Re: [gmx-users] PBC

[mah maz]

I thought so :D
Thanks!

On Thu, Oct 8, 2015 at 9:37 AM, mah maz  wrote:

> Hi Mark
>
> Thank you. I suppose grid can be used without PBC specially when the
> system is in vacuum.
> There are some parameters in the .mdp file that I haven't defined and I
> don't want them to be applied during simulation. However in the mdout.mdp
> They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role
> in the simulation?
>
> Thanks!
>
> On Mon, Oct 5, 2015 at 2:26 PM, mah maz  wrote:
>
>> Hi Mark,
>> Thanks. It seems the default is pbc =xyz. But my question is if I don't
>> use PBC, can I use grid, or grid is only meaningful when PBC is defined?
>>
>> On Mon, Oct 5, 2015 at 11:07 AM, mah maz  wrote:
>>
>>> Dear users,
>>>
>>> If I dont define pbc=no, what is the default type for gromacs? Is it
>>> right if I dont use pbc=no in my system while using grid for ns-type?
>>>
>>> thank you.
>>>
>>
>>
>
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Re: [gmx-users] PBC

[Mark Abraham]

Hi,

On Thu, Oct 8, 2015 at 8:08 AM mah maz  wrote:

> Hi Mark
>
> Thank you. I suppose grid can be used without PBC specially when the system
> is in vacuum.
> There are some parameters in the .mdp file that I haven't defined and I
> don't want them to be applied during simulation. However in the mdout.mdp
> They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role
> in the simulation?
>

Yes, gen-seed kills a kitten and ewald-rtol launches nuclear missiles ;-)
(Stuff that configures inactive algorithms isn't active.)

Mark
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Re: [gmx-users] A problem with potential energy values and openMP

[Mark Abraham]

Hi,

This is normal. See
http://www.gromacs.org/Documentation/Terminology/Reproducibility. You will
observe similar differences if you run with different numbers of MPI ranks.

Mark

On Thu, Oct 8, 2015 at 8:40 AM Milko Vesterinen <
milko.j.vesteri...@student.jyu.fi> wrote:

> Dear Gromacs users,
>
> I have been working with Gromacs v. 5.0.4 by
> using its MPI/OPENMP – parallelization. While studying outputs of
> mdrun with input argument ”ntomp” (shell command ”gmx_mpi mdrun
> -ntomp i” where i = 1,2 or 4), the potential energy values seemed
> to differ. My typical demo run included 100 steps and the potential energy
> values were checked for the first (initial) step.
>
> Below, the obtained potential energy values are presented for two different
> energy groups and for three different ”ntomp” values (unit for potential
> energy: kJ/mol)
>
> SystemProt – Sol
>
> ntomp: 1-193754.7-193733.2
>
> ntomp: 2 -193741.3-193795.4
>
> ntomp: 4 (”default” run)-193744.7-193758.7
>
> A more detailed investigation showed that the deviations can be seen in the
> values of short – range Coulomb forces (other Coulomb short - range values
> than the values of ”SOL-SOL” system in the ”Prot-Sol” simulations differed
> less than 1 kJ/mol. The values in "SOL-SOL" system
> mostly induced the differences). I use ”PME” as ”coulombtype” here, but the
> potential energy values also differed when using ”cut-off” and again, the
> differences were noticed especially in the case of the short – range
> Coulomb forces.
>
> The question is: can one expect such differences in potential energy values
> when using openMP parallelization or is this a simple user error?
>
> Gromacs was run in a server for which detailed
> information is printed below by using command ”lscpu”:
>
> "
> Architecture:  x86_64
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):4
> On-line CPU(s) list:   0-3
> Thread(s) per core:1
> Core(s) per socket:4
> Socket(s): 1
> NUMA node(s):  1
> Vendor ID: GenuineIntel
> CPU family:6
> Model: 44
> Stepping:  2
> CPU MHz:   2400.000
> BogoMIPS:  4799.98
> Virtualization:VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache:  256K
> L3 cache:  12288K
> NUMA node0 CPU(s): 0-3
> "
>
> For example, the ”default” run (with shell command ”gmx_mpi mdrun”)
> produces the following info:
>
> ”
> Using 1 MPI process
> Using 4 OpenMP threads
> No GPUs detected on host xxx.xxx.jyu.fi
> ”
>
> Thank you.
>
> M-J Vesterinen
>
> University of Jyväskylä
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi,
I can check all the possible combinations you listed in
http://redmine.gromacs.org/issues/1834. Since my programming capability is
limited, please direct me how to proceed for solving this issue?

On Tue, Oct 6, 2015 at 9:00 PM, Teemu Murtola 
wrote:

> Thanks for the clarification. I updated the Redmine issue (
> http://redmine.gromacs.org/issues/1834) with a summary and next steps. I
> unfortunately do not have access to various systems to test the issue, but
> I put some guesses on the possible reasons in the issue.
>
> Best regards,
> Teemu
>
> On Tue, Oct 6, 2015, 07:37 Venkat Reddy  wrote:
>
> > Hi,
> > Sorry for the confusion. Now I have generated a small xtc file and a very
> > big pdb file. I can able to access small xtc file but unable to read the
> > large pdb file (~10GB) (terminating with the same error as reported
> > earlier). Does it mean my installation has some problem?
> >
> > On Mon, Oct 5, 2015 at 7:41 PM, Teemu Murtola 
> > wrote:
> >
> > > Hi,
> > >
> > > That unfortunately doesn't tell us anything, since 1.5GB can still be
> > read
> > > with 32-bit file operations. You didn't answer any of the questions:
> can
> > > you open very small xtc files, or very large (requiring 64-bit access)
> > > gro/pdb files, or not? We are still thinking that you should be able to
> > > open any files smaller than 2GB just fine, but you are making confusing
> > > claims that seem to contradict this, so this needs to be sorted out
> > before
> > > we can really conclude anything.
> > >
> > > Best regards,
> > > Teemu
> > >
> > > On Mon, Oct 5, 2015, 08:32 Venkat Reddy  wrote:
> > >
> > > > Hi,
> > > > Sorry for the delay in reply.
> > > > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1
> > > version.
> > > > My Desktop is 32-bit whereas my xtc files were generated on our super
> > > > cluster, which runs on 64-bit O.S.
> > > >
> > > > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <
> teemu.murt...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <
> pall.szil...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <
> venkat...@gmail.com>
> > > > > wrote:
> > > > > > > Gromacs-5.1 version can not read xtc files. However, it can
> > access
> > > > > single
> > > > > > > frame gro/pdb files.
> > > > > > >
> > > > > >
> > > > > > That's a bold claim that IMO requires equally strong proof.
> > > > > >
> > > > >
> > > > > I agree with Szilard. Are you saying that you cannot even read a
> > > > > single-frame xtc file with just a few kB in size? How about other
> > > binary
> > > > > files (e.g., trr)? How about large (>2GB) gro files?
> > > > >
> > > > > In your other mail to the list you were talking about a 32-bit
> Ubuntu
> > > VM.
> > > > > > Are you sure you're not running into in incompatibility issue
> > between
> > > > the
> > > > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> > > > > >
> > > > >
> > > > > I would still suspect that the underlying reason is that for some
> > > reason,
> > > > > 5.1 gets compiled without large file support in your system, which
> > > makes
> > > > > even plain fopen() fail on large files. The build system should
> give
> > an
> > > > > error if it cannot find 64-bit file support, but the check may be
> > > > > imperfect. Someone who can reproduce the issue (i.e., has access
> to a
> > > > > similar OS and other environment) should try what is actually
> > required
> > > to
> > > > > get 64-bit file support working there. Based on the information you
> > > > posted
> > > > > in Redmine, the build system already checks that off_t is 64-bit
> > > without
> > > > > any extra defines on your system. The checks in the build system
> have
> > > not
> > > > > changed between 5.0 and 5.1, though.
> > > > >
> > > > > Teemu
> > > > > --
> > > > > 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
> > > > >
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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > With Best Wishes
> > > > Venkat Reddy Chirasani
> > > > PhD student
> > > > Laboratory of Computational Biophysics
> > > > Department of Biotechnology
> > > > IIT Madras
> > > > Chennai
> > > > INDIA-600036
> > > > --
> > > > 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 

Re: [gmx-users] PBC

[mah maz]

Hi Mark

Thank you. I suppose grid can be used without PBC specially when the system
is in vacuum.
There are some parameters in the .mdp file that I haven't defined and I
don't want them to be applied during simulation. However in the mdout.mdp
They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role
in the simulation?

Thanks!

On Mon, Oct 5, 2015 at 2:26 PM, mah maz  wrote:

> Hi Mark,
> Thanks. It seems the default is pbc =xyz. But my question is if I don't
> use PBC, can I use grid, or grid is only meaningful when PBC is defined?
>
> On Mon, Oct 5, 2015 at 11:07 AM, mah maz  wrote:
>
>> Dear users,
>>
>> If I dont define pbc=no, what is the default type for gromacs? Is it
>> right if I dont use pbc=no in my system while using grid for ns-type?
>>
>> thank you.
>>
>
>
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[gmx-users] A problem with potential energy values and openMP

[Milko Vesterinen]

Dear Gromacs users,

I have been working with Gromacs v. 5.0.4 by
using its MPI/OPENMP – parallelization. While studying outputs of
mdrun with input argument ”ntomp” (shell command ”gmx_mpi mdrun
-ntomp i” where i = 1,2 or 4), the potential energy values seemed
to differ. My typical demo run included 100 steps and the potential energy
values were checked for the first (initial) step.

Below, the obtained potential energy values are presented for two different
energy groups and for three different ”ntomp” values (unit for potential
energy: kJ/mol)

SystemProt – Sol

ntomp: 1-193754.7-193733.2

ntomp: 2 -193741.3-193795.4

ntomp: 4 (”default” run)-193744.7-193758.7

A more detailed investigation showed that the deviations can be seen in the
values of short – range Coulomb forces (other Coulomb short - range values
than the values of ”SOL-SOL” system in the ”Prot-Sol” simulations differed
less than 1 kJ/mol. The values in "SOL-SOL" system
mostly induced the differences). I use ”PME” as ”coulombtype” here, but the
potential energy values also differed when using ”cut-off” and again, the
differences were noticed especially in the case of the short – range
Coulomb forces.

The question is: can one expect such differences in potential energy values
when using openMP parallelization or is this a simple user error?

Gromacs was run in a server for which detailed
information is printed below by using command ”lscpu”:

"
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):4
On-line CPU(s) list:   0-3
Thread(s) per core:1
Core(s) per socket:4
Socket(s): 1
NUMA node(s):  1
Vendor ID: GenuineIntel
CPU family:6
Model: 44
Stepping:  2
CPU MHz:   2400.000
BogoMIPS:  4799.98
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  12288K
NUMA node0 CPU(s): 0-3
"

For example, the ”default” run (with shell command ”gmx_mpi mdrun”)
produces the following info:

”
Using 1 MPI process
Using 4 OpenMP threads
No GPUs detected on host xxx.xxx.jyu.fi
”

Thank you.

M-J Vesterinen

University of Jyväskylä
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Re: [gmx-users] Testing mpi version of Gromacs 5.1

[Szilárd Páll]

On Thu, Oct 8, 2015 at 11:56 AM, Joachim Hein 
wrote:

> Hi everyone
>
> I hope this is the right place to discuss this.
>
> I am having issues with checking the correctness of my mpi version of
> Gromacs 5.1.  I have build and tested earlier versions without issues (e.g.
> 5.0.4 is the latest I did).  I am also building float and double versions
> of the serial tools and they test without issue using: make check.
>
> I tried two things to test my MPI build (I’ll give a detailed account on
> how I build later):
>
>  make -j 8 check
>
> on a back-end node (slurm sbatch job asking for 8 cores) of our cluster.
> Tests 19 to 25 pass, while the first 18 fail in MPI_Init.  Is that how it
> is supposed to be?
>
> The other test I tried was as follows:
>
> - change into the regression test directory
> - source the GMXRC file of an install containing a float and a float mpi
> version
> - executing: ./gmxtest.pl all -np 4  (in a batch script asking for 4
> cores)
>
> I get the following:
>
>  gmx-completion.bash: line 258: `_gmx_convert-tpr_compl': not a valid
> identifier
>

This error clearly suggests that something is wrong with the bash
completion script when used with your bash version. This sounds like an
issue that likely requires some dev attention, so please file an issue at
redmine.gromacs.org (and include the info you provided + your bash version).

As a workaround, you could disable bash completion e.g. by removing
the $GMXBIN/gmx-completion.bash file or disabling loading it in
$GMXBIN/GMXRC.bash:75.

Cheers,
--
Szilárd


>
>
> So here comes the detail on the build:
> ---
>
> gcc/5.2.0
> openmpi 1.10.0 build for the above gcc 5.2.0
> fftw 3.3.4 build for the above gcc with sse and avx
> boost/1.59.0
>
> CMAKEFLAGS="-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DGMX_FFT_LIBRARY=fftw3 -DBUILD_SHARED_LIBS=ON
> -DCMAKE_INSTALL_PREFIX=$PREFIX -DGMX_DEFAULT_SUFFIX=ON -DREGRESSION
> TEST_PATH=$RTESTPATH -DGMX_SIMD=AVX_128_FMA
> -DCMAKE_PREFIX_PATH=$FFTW3_HOME"
>
> I build the serial and parallel version:
>
> # Building single precision without MPI
> BUILDDIR="bdir_float_boost"
> mkdir -p $BUILDDIR
> cd $BUILDDIR
>
> cmake ../ $CMAKEFLAGS
>
> make -j 16
>
> make -j 4 check
>
> make install
>
> cd ..
>
> # Building single precision with MPI
> BUILDDIR="bdir_float_mpi_boost"
> mkdir -p $BUILDDIR
> cd $BUILDDIR
>
> cmake ../ $CMAKEFLAGS -DGMX_MPI=ON -DBUILD_SHARED_LIBS=off
>
> make -j 16
>
> make install
>
>
> Both installs go to the same directory.  This procedure is essentially the
> same as I used fro Gromacs 5.0.4.
>
> I tested with gcc 4.9.0 and openmpi 1.8.3 (which I used for gromacs 5.0.4)
> and the results are similar, though the error message from the MPI_Init is
> slightly different.
>
> Any comments and help is greatly appreciated.
>
> Thanks and best wishes
>   Joachim
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Re: [gmx-users] Virtual sites error

[Erik Marklund]

Unfortunately, the parameters required for certain virtual sites in nucleic 
acids are not define in the force field files that are shipped with Gromacs.

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 7 Oct 2015, at 11:33, Timofey Tyugashev  wrote:
> 
> Trying to add hydrogen virtual sites to the model (using -vsites h option in 
> pdb2gmx) results in a salvo of error messages when running grommp to create 
> .tpr file after the solvation:
> 
> ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
>  No default Constr. No Conn. types
> 
> 
> ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
>  No default Constr. No Conn. types
> 
> This lines in constraints section in the .itp file refer to pairs of two MCH3 
> and one MC atoms, which should serve (the way I understand the situation) as 
> replacement methyl group in thymine. There are several more pairs of same 
> errors corresponding to different thymine methyl groups in the DNA strands.
> 
> Here is the relevant sections of the itp file for the first two errors:
> 
> [ constraints ]
> ;  aiaj functc0c1
>2 3 2
>  110   111 2
>  110   112 2
>  111   112 2
> 
> [ atoms ]
> 
>   110 CM321 DT C5110 0.0025 12.01   ; qtot -2.867
>   111   MCH3321 DT   MC71111  0 7.517   ; qtot -2.867
>   112   MCH3321 DT   MC72111  0 7.517   ; qtot -2.867
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Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 10/8/15 1:54 AM, Dries Van Rompaey wrote:

Thanks for the reply Justin. I unfortunately cannot currently disclose the
files that I'm working on. Based on the info presented, would you say that
it's an issue with the force field definition or with the actual protein
topology? I am not planning on using amber03 in my simulations at the
moment, so this specific warning is not that important, but I can't help
but wonder if this warning means something is off in the topology.



Given that error, there is no topology produced, so there's not going to be a 
problem with the topology itself.


I'm sorry to say that without your actual files, there's literally nothing we 
can do to diagnose this.  You say some prolines work with AMBER03 and others 
don't, which makes no sense at all.  Either the .rtp is sound or it isn't. 
Either it is unmodified (which will work) or someone has tampered with it and 
broken it.


If you're not going to use AMBER03 and the topology is produced with other force 
fields, then you know you have a problem with a hacked AMBER03 .rtp file.  It 
should be very straightforward to simply to a diff against the unmodified 
version (which you can get by downloading a fresh GROMACS tarball if you don't 
already have it).


-Justin


On 7 October 2015 at 23:05, Justin Lemkul  wrote:




On 10/7/15 5:03 PM, Dries Van Rompaey wrote:


Thanks Justin, that makes sense! I'm wondering why none of the other
proline residues triggered that warning though? The same procedure works
like a charm with other proteins.



Without access to all of the files you're looking at, the best I can do is
shrug my shoulders because that doesn't make any sense.  Some prolines work
and one doesn't?  That's just not logical.

-Justin


On 7 Oct 2015 10:59 pm, "Justin Lemkul"  wrote:





On 10/7/15 3:01 PM, Dries Van Rompaey wrote:

Hi Mark,


This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.


Non-terminal proline does not have an amide H.  If your force field .rtp

file claims to use such an atom used in a dihedral (which is what the
error
message tells you is happening), find out who altered the file and
reprimand them :)

-Justin

Kind regards,


Dries


On 7 October 2015 at 20:56, Mark Abraham 
wrote:

Hi,



Is it terminal? Are there specbonds in play? What's the GROMACS
version?
What's your pdb2gmx command line? :-)

Mark

On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
dries.vanromp...@gmail.com>
wrote:

Hi everyone,



I'm getting the following warning when I try to run pdb2gmx on my
protein
structure:

WARNING: WARNING: Residue 168 named PRO of a molecule in the input
file

was


mapped to an entry in the topology database, but the atom H used in an

interaction of type dihedral in that entry is not found in the input

file.


Perhaps your atom and/or residue naming needs to be fixed.


This warning is only present when I use the AMBER03 forcefield, all
other
forcefields seem to work fine. I have tried this with both a structure
without hydrogens as well as a structure with hydrogens added, both
with
and without the -ignh flag. I tried looking at the amber03 database
files
as well as the amber99sb-ildn database files (amber99sb-ildn works
just
fine), but I could not find any reason why this particular residue
would

be


problematic. pdb2gmx does not find any problems with the other proline

residues in the protein (which look identical), so I am puzzled as to
what's causing this.

The proline residue is:
ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
 N
ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
 C
ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
 C
ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
 C
ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
 C
ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
 C
ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
 O

Does anyone know what's going on here?

Thanks in advance!
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[gmx-users] Differences between gmx bar and pymbar free energy

[Gmx QA]

Hi gmx-users

I am running a series of free-energy of solvation calculations for small
molecules in water and octanol, to calculate partition coefficients.

For this, I have set up a series of lambda-points in water and in octanol,
and then haves used primarily gmx bar to evaluate the results.

Using gmx bar (v.5.0.4) with the following command line
$ gmx bar -f md*xvg -o -oi -oh -b 100 &>FEP.dat

I get for eg. ethanol in water a Delta-G of 14.33 kJ/mol (which is very
close to the value (14.42 kj/mol) reported by eg. Lundborg and Lindahl in
JPCB, 119, 2015, for the same combination of water model and forcefield, so
that is reassuring).

Then I tried the same analysis using pymbar (cloned today from git) like
this:
$ python alchemical_analysis.py -t 300 -p 1 -q xvg -p md -m BAR -v -s 100
&> FEP_pymbar.dat

Now, I get a Delta-G of 64.235 kJ/mol, so clearly not the same as with gmx
bar (and not simply a kJ vs kcal issue either I think)

I feel like I am missing something fundamental since I get so different
values, and would appreciate any feedback. The simulations have been run
using gmx 5.0.4 with a total of 47 lambda points, and each run is 10 ns in
length.

I can provide mdp-files and such if needed.

Cheers
/PK
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Re: [gmx-users] Differences between gmx bar and pymbar free energy

[Gmx QA]

Hello again

Scratch that, I had the input files numbered incorrectly for pymbar. Now
all is well.

Sorry for the confusion
/PK

2015-10-08 13:22 GMT+02:00 Gmx QA :

> Hi gmx-users
>
> I am running a series of free-energy of solvation calculations for small
> molecules in water and octanol, to calculate partition coefficients.
>
> For this, I have set up a series of lambda-points in water and in octanol,
> and then haves used primarily gmx bar to evaluate the results.
>
> Using gmx bar (v.5.0.4) with the following command line
> $ gmx bar -f md*xvg -o -oi -oh -b 100 &>FEP.dat
>
> I get for eg. ethanol in water a Delta-G of 14.33 kJ/mol (which is very
> close to the value (14.42 kj/mol) reported by eg. Lundborg and Lindahl in
> JPCB, 119, 2015, for the same combination of water model and forcefield, so
> that is reassuring).
>
> Then I tried the same analysis using pymbar (cloned today from git) like
> this:
> $ python alchemical_analysis.py -t 300 -p 1 -q xvg -p md -m BAR -v -s 100
> &> FEP_pymbar.dat
>
> Now, I get a Delta-G of 64.235 kJ/mol, so clearly not the same as with gmx
> bar (and not simply a kJ vs kcal issue either I think)
>
> I feel like I am missing something fundamental since I get so different
> values, and would appreciate any feedback. The simulations have been run
> using gmx 5.0.4 with a total of 47 lambda points, and each run is 10 ns in
> length.
>
> I can provide mdp-files and such if needed.
>
> Cheers
> /PK
>
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[gmx-users] Testing mpi version of Gromacs 5.1

[Joachim Hein]

Hi everyone

I hope this is the right place to discuss this.

I am having issues with checking the correctness of my mpi version of Gromacs 
5.1.  I have build and tested earlier versions without issues (e.g. 5.0.4 is 
the latest I did).  I am also building float and double versions of the serial 
tools and they test without issue using: make check.

I tried two things to test my MPI build (I’ll give a detailed account on how I 
build later):

 make -j 8 check

on a back-end node (slurm sbatch job asking for 8 cores) of our cluster.  Tests 
19 to 25 pass, while the first 18 fail in MPI_Init.  Is that how it is supposed 
to be?

The other test I tried was as follows:

- change into the regression test directory
- source the GMXRC file of an install containing a float and a float mpi version
- executing: ./gmxtest.pl all -np 4  (in a batch script asking for 4 cores)

I get the following:

 gmx-completion.bash: line 258: `_gmx_convert-tpr_compl': not a valid identifier



So here comes the detail on the build:
---

gcc/5.2.0
openmpi 1.10.0 build for the above gcc 5.2.0
fftw 3.3.4 build for the above gcc with sse and avx
boost/1.59.0

CMAKEFLAGS="-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ 
-DGMX_FFT_LIBRARY=fftw3 -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$PREFIX 
-DGMX_DEFAULT_SUFFIX=ON -DREGRESSION
TEST_PATH=$RTESTPATH -DGMX_SIMD=AVX_128_FMA -DCMAKE_PREFIX_PATH=$FFTW3_HOME"

I build the serial and parallel version:

# Building single precision without MPI
BUILDDIR="bdir_float_boost"
mkdir -p $BUILDDIR
cd $BUILDDIR

cmake ../ $CMAKEFLAGS

make -j 16

make -j 4 check

make install

cd ..

# Building single precision with MPI
BUILDDIR="bdir_float_mpi_boost"
mkdir -p $BUILDDIR
cd $BUILDDIR

cmake ../ $CMAKEFLAGS -DGMX_MPI=ON -DBUILD_SHARED_LIBS=off

make -j 16

make install


Both installs go to the same directory.  This procedure is essentially the same 
as I used fro Gromacs 5.0.4.

I tested with gcc 4.9.0 and openmpi 1.8.3 (which I used for gromacs 5.0.4) and 
the results are similar, though the error message from the MPI_Init is slightly 
different.

Any comments and help is greatly appreciated.

Thanks and best wishes
  Joachim
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[gmx-users] NMA run problem

[KARAKAS Esra]

Dear Gromacs Users,

I am trying to run a Normal Mode Analysis with Gromacs v5.0.4 of a structure of 
18081 atoms (without water) and I have a problem.
I did a several minimization of my structure (1 SD, 1 CD and 4 L-BFGS), and 
everything went well. You can see below the relative informations for my last 
L-BFGS minimization:

-- At the top of my .log file:
Using 10 BFGS correction steps.

   F-max =  9.76934e-06 on atom 15076
   F-Norm=  7.50769e-07

-- At the end of my .log file:
Low-Memory BFGS Minimizer converged to Fmax < 1e-07 in 132449 steps
Potential Energy  = -9.52896691013964e+04
Maximum force =  9.82970751734797e-08 on atom 17063
Norm of force =  1.69009515334513e-08

then, when I run my NMA, I see this message in my .log file:

Maximum force: 2.85412e+02
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.

My command line is :
grompp_mpi_d -f nma.mdp -c em_BFGS_4_NoWater.gro -t em_BFGS_4_NoWater.trr -e 
em_BFGS_4_NoWater.edr -p protein.top -o nma_NoWater.tpr

My question is why I have such a large force ?

Thank you in advance for your help.


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[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

[Nicolas Cheron]

Dear all,

I am joining a project where people are using the CHARMM22 force field.
They converted a .prmtop file from Amber to Gromacs format with acpype. In
the output topology, there are no Urey-Bradley potentials or improper
dihedrals (for example, all the [ angle ] functions are of type 1 and none
are 5 and all the [ dihedrals ] function are of type 9 and none are 2).

I am confused, and I am wondering if something went missing when using
acpype? Do you know how acpype handle this part of the amber topology? Or
did acpype converted the Urey-Bradley and improper dihedrals from the
.prmtop to other kind of functions? For an angle A-B-C with Urey-Bradley, I
thought it would be possible to have a force as if there was a bond between
A and C but I didn't find anything like that in the topology.

The manual says about Urey-Bradley potential "Although this can be easily
written as a simple sum of two terms, it is convenient to have it as a
single entry in the topology file and in the output as a separate energy
term" but I am not sure to understand if that means that Gromacs developers
have prefered to keep it as a single entry or not.

Thanks for your help

Nicolas
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Re: [gmx-users] Free Energy of Liquid Water

[Nathan K Houtz]

You were right, it's much faster when I only calculate free energy for one 
molecule. My simulation has 1000 water molecules in it, but I created a new 
topology file and gave one molecule a different name (but identical properties) 
and now it runs the same simulation in about 36% more time, which is much more 
manageable. Thank you very much for the help! I don't think there is a problem 
with my topology or mdp files now. 

Regards,
Nathan H.

- Original Message -
From: "Michael Shirts" 
To: "Discussion list for GROMACS users" 
Sent: Wednesday, October 7, 2015 11:14:29 PM
Subject: Re: [gmx-users] Free Energy of Liquid Water

If ALL the particles are changing with the free energy coupling
parameter, then GROMACS will slow down quite a bit.  If only one
molecule is changing, then it shouldn't be that much slower (20-30%
slower?)  But without .mdp and.top files, it's hard to say exactly
what is happening.


On Wed, Oct 7, 2015 at 11:08 PM, Nathan K Houtz  wrote:
> Thanks for explaining, (and Professor Farais de Moura as well) that makes 
> sense.
>
> On a different note, I've noticed a huge difference in performance between my 
> equillibration run and my actual simulation, and I'm wondering if this is 
> normal. For comparison, I ran a couple small (meaningless) simulations where 
> the only difference was the collection of free energy information and Gromacs 
> slows down by a factor of 39. I had been under the impression that I would be 
> able to do each simulation in just under an hour but now it looks like it 
> will take the better part of two days, which is too much. I'll just have to 
> run shorter or fewer simulations if I can't improve that, but I'm hoping I'm 
> just doing something wrong. I'm essentially using modified versions of the 
> .mdp file I found for this tutorial: 
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy.
>  I changed things like turning off the pressure coupling, changing the 
> temperature, etc. The settings for free energy calculations are unchanged. Is 
> the calculation of dh/dl 
 re
>  ally that expensive, or is this abnormal?
>
> Thank you for the help as always. Regards,
> Nathan H.
>
> - Original Message -
> From: "Michael Shirts" 
> To: "Discussion list for GROMACS users" 
> Cc: "gromacs org gmx-users" 
> Sent: Tuesday, October 6, 2015 3:05:38 PM
> Subject: Re: [gmx-users] Free Energy of Liquid Water
>
> For a pure fluid, G  = N \mu.  And \mu = (dG/dN)_(T,P).  So you only
> need to change one molecule to ideal gas to get the change in free
> energy. The free energy of transfer of water from liquid to gas is
> indeed the free energy of solvation of one water molecule in bath of
> water.  So there's a reason why you're just finding tutorials of
> solvation free energies!
>
> On Thu, Oct 1, 2015 at 10:44 PM, Nathan K Houtz  wrote:
>> Hi everyone,
>>
>> I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid 
>> water (TIP4P model) to an ideal gas, to find the relative free energy. To do 
>> this, I believe  one generally integrates above the critical point by 
>> increasing the temperature above the critical temperature and then relaxing 
>> the pressure until the system is a diffuse gas. The mdp options 
>> documentation is helpful, and I went through an ethanol solvation tutorial, 
>> but there doesn't appear to be a "pressure-lambda" or a "volume-lambda" 
>> option that I could use to do the second part. How can I get Gromacs to 
>> calculate the dh/dl derivative while relaxing the pressure?
>>
>> In addition, all of the tutorials I found for thermodynamic integration were 
>> for finding solvation free energies. The coulomb and VDW forces are 
>> essentially changed from "completely on" to "completely off". But in my 
>> case, I'd like to change the temperature and pressure between two nonzero 
>> values. I don't want to begin my simulation at 0K and 0atm, but lambda 
>> *must* go from 0 to 1. How can I define both starting and ending points for 
>> the temperature and pressure (or volume, or density)?
>>
>> Thanks for your help!
>> Nathan H.
>> --
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[gmx-users] GPU installation of gromacs:Tesla K20c

[Nikhil Maroli]

Dear all,
i have Tesla K20 GPU and ubuntu 15.04 and i installed cuda 7.5.after that i
executed the following commands

tar xfz gromacs-5.0.5.tar.gz
cd gromacs-5.0.5
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

-- 

everything is completed without any error
what i have to do next for gromacs installation in linux
i seen the files of gromacs in usr/local/gromacs/share/gromacs
but when i give mdrun or pdb2gmx it asking for install gromacs
sudo apt-get install gromacs?
what i have to do next to get a working gromacs in gpu?
thanks
Ragards,
Nikhil Maroli
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Re: [gmx-users] Dftb as qmmm method with gromacs

[Padmani Sandhu]

Hello Sir,


I have modified the file CMakeCache.txt as suggested by you followed by
make and sudo make install but while running mdrun I am getting the error:

 DFTB: SCC-DFTB mode 3!
  DFTB: PME will be done for QM/MM with QM atoms only, starting from 2nd
SCC iteration (partial PME)
  QM/MM: MM electric field scaled by a factor of 1.00
  DFTB: empirical dispersion -- with Grimme's DFT-D3



*cannot read file /path/to/skf/dftd3-pars.txt*





*I have exported all the paths as said in the tutorial
"http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3
".*





*Regards,*

*Padmani*







On Thu, Oct 8, 2015 at 7:04 PM, Groenhof, Gerrit  wrote:

> [image: Boxbe]  This message is eligible
> for Automatic Cleanup! (ggro...@gwdg.de) Add cleanup rule
> 
> | More info
> 
>
> Hi,
>
> Instead of the flag to Cmake you could also manually modify CMakeCache.txt
>
> //QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess,
> // orca
> GMX_QMMM_PROGRAM:STRING=dftb
>
> best,
>
> Gerrit
>
>
> Message: 4
> Date: Thu, 8 Oct 2015 09:51:38 +0530
> From: Padmani Sandhu 
> To: "gmx-us...@gromacs.org" 
> Subject: [gmx-users] Dftb as qmmm method with gromacs
> Message-ID:
>