Re: [gmx-users] installation of gromacs on windows using cygwin

[Mark Abraham]

On 5/11/2010 10:48 PM, bharat gupta wrote:
I followed the same instructions given in the gromacs manual , step by 
step ... I first tried installing gromacs with the first command given 
in the manual and then again I installed with the options for FLAGS 
but finally ended up with the following error in both the above 
mentioned conditions :-


checking dynamic linker characteristics... Win32 ld.exe


I think here's a problem.  Your cygwin installation doesn't have a 
proper linker installed. win32 ld.exe is not up to the job, IIRC. You 
need (at least) the gcc and binutils packages.


When asking for free help, you should copy and paste into these emails 
the command that is failing. If you'd really followed the instructions, 
we expect they'd have worked. So in the absence of evidence that you've 
done it right, we'll have to assume you've made a typo. We don't want to 
guess what you've done wrong :-)


Mark


checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for sqrt in -lm... yes
checking for fftw3.h... configure: error: Cannot find the default 
external FFT l

ibrary (fftw3).
Other alternatives are 'fftw2', or 'mkl' for Intel MKL.
You are STRONGLY recommended to use one of these - fftw is free.

Use CPPFLAGS and LDFLAGS if the library is installed in a
non-standard location. (see FAQ at http://www.gromacs.org)

If you dont care about performance you can also specify 'fftpack'
to use a slower set of FFTs built into Gromacs.
(Just install FFTW3 unless you really know what you are doing).


I have installed fftw2.1.5  ...


Pls help me rectify the error


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



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Re: [gmx-users] problem in executing genbox command

[Mark Abraham]

On 6/11/2010 4:02 PM, bharat gupta wrote:

Hi all ,

Whenever i am running the genbox command I am getting the following 
error  :-



genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

 :-)  G  R  O  M  A  C  S  (-:

Segmentation fault (core dumped)


The most likely scenario is some shared library is not available when it 
should be. That means the environment in which you ran the above command 
is different from the one in which GROMACS was built. That means 
most/all GROMACS commands will fail. A possibility is that there's a bug 
in GROMACS, but I doubt it. Do other GROMACS commands, or other genbox 
runs work?


Mark



Can anybody tell me whats the reason for such an error ...

--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



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Re: [gmx-users] problem in executing genbox command

[bharat gupta]

yes the first two commands namely - pdb2gmx and editconf are working ...
-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] g_sas resarea.xvg

[Mark Abraham]

On 4/11/2010 11:04 PM, Justin A. Lemkul wrote:



Carla Jamous wrote:

Hi everyone,

I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg

What I don't understand is why there are 3 columns in the file 
resarea.xvg although this is what's written in my file:

# g_sas is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Area per residue"
@xaxis  label "Residue"
@yaxis  label "Area (nm\S2\N)"
@TYPE xy

So I would expect this file to contain only two columns. I'm using 
gromacs version 4.0.3.




Residue, average area, standard deviation.


Fixed in git.

Mark


-Justin


Thanks for your help,
Carla





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[gmx-users] Using mdrun -rerun to get energy values

[Martin Kamp Jensen]

Hello,

Hopefully someone can help me understand how to use the mdrun -rerun
functionality, because currently I am confused. I would like to be able to
look up potential energy values for a number of conformations by calling
mdrun -rerun once.

The idea to use mdrun -rerun is from advice given to me by Mark Abraham on
the gmx-developers list (
http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html
 and
http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html):

You want GROMACS to find the energy of a potentially infinite set of
> coordinates that appear magically, and that is what mdrun -rerun does.


> The elegant way to do that is to write your series of conformations to a
> pseudo-trajectory (in whichever of GROMACS many trajectory formats is
> convenient to you), and then invoke mdrun -rerun on that trajectory with a
> suitable .tpr. Then you either parse the .log file or the output .edr file
> for the energies.


I wanted to find out how this works so I have been experimenting. I started
out by looking at the Peptide tutorial at
http://manual.gromacs.org/current/online/speptide.html. I used three
different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me
three conformations and their energy values. For testing purposes I then
wanted to get the energy values for those three conformations using mdrun
-rerun (and since I already have the correct energy values it is easy to
verify the results).

First, I created a trajectory by concatenating the three conformations (gro
files) into one gro file (which is okay according to
http://manual.gromacs.org/current/online/gro.html: "gro files can be used as
trajectory by simply concatenating files"). I then used an mdp file with
integrator = steep and nsteps = 0 indicating that I just want the energy
value (listed in the output, in the log file or by using g_energy). Now, by
using mdrun -s  -rerun  I only get the energy
value for the first conformation listed in the gro file used to create the
tpr file. The -rerun option does not seem to have any effect at all.

I used the following commands three times to create three different
conformations (one conf_mdrun.gro file for each time) with different energy
values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in
em.mdp.

pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx << EOF

1

1

EOF


> editconf -f conf_pdb2gmx -o conf_editconf -d 0.5


> genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox

mv top_pdb2gmx.top top_genbox.top

mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top


> grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp


> mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun


I was hoping the following would give me the three energy values for the
three conformations in 2+1+0.gro, which is the concatenation of the three
conf_mdrun.gro files from before. However, I just get the energy value from
the first conformation in the file. Using the -rerun option does not make a
difference (I can put whatever after -rerun, even files that do not exist,
without any effect).

grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp


> mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro


Regards,
Martin.
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Re: [gmx-users] Using mdrun -rerun to get energy values

[Krzysztof Mlynarczyk]

Hi,

You need to use md integrator for -rerun to work.

Good luck,
Chris

2010/11/6 Martin Kamp Jensen 

> Hello,
>
> Hopefully someone can help me understand how to use the mdrun -rerun
> functionality, because currently I am confused. I would like to be able to
> look up potential energy values for a number of conformations by calling
> mdrun -rerun once.
>
> The idea to use mdrun -rerun is from advice given to me by Mark Abraham on
> the gmx-developers list (
> http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html
>  and
> http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html
> ):
>
> You want GROMACS to find the energy of a potentially infinite set of
>> coordinates that appear magically, and that is what mdrun -rerun does.
>
>
>> The elegant way to do that is to write your series of conformations to a
>> pseudo-trajectory (in whichever of GROMACS many trajectory formats is
>> convenient to you), and then invoke mdrun -rerun on that trajectory with a
>> suitable .tpr. Then you either parse the .log file or the output .edr file
>> for the energies.
>
>
> I wanted to find out how this works so I have been experimenting. I started
> out by looking at the Peptide tutorial at
> http://manual.gromacs.org/current/online/speptide.html. I used three
> different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me
> three conformations and their energy values. For testing purposes I then
> wanted to get the energy values for those three conformations using mdrun
> -rerun (and since I already have the correct energy values it is easy to
> verify the results).
>
> First, I created a trajectory by concatenating the three conformations (gro
> files) into one gro file (which is okay according to
> http://manual.gromacs.org/current/online/gro.html: "gro files can be used
> as trajectory by simply concatenating files"). I then used an mdp file with
> integrator = steep and nsteps = 0 indicating that I just want the energy
> value (listed in the output, in the log file or by using g_energy). Now, by
> using mdrun -s  -rerun  I only get the energy
> value for the first conformation listed in the gro file used to create the
> tpr file. The -rerun option does not seem to have any effect at all.
>
> I used the following commands three times to create three different
> conformations (one conf_mdrun.gro file for each time) with different energy
> values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in
> em.mdp.
>
> pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx << EOF
>
> 1
>
> 1
>
> EOF
>
>
>> editconf -f conf_pdb2gmx -o conf_editconf -d 0.5
>
>
>> genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox
>
> mv top_pdb2gmx.top top_genbox.top
>
> mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top
>
>
>> grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp
>
>
>> mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun
>
>
> I was hoping the following would give me the three energy values for the
> three conformations in 2+1+0.gro, which is the concatenation of the three
> conf_mdrun.gro files from before. However, I just get the energy value from
> the first conformation in the file. Using the -rerun option does not make a
> difference (I can put whatever after -rerun, even files that do not exist,
> without any effect).
>
> grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp
>
>
>> mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro
>
>
> Regards,
> Martin.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] Using mdrun -rerun to get energy values

[Martin Kamp Jensen]

Hi Chris,

On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk
wrote:

> Hi,
>
> You need to use md integrator for -rerun to work.
>

Aha, now it seems to work. Thanks!

I am just sad that I did not find that information. According to
http://manual.gromacs.org/current/online/mdrun.html "With -rerun an input
trajectory can be given for which forces and energies will be
(re)calculated. Neighbor searching will be performed for every frame, unless
nstlist is zero (see the .mdp file)."


>
> Good luck,
> Chris
>
> 2010/11/6 Martin Kamp Jensen 
>
>> Hello,
>>
>> Hopefully someone can help me understand how to use the mdrun -rerun
>> functionality, because currently I am confused. I would like to be able to
>> look up potential energy values for a number of conformations by calling
>> mdrun -rerun once.
>>
>> The idea to use mdrun -rerun is from advice given to me by Mark Abraham on
>> the gmx-developers list (
>> http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html
>>  and
>> http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html
>> ):
>>
>> You want GROMACS to find the energy of a potentially infinite set of
>>> coordinates that appear magically, and that is what mdrun -rerun does.
>>
>>
>>> The elegant way to do that is to write your series of conformations to a
>>> pseudo-trajectory (in whichever of GROMACS many trajectory formats is
>>> convenient to you), and then invoke mdrun -rerun on that trajectory with a
>>> suitable .tpr. Then you either parse the .log file or the output .edr file
>>> for the energies.
>>
>>
>> I wanted to find out how this works so I have been experimenting. I
>> started out by looking at the Peptide tutorial at
>> http://manual.gromacs.org/current/online/speptide.html. I used three
>> different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me
>> three conformations and their energy values. For testing purposes I then
>> wanted to get the energy values for those three conformations using mdrun
>> -rerun (and since I already have the correct energy values it is easy to
>> verify the results).
>>
>> First, I created a trajectory by concatenating the three conformations
>> (gro files) into one gro file (which is okay according to
>> http://manual.gromacs.org/current/online/gro.html: "gro files can be used
>> as trajectory by simply concatenating files"). I then used an mdp file with
>> integrator = steep and nsteps = 0 indicating that I just want the energy
>> value (listed in the output, in the log file or by using g_energy). Now, by
>> using mdrun -s  -rerun  I only get the energy
>> value for the first conformation listed in the gro file used to create the
>> tpr file. The -rerun option does not seem to have any effect at all.
>>
>> I used the following commands three times to create three different
>> conformations (one conf_mdrun.gro file for each time) with different energy
>> values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in
>> em.mdp.
>>
>> pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx << EOF
>>
>> 1
>>
>> 1
>>
>> EOF
>>
>>
>>> editconf -f conf_pdb2gmx -o conf_editconf -d 0.5
>>
>>
>>> genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox
>>
>> mv top_pdb2gmx.top top_genbox.top
>>
>> mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top
>>
>>
>>> grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp
>>
>>
>>> mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun
>>
>>
>> I was hoping the following would give me the three energy values for the
>> three conformations in 2+1+0.gro, which is the concatenation of the three
>> conf_mdrun.gro files from before. However, I just get the energy value from
>> the first conformation in the file. Using the -rerun option does not make a
>> difference (I can put whatever after -rerun, even files that do not exist,
>> without any effect).
>>
>> grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp
>>
>>
>>> mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro
>>
>>
>> Regards,
>> Martin.
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>

Regards,
Martin.
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Please search the ar

Re: [gmx-users] ./mdrun-gpu fatal error

[Szilárd Páll]

You can try the systems we provided on the GROMACS-GPU page:
http://www.gromacs.org/gpu#GPU_Benchmarks

--
Szilárd




On Sat, Nov 6, 2010 at 12:59 AM, lin hen  wrote:
> Yeah, I think my problem is the input, but I don't have the .mpd file,  I am
> using the existing input which has no problem with Gromacs 4.0.5
> using ./mdrun-openmm.
>
> So is there any other way I could modify?
> Thanks,
>
> YY
>
>> Date: Fri, 5 Nov 2010 19:54:10 -0400
>> From: jalem...@vt.edu
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] ./mdrun-gpu fatal error
>>
>>
>>
>> lin hen wrote:
>> > Thanks a lot for your reply, I didn't have this .mdp file, and I
>> > attached the log file, how to modify?
>> >
>>
>> You don't have an .mdp file? Then how did you create your input .tpr file?
>> This is the only way to fix your problem - specify proper input parameters
>> in
>> the .mdp file.
>>
>> > Just wonder the gcc compiler, I am using gcc 4.1.2, but I saw the
>> > requirements listed for gcc is 4.4, is it a problem?
>> >
>>
>> I think there have been some issues associated with gcc-4.1.x, but I am
>> not sure
>> that they were specifically related to the compiler or some
>> incompatibility with
>> the code that was addressed. In any case, your compiler is not your
>> problem.
>> You have an error in your input file, and the fatal error is very clear
>> about this.
>>
>> -Justin
>>
>> > Thanks,
>> >
>> > yy
>> >
>> > > Date: Fri, 5 Nov 2010 19:29:09 -0400
>> > > From: jalem...@vt.edu
>> > > To: gmx-users@gromacs.org
>> > > Subject: Re: [gmx-users] ./mdrun-gpu fatal error
>> > >
>> > >
>> > >
>> > > lin hen wrote:
>> > > > Hi,
>> > > >
>> > > > I am new for gromacs, I am trying to run the mdrun-gpu executable:
>> > > >
>> > > > the step to build the mdrun-gpu:
>> > > >
>> > > > 1. disable the shared libraries:
>> > > > //disable shared libraries (can be problematic with MPI, Windows)
>> > > > BUILD_SHARED_LIBS:BOOL=OFF
>> > > > 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$
>> > LD_LIBRARY_PATH
>> > > > 3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
>> > > > 4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
>> > > > 5. ./configure
>> > > > 6. cmake -DGMX_OPENMM=ON
>> > > > 7. make mdrun
>> > > > 8. make install
>> > > >
>> > > > when I got the mdrun-gpu in /src/kernel.
>> > > >
>> > > > I put all the shared libs in one folder, point the LD_LIBRARY_PATH
>> > > > to
>> > > > this folder, also openmm libs
>> > > >
>> > > > The attached is the .tpr file I use in the same folder with
>> > > > mdrun-gpu.
>> > > >
>> > > > when i run ./mdrun-gpu
>> > > > it shows:
>> > > >
>> > > > :-) G R O M A C S (-:
>> > > > GROningen MAchine for Chemical Simulation
>> > > > :-) VERSION 4.5.1 (-:
>> > > > Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>> > > > Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>> > > > Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
>> > > > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
>> > > > Michael Shirts, Alfons Sijbers, Peter Tieleman,
>> > > > Berk Hess, David van der Spoel, and Erik Lindahl.
>> > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> > > > Copyright (c) 2001-2010, The GROMACS development team at
>> > > > Uppsala University & The Royal Institute of Technology, Sweden.
>> > > > check out http://www.gromacs.org 
>> > > > for more information.
>> > > > This program is free software; you can redistribute it and/or
>> > > > modify it under the terms of the GNU General Public License
>> > > > as published by the Free Software Foundation; either version 2
>> > > > of the License, or (at your option) any later version.
>> > > > :-) ./mdrun-gpu (-:
>> > > > Option Filename Type Description
>> > > > 
>> > > > -s topol.tpr Input Run input file: tpr tpb tpa
>> > > > -o traj.trr Output Full precision trajectory: trr trj cpt
>> > > > -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
>> > > > format)
>> > > > -cpi state.cpt Input, Opt. Checkpoint file
>> > > > -cpo state.cpt Output, Opt. Checkpoint file
>> > > > -c confout.gro Output Structure file: gro g96 pdb etc.
>> > > > -e ener.edr Output Energy file
>> > > > -g md.log Output Log file
>> > > > -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
>> > > > -field field.xvg Output, Opt. xvgr/xmgr file
>> > > > -table table.xvg Input, Opt. xvgr/xmgr file
>> > > > -tablep tablep.xvg Input, Opt. xvgr/xmgr file
>> > > > -tableb table.xvg Input, Opt. xvgr/xmgr file
>> > > > -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
>> > > > -tpi tpi.xvg Output, Opt. xvgr/xmgr file
>> > > > -tpid tpidist.xvg Output, Opt. xvgr/xmgr file
>> > > > -ei sam.edi Input, Opt. ED sampling input
>> > > > -eo sam.edo Output, Opt. ED sampling output
>> > > > -j wham.gct Input, Opt. General coupling stuff
>> > > > -jo bam.gct Output, Opt. General coupling stuff
>> > > > 

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

[Diana Lousa]

Hello,

No, the hole don't correspond to parts of the protein sticking out on the
other side. The protein is in the center of the box and the holes are not
due to pbc issues.


Diana

On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar  wrote:

> Hey,
>
> Do the holes match the parts of the protein sticking out on the other side?
>
>
> Tsjerk
>
> On Nov 5, 2010 8:14 PM, "Vitaly Chaban"  wrote:
>
> On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz  wrote:
> > hi vitaly,
> >
> > the only acetonitrile boxe that i was able to find is the one provided by
> > christoph freudenberger in 2003:
> >
> > http://www.gromacs.org/@api/deki/files/34/=mecn_box.tgz
>
> Maybe somewhere on other old website if they lost it while migrating
> to the new one - there should have been a few carbon nanotubes + ACN
> systems. If you need a 6-point ACN box, I can find it on my own
> archives.
>
> > where exactly is yours? i am simulating with that solvent at the moment
> but
> > the charges are different from the the ones mentioned above .. and the
> > density is a little less than it should be (640g/ml).
>
> Hmm... Is 640 kg/m3 the density with protein? What it should be then
> (if with protein)?
>
> The density of the bulk ACN is 770kg/m3 at 300K, and the model, which
> we used, reproduces it perfectly.
>
> -
> Dr. Vitaly V. Chaban
>
>
>
> > Am 05.11.2010 19:16, schrieb Vitaly Chaban:
>
> >> >> Diana - >> >> I just wonder how the density of your system behaves
> while you run NPT >> equili...
>
>
> --
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Protein Modeling Laboratory
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Oeiras, Portugal
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Re: [gmx-users] Using mdrun -rerun to get energy values

[Krzysztof Mlynarczyk]

Hi Martin,

Well, I was browsing the source code just yesterday cause I also noticed
that with steep integrator mdrun does not notice -rerun presence. And it
turned out that in do_steep() no one cares if -rerun is on. And if you think
for a moment what it does, it makes sense. However, it would be good to add
a check in the future releases so that gmx_fatal() is called in case someone
combines -rerun with integrators from minimize.c.

I'm happy that I was helpful.

Chris

2010/11/6 Martin Kamp Jensen 

> Hi Chris,
>
> On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk  > wrote:
>
>> Hi,
>>
>> You need to use md integrator for -rerun to work.
>>
>
> Aha, now it seems to work. Thanks!
>
> I am just sad that I did not find that information. According to
> http://manual.gromacs.org/current/online/mdrun.html "With -rerun an input
> trajectory can be given for which forces and energies will be
> (re)calculated. Neighbor searching will be performed for every frame, unless
> nstlist is zero (see the .mdp file)."
>
>
>>
>> Good luck,
>> Chris
>>
>> 2010/11/6 Martin Kamp Jensen 
>>
>>> Hello,
>>>
>>> Hopefully someone can help me understand how to use the mdrun -rerun
>>> functionality, because currently I am confused. I would like to be able to
>>> look up potential energy values for a number of conformations by calling
>>> mdrun -rerun once.
>>>
>>> The idea to use mdrun -rerun is from advice given to me by Mark Abraham
>>> on the gmx-developers list (
>>> http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html
>>>  and
>>> http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html
>>> ):
>>>
>>> You want GROMACS to find the energy of a potentially infinite set of
 coordinates that appear magically, and that is what mdrun -rerun does.
>>>
>>>
 The elegant way to do that is to write your series of conformations to a
 pseudo-trajectory (in whichever of GROMACS many trajectory formats is
 convenient to you), and then invoke mdrun -rerun on that trajectory with a
 suitable .tpr. Then you either parse the .log file or the output .edr file
 for the energies.
>>>
>>>
>>> I wanted to find out how this works so I have been experimenting. I
>>> started out by looking at the Peptide tutorial at
>>> http://manual.gromacs.org/current/online/speptide.html. I used three
>>> different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me
>>> three conformations and their energy values. For testing purposes I then
>>> wanted to get the energy values for those three conformations using mdrun
>>> -rerun (and since I already have the correct energy values it is easy to
>>> verify the results).
>>>
>>> First, I created a trajectory by concatenating the three conformations
>>> (gro files) into one gro file (which is okay according to
>>> http://manual.gromacs.org/current/online/gro.html: "gro files can be
>>> used as trajectory by simply concatenating files"). I then used an mdp file
>>> with integrator = steep and nsteps = 0 indicating that I just want the
>>> energy value (listed in the output, in the log file or by using g_energy).
>>> Now, by using mdrun -s  -rerun  I only get
>>> the energy value for the first conformation listed in the gro file used to
>>> create the tpr file. The -rerun option does not seem to have any effect at
>>> all.
>>>
>>> I used the following commands three times to create three different
>>> conformations (one conf_mdrun.gro file for each time) with different energy
>>> values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in
>>> em.mdp.
>>>
>>> pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx << EOF
>>>
>>> 1
>>>
>>> 1
>>>
>>> EOF
>>>
>>>
 editconf -f conf_pdb2gmx -o conf_editconf -d 0.5
>>>
>>>
 genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox
>>>
>>> mv top_pdb2gmx.top top_genbox.top
>>>
>>> mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top
>>>
>>>
 grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp
>>>
>>>
 mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun
>>>
>>>
>>> I was hoping the following would give me the three energy values for the
>>> three conformations in 2+1+0.gro, which is the concatenation of the three
>>> conf_mdrun.gro files from before. However, I just get the energy value from
>>> the first conformation in the file. Using the -rerun option does not make a
>>> difference (I can put whatever after -rerun, even files that do not exist,
>>> without any effect).
>>>
>>> grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp
>>>
>>>
 mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro
>>>
>>>
>>> Regards,
>>> Martin.
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> www interface or send it to gm

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

[Tsjerk Wassenaar]

Hi Diana,

Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
reading, sorry. But are these holes created by genbox, or are they already
present in the acn solven box? Have you already checked all intermediate
structures?

Cheers,

Tsjerk

On Nov 6, 2010 7:25 PM, "Diana Lousa"  wrote:

Hello,

No, the hole don't correspond to parts of the protein sticking out on the
other side. The protein is in the center of the box and the holes are not
due to pbc issues.


Diana

On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar  wrote:


> > > Hey, > > Do the holes match the parts of the protein sticking out on
> the other side? > > Tsjerk ...
> --
>
> > gmx-users mailing listgmx-users@gromacs.org >
> http://lists.gromacs.org/mailman/listinfo/gmx-u...
>



-- 

Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras,
Portugal

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Re: [gmx-users] Re: genbox generating acetonitrile box with holes

[Diana Lousa]

Hi,

It seems to me that the holes are created by genbox because I don't have
them in the original solvent box. The intermediate box (outputed by trjconv)
with the protein solvated but not converted is difficult to analyze, because
the box doesn't have the right shape and of pbc issues, but it seems to me
that the holes are present in this box, i.e. I don't think they are an
artifact of trjconv.

Thanks for the help

Diana

On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar  wrote:

> Hi Diana,
>
> Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
> reading, sorry. But are these holes created by genbox, or are they already
> present in the acn solven box? Have you already checked all intermediate
> structures?
>
> Cheers,
>
> Tsjerk
>
> On Nov 6, 2010 7:25 PM, "Diana Lousa"  wrote:
>
> Hello,
>
> No, the hole don't correspond to parts of the protein sticking out on the
> other side. The protein is in the center of the box and the holes are not
> due to pbc issues.
>
>
> Diana
>
> On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar 
> wrote:
>
>> > > Hey, > > Do the holes match the parts of the protein sticking out on
>> the other side? > > Tsjerk ...
>> --
>>
>> > gmx-users mailing listgmx-users@gromacs.org >
>> http://lists.gromacs.org/mailman/listinfo/gmx-u...
>>
>
>
>
> --
>
> Diana Lousa PhD student Protein Modeling Laboratory ITQB/UNL Oeiras,
> Portugal
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
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-- 
Diana Lousa
PhD student
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
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Re: [gmx-users] Re: genbox generating acetonitrile box with holes

[Tsjerk Wassenaar]

Hi Diana,

Does it also happen if you solvate the box without the protein? And are the
holes close to the protein or just anywhere? And what makes it difficult to
analyze the structure output by genbox directly, perhaps specifying that the
output be .pdb? It's what I usually do.

Cheers,

Tsjerk

On Nov 6, 2010 9:15 PM, "Diana Lousa"  wrote:

Hi,

It seems to me that the holes are created by genbox because I don't have
them in the original solvent box. The intermediate box (outputed by trjconv)
with the protein solvated but not converted is difficult to analyze, because
the box doesn't have the right shape and of pbc issues, but it seems to me
that the holes are present in this box, i.e. I don't think they are an
artifact of trjconv.

Thanks for the help

Diana

On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar  wrote:
> > Hi Diana, > > Yeah...

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[gmx-users] Re: genbox generating acetonitrile box with holes

[Vitaly Chaban]

Holes... Holes... What is the size of these holes? Use g_density,
g_rdf, make plots, observe peaks...



> Hi Diana,
>
> Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
> reading, sorry. But are these holes created by genbox, or are they already
> present in the acn solven box? Have you already checked all intermediate
> structures?
>
> Cheers,
>
> Tsjerk
>
> On Nov 6, 2010 7:25 PM, "Diana Lousa"  wrote:
>
> Hello,
>
> No, the hole don't correspond to parts of the protein sticking out on the
> other side. The protein is in the center of the box and the holes are not
> due to pbc issues.
>
>
> Diana
>
> On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar  wrote:
>
>
>> > > Hey, > > Do the holes match the parts of the protein sticking out on
>> the other side? > > Tsjerk ...
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[gmx-users] High Temprature MD with scaled params

[Sai Pooja]

Hi,

I have scaled the non-bonded parameters(charges and epsilon) of tip3p atoms
in ffnonbonded.itp file(charmm forcefield). They are scaled by a ratio of
3/5. The simulation is then run at 500K for the protein water system. The
temperature exploded after first 20 steps. This does not happen if I run the
simulations with the unscaled parameters. I have also tried this with T=400
and temperature remains stable.

Pooja

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[gmx-users] High Temprature MD with scaled params

[chris . neale]

I suspect that you need to re-equilibrate your box volume to the new  
solute parameters -- the volume probably needs to increase. Run a  
simulation with a much smaller timestep and the Berendsen barostat and  
the SD integrator. If this is stable, then use the output coordinates  
of that to start your simulation with your desired parameters.


-- original message --

Hi,

I have scaled the non-bonded parameters(charges and epsilon) of tip3p atoms
in ffnonbonded.itp file(charmm forcefield). They are scaled by a ratio of
3/5. The simulation is then run at 500K for the protein water system. The
temperature exploded after first 20 steps. This does not happen if I run the
simulations with the unscaled parameters. I have also tried this with T=400
and temperature remains stable.

Pooja

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Re: [gmx-users] Using mdrun -rerun to get energy values

[Mark Abraham]

On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:

Hi Chris,

On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk 
mailto:mitomas...@gmail.com>> wrote:


Hi,

You need to use md integrator for -rerun to work.


Aha, now it seems to work. Thanks!

I am just sad that I did not find that information. According to 
http://manual.gromacs.org/current/online/mdrun.html "With -rerun an 
input trajectory can be given for which forces and energies will be 
(re)calculated. Neighbor searching will be performed for every frame, 
unless nstlist is zero (see the .mdp file)."


Writing and documenting bulletproof software is tough work :-(

I've fixed the code so that -rerun and EM or NM integrators flag a fatal 
error.


Mark



Good luck,
Chris

2010/11/6 Martin Kamp Jensen mailto:martin.kamp.jen...@gmail.com>>

Hello,

Hopefully someone can help me understand how to use the mdrun
-rerun functionality, because currently I am confused. I would
like to be able to look up potential energy values for a
number of conformations by calling mdrun -rerun once.

The idea to use mdrun -rerun is from advice given to me by
Mark Abraham on the gmx-developers list

(http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html 
and

http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html):

You want GROMACS to find the energy of a potentially
infinite set of coordinates that appear magically, and
that is what mdrun -rerun does.


The elegant way to do that is to write your series of
conformations to a pseudo-trajectory (in whichever of
GROMACS many trajectory formats is convenient to you), and
then invoke mdrun -rerun on that trajectory with a
suitable .tpr. Then you either parse the .log file or the
output .edr file for the energies.


I wanted to find out how this works so I have been
experimenting. I started out by looking at the Peptide
tutorial at
http://manual.gromacs.org/current/online/speptide.html. I used
three different mdp files (integrator = steep, nsteps = 0, 1,
2). This gave me three conformations and their energy values.
For testing purposes I then wanted to get the energy values
for those three conformations using mdrun -rerun (and since I
already have the correct energy values it is easy to verify
the results).

First, I created a trajectory by concatenating the three
conformations (gro files) into one gro file (which is okay
according to
http://manual.gromacs.org/current/online/gro.html: "gro files
can be used as trajectory by simply concatenating files"). I
then used an mdp file with integrator = steep and nsteps = 0
indicating that I just want the energy value (listed in the
output, in the log file or by using g_energy). Now, by using
mdrun -s  -rerun  I only get
the energy value for the first conformation listed in the gro
file used to create the tpr file. The -rerun option does not
seem to have any effect at all.

I used the following commands three times to create three
different conformations (one conf_mdrun.gro file for each
time) with different energy values. I am just setting nsteps
to 0, 1, or 2 (integrator = steep) in em.mdp.

pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i
top_pdb2gmx << EOF

1

1

EOF


editconf -f conf_pdb2gmx -o conf_editconf -d 0.5


genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox

mv top_pdb2gmx.top top_genbox.top

mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top


grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o
em_grompp


mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun


I was hoping the following would give me the three energy
values for the three conformations in 2+1+0.gro, which is the
concatenation of the three conf_mdrun.gro files from before.
However, I just get the energy value from the first
conformation in the file. Using the -rerun option does not
make a difference (I can put whatever after -rerun, even files
that do not exist, without any effect).

grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o
em_grompp


mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro


Regards,
Martin.

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[gmx-users] Re: High Temprature MD with scaled params

[Vitaly Chaban]

> Hi,
>
> I have scaled the non-bonded parameters(charges and epsilon) of tip3p atoms
> in ffnonbonded.itp file(charmm forcefield). They are scaled by a ratio of
> 3/5.

What's the idea behind this scaling please?


>The simulation is then run at 500K for the protein water system. The
> temperature exploded after first 20 steps. This does not happen if I run the
> simulations with the unscaled parameters. I have also tried this with T=400
> and temperature remains stable.

Do you run NPT or NVT here? I believe the decrease of time-step can
solve any problem with a poorly equilibrated system.


Vitaly Chaban, Ph.D.
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