HA6   6.878   4.489   7.582
   27MET CB7   7.015   4.420   7.432
   27METHB18   7.103   4.416   7.481
   27METHB29   7.011   4.346   7.365
   27MET CG   10   7.002   4.555   7.361
   27METHG1   11   7.052   4.545   7.275
   27METHG2   12   6.905   4.567   7.343
   27MET SD   13   7.071   4.684   7.468
   27MET CE   14   7.025   4.812   7.348
   27METHE1   15   7.053   4.901   7.383
   27METHE2   16   7.071   4.794   7.261
   27METHE3   17   6.926   4.811   7.334
   27MET  C   18   6.782   4.355   7.451
   27MET  O   19   6.698   4.426   7.397
   28ALA  N   20   6.750   4.225   7.452
   28ALA  H   21   6.820   4.162   7.486
   28ALA CA   22   6.625   4.167   7.410
   28ALA HA   23   6.620   4.184   7.311
   28ALA CB   24   6.632   4.017   7.440
   28ALAHB1   25   6.547   3.973   7.411
   28ALAHB2   26   6.709   3.976   7.389
   28ALAHB3   27   6.646   4.003   7.538
   28ALA  C   28   6.497   4.239   7.447
   28ALA  O   29   6.406   4.254   7.365
   29GLU  N   30   6.484   4.273   7.576
   29GLU  H   31   6.562   4.257   7.636
   29GLU CA   32   6.366   4.332   7.633
   29GLU HA   33   6.289   4.281   7.594
   29GLU CB   34   6.366   4.314   7.785
   29GLUHB1   35   6.281   4.352   7.822
   29GLUHB2   36   6.371   4.217   7.806
   29GLU CG   37   6.482   4.384   7.855
   29GLUHG1   38   6.568   4.346   7.820
   29GLUHG2   39   6.478   4.481   7.836
   29GLU CD   40   6.479   4.364   8.005
   29GLUOE1   41   6.380   4.406   8.069
   29GLUOE2   42   6.576   4.308   8.060
   29GLU  C   43   6.357   4.479   7.595
   29GLU  O   44   6.248   4.535   7.585

and this is the output from editconf.

Giant Rising Ordinary Mutants for A Clerical Setup
16231
   27MET  N1-nan-nan-nan
   27MET H12-nan-nan-nan
   27MET H23-nan-nan-nan
   27MET H34-nan-nan-nan
   27MET CA5-nan-nan-nan
   27MET HA6-nan-nan-nan
   27MET CB7-nan-nan-nan
   27METHB18-nan-nan-nan
   27METHB29-nan-nan-nan
   27MET CG   10-nan-nan-nan
   27METHG1   11-nan-nan-nan
   27METHG2   

Re: [gmx-users] GPU low performance

[Barnett, James W]

What's your exact command?

Have you reviewed this page: 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization

James Wes Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Carmen Di 
Giovanni cdigi...@unina.it
Sent: Wednesday, February 18, 2015 10:06 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] GPU low performance

I post the message of a md run :


Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677
For optimal performance this ratio should be close to 1!


NOTE: The GPU has 20% more load than the CPU. This imbalance causes
   performance loss, consider using a shorter cut-off and a finer PME grid.

As can I solved this problem ?
Thank you in advance


--
Carmen Di Giovanni, PhD
Dept. of Pharmaceutical and Toxicological Chemistry
Drug Discovery Lab
University of Naples Federico II
Via D. Montesano, 49
80131 Naples
Tel.: ++39 081 678623
Fax: ++39 081 678100
Email: cdigi...@unina.it



Quoting Justin Lemkul jalem...@vt.edu:



 On 2/18/15 10:30 AM, Carmen Di Giovanni wrote:
 Daear all,
 I'm working on a machine with an INVIDIA Teska K20.
 After a minimization on a protein of 1925 atoms this is the mesage:

 Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
 For optimal performance this ratio should be close to 1!


 Minimization is a poor indicator of performance.  Do a real MD run.


 NOTE: The GPU has 25% less load than the CPU. This imbalance causes
 performance loss.

 Core t (s) Wall t (s) (%)
 Time: 3289.010 205.891 1597.4
 (steps/hour)
 Performance: 8480.2
 Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015


 Cai I improve the performance?
 At the moment in the forum I didn't full informations to solve this problem.
 In attachment there is the log. file


 The list does not accept attachments.  If you wish to share a file,
 upload it to a file-sharing service and provide a URL.  The full
 .log is quite important for understanding your hardware,
 optimizations, and seeing full details of the performance breakdown.
  But again, base your assessment on MD, not EM.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 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] Can only find GPU'S on first node

[Barnett, James W]

Have you tried using:

 mpirun -np (number of mpi-processes total)  -npernode (number of gpus per 
 node) .

when you execute mdrun? Not sure if it will do the trick, but it looks like it 
may work. What that command should do it limit the number of mpi-process to 
the number of gpus (so that each node uses all of the gpus, one per mpi 
process).

-Micholas

Hey Micholas, works perfectly. Thanks. Wes
-- 
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] [ constraints ] in .rtp database not recognized by pdb2gmx

[Barnett, James W]

I'm using fixed bond lengths from TRAPPE-UA with [ constraints ] type 1. I'm 
attempting to place constraints in an .rtp file for use with pdb2gmx, but it 
looks like GROMACS doesn't recognize the keyword in that case. It thinks it is 
a new residue name:

Fatal error:
in .rtp file in residue constraints at line:
   C1C

This is my .rtp 
filehttps://gist.githubusercontent.com/wesbarnett/93b27158fd49994eeac4/raw/845c56be6e4f0374c4ade7b901ec76f7184ba38b/npa.rtp.
 The force field is set up properly, since when I replace [ constraints ]  
with [ bonds ]  pdb2gmx works fine (after which I manually change [ bonds ] 
to [ constraints ] in the generated topol.top file and am able to run the 
simulation normally).


Is the [ constraints ] directive supported for pdb2gmx? I've searched the 
manual but don't see if this is supported.


Thanks,


James Wes Barnett

Ph.D. Candidate

Chemical and Biomolecular Engineering


Tulane University

Boggs Center for Energy and Biotechnology, Room 341-B
-- 
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] Comb. Rule 2 LJ Params. Being Stored in .tpr as Rule 1 and Vice Versa?

[Barnett, James W]

I have combination rule set as 2 in my [ defaults ] section. However, when I do 
gmx grompp and then gmx dump on the .tpr file, the values indicate they are 
being stored as combination 1. My understanding from the manual section 5.3.2 
is that for combination rule 2 the last two values on an [ atomtypes ] line are 
sigma and epsilon. But, the values stored in the .tpr file are c6 (4*eps*sig^6) 
and c12 (4*eps*sig^12) according to gmx dump.


Here is an example line from my topology and the corresponding line from gmx 
dump for both comb. rule 2 and 1:


[ atomtypes ]
; name  bond_typemass   charge   ptype   sigmaepsilon
  CH3_C CH3  15.03500   0.000A   3.75000e-01  8.14817e-01; 
[CH3]-CHX


[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
 1  CH3_C  1NPA C1  1  0 15.035   ; qtot 0


Combination rule 2 yields in the .tpr file (should be epsilon and sigma, but 
are actually c6 and c12):

functype[0]=LJ_SR, c6= 9.06374492e-03, c12= 2.52054979e-05


Combination rule 1 yields in the .tpr file (should be c6 and c12, but are 
actually epsilon and sigma):

functype[0]=LJ_SR, c6= 3.7500e-01, c12= 8.14817011e-01


I am just concerned that this is behavior is opposite of what I expected. 
Perhaps I am misunderstanding how GROMACS stores these values in the tpr file 
or the section in the manual? Can someone point me in the right direction?


James Wes Barnett

Ph.D. Candidate

Chemical and Biomolecular Engineering


Tulane University

Boggs Center for Energy and Biotechnology, Room 341-B
-- 
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] Coul. Recip. in Logfile for Classical Ewald

[Barnett, James W.]

I'm doing a classical Ewald simulation with GROMACS (obviously I should 
be using something other than Ewald in my simulations like PME, but I am 
just trying to understand the concept and write some analysis code.). In 
the logfile does Coul. Recip. include the self correction (or any 
other kind of correction)? I'm having a little trouble seeing where the 
specific number comes from and am trying to understand. Adding up the 
kspace contribution (from GROMACS) and self contribution (my own 
calculation) doesn't seem to get me the number from the logfile. I know 
I'm missing something.


As an example I ran 33 SPC waters in a 1 x 1 x 1 box with cutoffs at 0.4 
(this is just a small quick simulation to get some numbers for this 
purpose). Again this is classical Ewald, fourierspacing is the default 
0.12, and ewald-rtol is the default 1e-5.


I added the following line to src/mdlib/ewald.c just before return 
energy; in the do_ewald function and recompiled :


   printf(%5.6f\n,energy);

This prints out the k-space contribution to the electrostatic energy at 
each step. As an example, at step 0 this it printed out 1008.472290 
(kJ/mol).


After getting this I calculated the self contribution as follows. The 
logfile says that 1/beta (the Gaussian width) is 0.128065 nm, so beta = 
7.808535 for this simulation. There are 33 water oxygens with a charge 
of -0.82 and 66 water hydrogens with a charge of 0.41. The following 
equation for the self term comes from section 4.9.1 of the manual (f = 
138.935485):


-f * beta / sqrt(pi) * [ (33)(-0.82)^2 + (66)(0.41)^2 ]  = -20372.33 kJ/mol

The logfile states for step 0 that Coulomb (Recip.) is -1.23120e+03 
kJ/mol, but this does not equal the total of the k-space and self 
correction terms:


1008.5 + -20372.3 = -19363.8

I appreciate anybody's help with understanding what I'm missing here in 
understanding how GROMACS calculates the self correction or if Coul. 
Recip. is something else.


Thanks,
Wes Barnett

--
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] Length of .xtc file in frames for C-Code

[Barnett, James W.]

 I have a question to all the people who are familiar with C-code. How can I
 read in the total number of frames in my *.xtc file? Especially when I do
 the analysis somewhere in the middle?

Are you using the XDR library or something else? In the XDR library there is a 
way to get the status each time you read in a frame. At the end of the file 
you get a different status, signaling there is nothing else to read in (or 
maybe signaling an error).

Typically I read in a frame, do my calcs, etc, and then when I'm at the end of 
the file the loop is exited.  To start somewhere in the middle of the file I 
set it up to read in X frames before I do my calcs (just cycle through the 
loop but skip the calcs).  I don't use C in particular, but the principle 
remains.

Alternatively you can use the trjconv tool to get rid of unneeded frames and 
then use your analysis program.

James Barnett

 
 E.g: I have a file with 100.000 frames. When I start the programm with
 
 ./program -f traj.xtc 
 
 then I want somewhere in my code something like:
 
 int totalnumerbofframesyouareanalyzing = 100.000
 
 
 When I do the same with:
 
 ./program -f traj.xtc -b 20.000
 
 then I want in my code:
 
 int totalnumerbofframesyouareanalyzing = 80.000
 
 Thanks for your help!
 GtrAngus
 
-- 
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: sigma unit conversion

[Barnett, James W.]

The Amber molecular dynamics program (sander) uses a different format of the 
van der Waals equation, so Amber force fields are designed to use different 
parameters than those used in Gromacs. So, it's not as simple as converting 
from Angstroms to nanometers. The coefficents used in the Amber force fields 
are not simply Gromacs sigma and epsilon.

Here is a document related to your question from the Amber site:
http://ambermd.org/Questions/vdwequation.pdf

Additionally combination rule 2 in Gromacs is a Lorentz-Berthelot rule (see 
section 5.3.2 in the Gromacs manual). This is just how the force field was 
designed. 

I'm just someone who uses acpype occasionally, so I hope this is helpful.

James Barnett

On Wed, Mar 05, 2014 at 10:17:27PM -0600, Chetan Mahajan wrote:
 Hi all,
 
 I am using Amber2gromacs tool called as acpype for converting input files
 to Amber to input files for gromacs. I have a question regarding atomtypes
 section of .top file. Here are first two rows of that section in my file:
 
 name   bond_type mass charge   ptype   sigma epsilon
  Amb
  Ti   Ti0.0  0.0A 1.39461e-01
 6.08772e-02 ; 0.78  0.0145
  OT   OT0.0  0.0A 2.87832e-01   8.29687e-02
 ; 1.62  0.0198
 
 Now, in my .top file, each row contains, at the end, Amber force field
 values for sigma and epsilon are given. Values on the left indicate unit
 converted values. However, given that Amber units are A0 for sigma,
 converted value for gromacs, which should be in nanometer does not match.
 Combination rule chosen is 2. ( by the way, how is this rule chosen ?)
 
 Thanks
 Chetan
-- 
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] Amber to Gromacs conversion

[Barnett, James W.]

On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
 are there other tools to convert Amber input files
 into the ones for Gromacs?

I've had success with acpype:
https://code.google.com/p/acpype/

Use the amb2gmx mode:

acpype -p _prmtop_ -x _inpcrd_

-- 
Wes Barnett | jbarn...@tulane.edu
-- 
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] Amber to Gromacs conversion

[Barnett, James W.]

You shouldn't change any of the code unless you know what you're doing. If you 
remove lines it will not work as intended. 

I think you simply need to upgrade your version of Python 2, according to the 
error message.

jbarn...@tulane.edu | from mobile

Chetan Mahajan chetanv...@gmail.com wrote:

I did play around lines 1231 and 1232, by keeping 1232, while removing
1231, etc etc. No success so far!


On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan chetanv...@gmail.com wrote:

 THis looks interesting, However, any version is giving following error on
 test mentioned in README:

 ../acpype.py -i FFF.pdb
   File ../acpype.py, line 1231
 with open(pklFile, wb) as f:  # for python 2.6 or higher
 ^
 SyntaxError: invalid syntax

 Unfortunately, I do not know python.

 Thanks


 On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. 
 jbarn...@tulane.eduwrote:

 On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
  are there other tools to convert Amber input files
  into the ones for Gromacs?

 I've had success with acpype:
 https://code.google.com/p/acpype/

 Use the amb2gmx mode:

 acpype -p _prmtop_ -x _inpcrd_

 --
 Wes Barnett | jbarn...@tulane.edu
 --
 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.