Re: [gmx-users] Gromacs 4.0.6 installation error

[Dian Jiao]

I got it to work finally. Didn't install fftw earlier. Thanks.

On Fri, Mar 5, 2010 at 4:02 PM, Mark Abraham wrote:

> On 6/03/2010 5:05 AM, Dian Jiao wrote:
>
>> Actually, I tried 4.0.7 first from this link,
>> http://www.gromacs.org/index.php?title=Download_%26_Installation
>>
>> It didn't work (same error). That's why I downloaded 4.0.6 from the same
>> webpage.
>>
>> On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul > > wrote:
>>
>>
>>
>>Dian Jiao wrote:
>>
>>I was following the instruction to install gromacs 4.0.6 on my
>>machine.
>>
>>./configure --enable-threads --enable-float --|enable-sse
>>--prefix=[mypath]|
>>
>
> Don't enable threads. Do follow an actual installation guide like on the
> GROMACS webpage.
>
> Mark
>
> make
>>make install
>>The configure looks ok but no Makefile is generated. When I do
>>make or make install, it gives me the error:
>>
>>make: *** No targets specified and no makefile found.  Stop.
>>
>>There are couple makefiles in the directory though, Makefile.in
>>and Makefile.am, do I need to rename one of them to Makefile to
>>make it work?
>>
>>
>>Per the warning on the Gromacs homepage, version 4.0.6 is a broken
>>distribution.  Use version 4.0.7 instead.
>>
>>-Justin
>>
>>Dian
>>
>>
>>--
>>
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
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Re: [gmx-users] pdb & gro files

[Mark Abraham]

On 6/03/2010 1:19 AM, Carla Jamous wrote:

Hi,
please I'm having a problem while running a minimisation.

I prepared my system with pdb2gmx and generated .pdb files. From the
last pdb file, I did grompp & generated the tpr file that I used to
start my minimization. At the 46th step, I encountered the
problem:"water molecule cannot be settled".
I looked at the pdb file and found that many water residues have the
same number because above residue , it restarts to count residue 0,
1, etc...

I prepared the same system but I generated .gro files instead of .pdb &
started my minimization. But did't encounter the same problem.
I looked at the gro file & here, it's the atomic number that can't be
above 9.

So did anyone encounter this problem before, & if yes, please do you
have a solution to propose?


Just use .gro files for these intermediate output files. There are very 
limited reasons to want .pdb for such intermediate output, such as 
visualization. If your visualization program can't read .gro, either get 
a new one (e.g. VMD), or use editconf to convert .gro -> .pdb before 
visualization.


Mark
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Re: [gmx-users] Gromacs 4.0.6 installation error

[Mark Abraham]

On 6/03/2010 5:05 AM, Dian Jiao wrote:

Actually, I tried 4.0.7 first from this link,
http://www.gromacs.org/index.php?title=Download_%26_Installation

It didn't work (same error). That's why I downloaded 4.0.6 from the same
webpage.

On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Dian Jiao wrote:

I was following the instruction to install gromacs 4.0.6 on my
machine.

./configure --enable-threads --enable-float --|enable-sse
--prefix=[mypath]|


Don't enable threads. Do follow an actual installation guide like on the 
GROMACS webpage.


Mark


make
make install
The configure looks ok but no Makefile is generated. When I do
make or make install, it gives me the error:

make: *** No targets specified and no makefile found.  Stop.

There are couple makefiles in the directory though, Makefile.in
and Makefile.am, do I need to rename one of them to Makefile to
make it work?


Per the warning on the Gromacs homepage, version 4.0.6 is a broken
distribution.  Use version 4.0.7 instead.

-Justin

Dian


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] isopropanol parameters?

[Jose Borreguero]

I am using SPC/E water model. Regarding isopropanol, these are the partial
charges:
 "H1"0.038594
 "C1"0.147250
 "HC1"  0.038591
 "C2"-0.106023
 "HC2"  0.038591
 "HC3"  0.038591
 "HA1"  0.038591
 "C3"-0.106023
 "HA2"   0.038591
 "HA3"   0.038591
 "O1"-0.579340
 "HO1"  0.373996
And the VdW radii and epsilon:
  HC  1.3770  0.0150
  OH  1.7210  0.2104
  CT  1.9080   0.1094
  HO  0.0  0.0


On Fri, Mar 5, 2010 at 3:21 PM, David van der Spoel wrote:

> On 2010-03-05 20.51, Jose Borreguero wrote:
>
>> Dear GROMACS users,
>>
>> I am simulating aqueous isopropanol. Unfortunately I observe segregation
>> of isopropanol from SPC water at isopropanol fraction volume of 0.25.
>> Since isopropanol is miscible in water, my parameters stress too much
>> the hydrophobic character of this solute. Only a few interstitial waters
>> are present in the isopropanol cluster, in order to saturate the
>> hydrogen bonds of the isopropanol hydroxyl groups.
>>
>> If anybody has good isopropanol parameters for simulation in aqueous
>> environment, please let me know.
>>
>> Best regards,
>> Jose M. Borreguero
>>
>>  Which ones did you use? OPLS will be miscible I'm sure, since I did
> 1-propanol sims at 11 concentrations from 0 to 100 Mass%. (With TIP4P).
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
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[gmx-users] problem with icc compiler

[Thomas Schlesier]

Hi,
i observed the following problem. if i simulate water (spc or tip4p) 
with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the 
wrong temperature (ref_t = 300K -> average around 425K, in about 1-2ps), 
but only in serial, not in parallel runs.

non-water molecules or nose-hoover thermostat make no problems.
see also http://lists.gromacs.org/pipermail/gmx-users/2010-March/049248.html
for mdp and log file.

gromacs was compiled with the following comands:
and in the file 'configure' all '-lmkl' were deleted (don't ask me why, 
i don't really understand that stuff, the command were from our previous 
phd student).


./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5"
make
make install
make clean
./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5" --enable-mpi --disable-nice
--program-suffix=_mpi
make mdrun
make install-mdrun

for gromacs 4.0.5 i used the icc 9.1.046 compiler.

i also tried gromacs 4.0.7 with icc 9.1.046 and icc 10.1.008 with spc 
water, v-rescale thermostat.

-> serial: too high temperature 425K iso 300K
-> parallel: no problems
with non-water (mesitylene) i have no problem in serial.

the problem does not come from grompp because i can use same tpr-file 
for serial and parallel runs with the above results.


if someone needs more informations about this please tell me.

greetings
thomas
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Re: [gmx-users] isopropanol parameters?

[David van der Spoel]

On 2010-03-05 20.51, Jose Borreguero wrote:

Dear GROMACS users,

I am simulating aqueous isopropanol. Unfortunately I observe segregation
of isopropanol from SPC water at isopropanol fraction volume of 0.25.
Since isopropanol is miscible in water, my parameters stress too much
the hydrophobic character of this solute. Only a few interstitial waters
are present in the isopropanol cluster, in order to saturate the
hydrogen bonds of the isopropanol hydroxyl groups.

If anybody has good isopropanol parameters for simulation in aqueous
environment, please let me know.

Best regards,
Jose M. Borreguero

Which ones did you use? OPLS will be miscible I'm sure, since I did 
1-propanol sims at 11 concentrations from 0 to 100 Mass%. (With TIP4P).


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] isopropanol parameters?

[Jose Borreguero]

Dear GROMACS users,

I am simulating aqueous isopropanol. Unfortunately I observe segregation of
isopropanol from SPC water at isopropanol fraction volume of 0.25. Since
isopropanol is miscible in water, my parameters stress too much the
hydrophobic character of this solute. Only a few interstitial waters are
present in the isopropanol cluster, in order to saturate the hydrogen bonds
of the isopropanol hydroxyl groups.

If anybody has good isopropanol parameters for simulation in aqueous
environment, please let me know.

Best regards,
Jose M. Borreguero
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Re: [gmx-users] Gromacs 4.0.6 installation error

[Justin A. Lemkul]

Dian Jiao wrote:

Actually, I tried 4.0.7 first from this link,
http://www.gromacs.org/index.php?title=Download_%26_Installation

It didn't work (same error). That's why I downloaded 4.0.6 from the same 
webpage.




Well, downgrading is usually not the answer, especially if you're downgrading to 
a broken distribution.  Maybe this should be removed from the downloads page...


In any case, if a Makefile wasn't generated, then the configuration can't be OK. 
 Some error must have come up.  Check the screen output and config.log, if 
necessary.  Once you have an actual error message, you stand to get better 
advice on how to fix it.


-Justin

On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul > wrote:




Dian Jiao wrote:

I was following the instruction to install gromacs 4.0.6 on my
machine.

./configure --enable-threads --enable-float --|enable-sse
--prefix=[mypath]|
make
make install
The configure looks ok but no Makefile is generated. When I do
make or make install, it gives me the error:

make: *** No targets specified and no makefile found.  Stop.

There are couple makefiles in the directory though, Makefile.in
and Makefile.am, do I need to rename one of them to Makefile to
make it work?


Per the warning on the Gromacs homepage, version 4.0.6 is a broken
distribution.  Use version 4.0.7 instead.

-Justin

Dian


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Gromacs 4.0.6 installation error

[Dian Jiao]

Actually, I tried 4.0.7 first from this link,
http://www.gromacs.org/index.php?title=Download_%26_Installation

It didn't work (same error). That's why I downloaded 4.0.6 from the same
webpage.

On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul  wrote:

>
>
> Dian Jiao wrote:
>
>> I was following the instruction to install gromacs 4.0.6 on my machine.
>>
>> ./configure --enable-threads --enable-float --|enable-sse
>> --prefix=[mypath]|
>> make
>> make install
>> The configure looks ok but no Makefile is generated. When I do make or
>> make install, it gives me the error:
>>
>> make: *** No targets specified and no makefile found.  Stop.
>>
>> There are couple makefiles in the directory though, Makefile.in and
>> Makefile.am, do I need to rename one of them to Makefile to make it work?
>>
>>
> Per the warning on the Gromacs homepage, version 4.0.6 is a broken
> distribution.  Use version 4.0.7 instead.
>
> -Justin
>
>  Dian
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Gromacs 4.0.6 installation error

[Justin A. Lemkul]

Dian Jiao wrote:

I was following the instruction to install gromacs 4.0.6 on my machine.

./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]|
make
make install 

The configure looks ok but no Makefile is generated. When I do make or 
make install, it gives me the error:


make: *** No targets specified and no makefile found.  Stop.

There are couple makefiles in the directory though, Makefile.in and 
Makefile.am, do I need to rename one of them to Makefile to make it work?




Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. 
 Use version 4.0.7 instead.


-Justin


Dian



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Gromacs 4.0.6 installation error

[Dian Jiao]

I was following the instruction to install gromacs 4.0.6 on my machine.

./configure --enable-threads --enable-float --enable-sse --prefix=[mypath]
make
make install

The configure looks ok but no Makefile is generated. When I do make or make
install, it gives me the error:

make: *** No targets specified and no makefile found.  Stop.

There are couple makefiles in the directory though, Makefile.in and
Makefile.am, do I need to rename one of them to Makefile to make it work?

Dian
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Re: [gmx-users] NVT simulation and mdp file

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:

Hi Justin,

That is really confusing. I tried to run this PDB file many times. But 
still I could not get it the topology file. I waited for so long (10 
hrs)but still the code looks in a deadlock.


Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading JUsti.pdb...
Read 'Tolene.pdb', 7 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 7 atoms

  chain  #res #atoms
  1 ' ' 1  7

All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
Atomtype 1

[1]+  Stopped

REMARK   This PDB file is created by CS Chem3D

REMARK

COMPND   Tolene.pdb

ATOM1  CB  PHE 1  -1.158   0.001   
0.000   C


ATOM2  CG  PHE 1  -1.158  -1.336   
0.000   C


ATOM3  CD1 PHE 1  -0.000  -2.004   
0.000   C


ATOM4  CD2 PHE 1   1.158  -1.336   
0.000   C


ATOM5  CE1 PHE 1   1.158   0.001   
0.000   C


ATOM6  CE2 PHE 1  -0.000   0.670   
0.000   C


ATOM7  CZ  PHE 1  -0.000   2.167   
0.000   C


END



can you please tell me what modifications you have done so that your 
pdb2gmx works fine.




I assumed the blank lines between each ATOM entry were a consequence of my email 
client; is your .pdb file actually double-spaced?  If so, that's the wrong 
format.  Other than that, I have no idea, it worked fine for me.  Does pdb2gmx 
correctly work on other .pdb files?


-Justin


thank you for your time

Rob


Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Hi Justin,

Thank you pointing out that!

I made all the changes and still cannot go past this line.

REMARK   This PDB file is created by CS Chem3D

REMARK

COMPND   Tolene.pdb

HETATM1  CB  PHE 0  -1.158   0.001   0.000  
 C


HETATM2  CG  PHE 0  -1.158  -1.336   0.000  
 C


HETATM3  CD1 PHE 0  -0.000  -2.004   0.000  
 C


HETATM4  CD2 PHE 0   1.158  -1.336   0.000  
 C


HETATM5  CE1 PHE 0   1.158   0.001   0.000  
 C


HETATM6  CE2 PHE 0  -0.000   0.670   0.000  
 C


HETATM7  CZ  PHE 0  -0.000   2.167   0.000  
 C


END


As you can see I used this PDB file but still no topology out put.

Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges

Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file

Re: [gmx-users] NVT simulation and mdp file

[teklebrh]

Hi Justin,

That is really confusing. I tried to run this PDB file many times. But  
still I could not get it the topology file. I waited for so long (10  
hrs)but still the code looks in a deadlock.


Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading JUsti.pdb...
Read 'Tolene.pdb', 7 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 7 atoms

  chain  #res #atoms
  1 ' ' 1  7

All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
Atomtype 1

[1]+  Stopped

REMARK   This PDB file is created by CS Chem3D

REMARK

COMPND   Tolene.pdb

ATOM1  CB  PHE 1  -1.158   0.001   0.000   C

ATOM2  CG  PHE 1  -1.158  -1.336   0.000   C

ATOM3  CD1 PHE 1  -0.000  -2.004   0.000   C

ATOM4  CD2 PHE 1   1.158  -1.336   0.000   C

ATOM5  CE1 PHE 1   1.158   0.001   0.000   C

ATOM6  CE2 PHE 1  -0.000   0.670   0.000   C

ATOM7  CZ  PHE 1  -0.000   2.167   0.000   C

END



can you please tell me what modifications you have done so that your  
pdb2gmx works fine.


thank you for your time

Rob


Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Hi Justin,

Thank you pointing out that!

I made all the changes and still cannot go past this line.

REMARK   This PDB file is created by CS Chem3D

REMARK

COMPND   Tolene.pdb

HETATM1  CB  PHE 0  -1.158   0.001   0.000   
 C


HETATM2  CG  PHE 0  -1.158  -1.336   0.000   
 C


HETATM3  CD1 PHE 0  -0.000  -2.004   0.000   
 C


HETATM4  CD2 PHE 0   1.158  -1.336   0.000   
 C


HETATM5  CE1 PHE 0   1.158   0.001   0.000   
 C


HETATM6  CE2 PHE 0  -0.000   0.670   0.000   
 C


HETATM7  CZ  PHE 0  -0.000   2.167   0.000   
 C


END


As you can see I used this PDB file but still no topology out put.

Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges

Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined base

RE: [gmx-users] Turn-off water optimisation

[Thomas Schlesier]

Hi all,
to summerize the

seems really like a compiler problem. i have now compiled 4.0.5 with gcc 
and had no problems.
i don't really know which icc compiler it was (but had send the guy who 
installed gromacs a mail), but with 'which icc' i find:

/share/apps/intel/cce/9.1.046/bin/icc

i will try now 4.0.7 with the icc compiler

Greetings
Thomas
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Re: [gmx-users] Turn-off water optimisation

[Thomas Schlesier]

ter optimisation

Hi,
i have the following problem: (GROMACS 4.0.5)

when i simulated water in serial on our cluster with the brendsen or
v-rescale thermostat i get to high temperatures (300 K goes in very
short time up to around 425 K). If i simulate in parallel or at my

local

machine i get no problems. Also if i change water to another molecule
there are no such problems. (I use the same mdp file for all the
simulations).

Because the problem appears with water (spc and tip4p) but not with
mesitylene i thought probably the special things for water (settle, and
so on) could be the problem. So i wanted to simulate water without that
fancy stuff.
Thanks for the info with the enviroment variable, but where can i

set it?

For the other problems (why it works on the cluster in parallel, but

not

in serial, but works on the local-pc in serial) i have so far no idea,
where to look. But first i'm happy to know if the problem comes from

the

special water-loops.

Thomas




Hi,

You don't want to mess with the topology, you will be simulating a

quit >different

system when you turn off constraints. Also Gromacs does not optimize
based
on names, since the name might not say anything about the molecule.
I don't know what effect of what optimizations you want to test,
but setting the environment variable GMX_NO_SOLV_OPT will turn off
the special inner-loops for water.

Berk
Date: Fri, 5 Mar 2010 11:31:50 +0100
From: schlesi at uni-mainz.de
To: gmx-users at gromacs.org
Subject: [gmx-users] Turn-off water optimisation

Dear all,
I simulated water (spc) with the ffG53a5 force field. For testing
propose i want to turn of the water optimisation. How do i do this?
So far i have tried:
* contraints = none
* define = -DFLEXIBLE
* took the spc.itp file and deleted all the stuff for settle and the
other force fields, changed resname from SOL to WAT (also spc.itp ->
wat.itp)

But all the time i the log file there is this line:
Enabling SPC water optimization for 1184 molecules.

Espically with the last option (change of the spc.itp) i don't how
GROMACS recorgnises that i simulate SPC water, because i has a

different

name and so.

Thanks for your help in advance.
Greetings
Thomas
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Re: [gmx-users] pdb & gro files

[Andrea]

I don't think the atom number is the problem. I also have systems with more
than 9 atoms, and in the gro file the atom number after 9 is reset
to 0, but that was never a problem for the simulations. I would check the
parameters again, but I don't have a more exact answer to your problem.

2010/3/5 Carla Jamous 

> Hi,
> please I'm having a problem while running a minimisation.
>
> I prepared my system with pdb2gmx and generated .pdb files. From the last
> pdb file, I did grompp & generated the tpr file that I used to start my
> minimization. At the 46th step, I encountered the problem:"water molecule
> cannot be settled".
> I looked at the pdb file and found that many water residues have the same
> number because above residue , it restarts to count residue 0, 1, etc...
>
> I prepared the same system but I generated .gro files instead of .pdb &
> started my minimization. But did't encounter the same problem.
> I looked at the gro file & here, it's the atomic number that can't be above
> 9.
>
> So did anyone encounter this problem before, & if yes, please do you have a
> solution to propose?
>
> Thanks
>
> Carla
>
>
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[gmx-users] pdb & gro files

[Carla Jamous]

Hi,
please I'm having a problem while running a minimisation.

I prepared my system with pdb2gmx and generated .pdb files. From the last
pdb file, I did grompp & generated the tpr file that I used to start my
minimization. At the 46th step, I encountered the problem:"water molecule
cannot be settled".
I looked at the pdb file and found that many water residues have the same
number because above residue , it restarts to count residue 0, 1, etc...

I prepared the same system but I generated .gro files instead of .pdb &
started my minimization. But did't encounter the same problem.
I looked at the gro file & here, it's the atomic number that can't be above
9.

So did anyone encounter this problem before, & if yes, please do you have a
solution to propose?

Thanks

Carla
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Re: [gmx-users] Turn-off water optimisation

[Ran Friedman]

Hi,

Can you also post your .mdp?

Ran

Berk Hess wrote:
> Hi,
>
> I have never heard about problems like this before.
> It seems highly unlikely to me that the innerloops are causing this.
>
> Are your running exacly the same tpr file on your local machine
> and the cluster?
>
> You probably want to update to version 4.0.7 to be sure you have
> all the latest bugfixes.
>
> Please keep us updated on this issue, since things like this should
> never happen (unless there is a compiler bug).
>
> Berk
>
> > Date: Fri, 5 Mar 2010 14:41:02 +0100
> > From: schl...@uni-mainz.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] Turn-off water optimisation
> >
> > Hi,
> > i have the following problem: (GROMACS 4.0.5)
> >
> > when i simulated water in serial on our cluster with the brendsen or
> > v-rescale thermostat i get to high temperatures (300 K goes in very
> > short time up to around 425 K). If i simulate in parallel or at my
> local
> > machine i get no problems. Also if i change water to another molecule
> > there are no such problems. (I use the same mdp file for all the
> > simulations).
> >
> > Because the problem appears with water (spc and tip4p) but not with
> > mesitylene i thought probably the special things for water (settle, and
> > so on) could be the problem. So i wanted to simulate water without that
> > fancy stuff.
> > Thanks for the info with the enviroment variable, but where can i
> set it?
> >
> > For the other problems (why it works on the cluster in parallel, but
> not
> > in serial, but works on the local-pc in serial) i have so far no idea,
> > where to look. But first i'm happy to know if the problem comes from
> the
> > special water-loops.
> >
> > Thomas
> >
> >
> >
> > >Hi,
> > >
> > >You don't want to mess with the topology, you will be simulating a
> > quit >different
> > >system when you turn off constraints. Also Gromacs does not optimize
> > >based
> > >on names, since the name might not say anything about the molecule.
> > >I don't know what effect of what optimizations you want to test,
> > >but setting the environment variable GMX_NO_SOLV_OPT will turn off
> > >the special inner-loops for water.
> > >
> > >Berk
> >
> > > Date: Fri, 5 Mar 2010 11:31:50 +0100
> > > From: schlesi at uni-mainz.de
> > > To: gmx-users at gromacs.org
> > > Subject: [gmx-users] Turn-off water optimisation
> > >
> > > Dear all,
> > > I simulated water (spc) with the ffG53a5 force field. For testing
> > > propose i want to turn of the water optimisation. How do i do this?
> > > So far i have tried:
> > > * contraints = none
> > > * define = -DFLEXIBLE
> > > * took the spc.itp file and deleted all the stuff for settle and the
> > > other force fields, changed resname from SOL to WAT (also spc.itp ->
> > > wat.itp)
> > >
> > > But all the time i the log file there is this line:
> > > Enabling SPC water optimization for 1184 molecules.
> > >
> > > Espically with the last option (change of the spc.itp) i don't how
> > > GROMACS recorgnises that i simulate SPC water, because i has a
> different
> > > name and so.
> > >
> > > Thanks for your help in advance.
> > > Greetings
> > > Thomas
> > > --
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > --
> > gmx-users mailing list gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
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>
> 
> New Windows 7: Simplify what you do everyday. Find the right PC for
> you. 

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RE: [gmx-users] Turn-off water optimisation

[Berk Hess]

Hi,

I have never heard about problems like this before.
It seems highly unlikely to me that the innerloops are causing this.

Are your running exacly the same tpr file on your local machine
and the cluster?

You probably want to update to version 4.0.7 to be sure you have
all the latest bugfixes.

Please keep us updated on this issue, since things like this should
never happen (unless there is a compiler bug).

Berk

> Date: Fri, 5 Mar 2010 14:41:02 +0100
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Turn-off water optimisation
> 
> Hi,
> i have the following problem: (GROMACS 4.0.5)
> 
> when i simulated water in serial on our cluster with the brendsen or 
> v-rescale thermostat i get to high temperatures (300 K goes in very 
> short time up to around 425 K). If i simulate in parallel or at my local 
> machine i get no problems. Also if i change water to another molecule 
> there are no such problems. (I use the same mdp file for all the 
> simulations).
> 
> Because the problem appears with water (spc and tip4p) but not with 
> mesitylene i thought probably the special things for water (settle, and 
> so on) could be the problem. So i wanted to simulate water without that 
> fancy stuff.
> Thanks for the info with the enviroment variable, but where can i set it?
> 
> For the other problems (why it works on the cluster in parallel, but not 
> in serial, but works on the local-pc in serial) i have so far no idea, 
> where to look. But first i'm happy to know if the problem comes from the 
>   special water-loops.
> 
> Thomas
> 
> 
> 
>  >Hi,
>  >
>  >You don't want to mess with the topology, you will be simulating a 
> quit >different
>  >system when you turn off constraints. Also Gromacs does not optimize 
>  >based
>  >on names, since the name might not say anything about the molecule.
>  >I don't know what effect of what optimizations you want to test,
>  >but setting the environment variable GMX_NO_SOLV_OPT will turn off
>  >the special inner-loops for water.
>  >
>  >Berk
> 
>  > Date: Fri, 5 Mar 2010 11:31:50 +0100
>  > From: schlesi at uni-mainz.de
>  > To: gmx-users at gromacs.org
>  > Subject: [gmx-users] Turn-off water optimisation
>  >
>  > Dear all,
>  > I simulated water (spc) with the ffG53a5 force field. For testing
>  > propose i want to turn of the water optimisation. How do i do this?
>  > So far i have tried:
>  > * contraints = none
>  > * define = -DFLEXIBLE
>  > * took the spc.itp file and deleted all the stuff for settle and the
>  > other force fields, changed resname from SOL to WAT (also spc.itp ->
>  > wat.itp)
>  >
>  > But all the time i the log file there is this line:
>  > Enabling SPC water optimization for 1184 molecules.
>  >
>  > Espically with the last option (change of the spc.itp) i don't how
>  > GROMACS recorgnises that i simulate SPC water, because i has a different
>  > name and so.
>  >
>  > Thanks for your help in advance.
>  > Greetings
>  > Thomas
>  > --
>  > gmx-users mailing list gmx-users at gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at http://www.gromacs.org/search before 
> posting!
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>  > www interface or send it to gmx-users-request at gromacs.org.
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Re: [gmx-users] Turn-off water optimisation

[Thomas Schlesier]

Hi,
i have the following problem: (GROMACS 4.0.5)

when i simulated water in serial on our cluster with the brendsen or 
v-rescale thermostat i get to high temperatures (300 K goes in very 
short time up to around 425 K). If i simulate in parallel or at my local 
machine i get no problems. Also if i change water to another molecule 
there are no such problems. (I use the same mdp file for all the 
simulations).


Because the problem appears with water (spc and tip4p) but not with 
mesitylene i thought probably the special things for water (settle, and 
so on) could be the problem. So i wanted to simulate water without that 
fancy stuff.

Thanks for the info with the enviroment variable, but where can i set it?

For the other problems (why it works on the cluster in parallel, but not 
in serial, but works on the local-pc in serial) i have so far no idea, 
where to look. But first i'm happy to know if the problem comes from the 
 special water-loops.


Thomas



>Hi,
>
>You don't want to mess with the topology, you will be simulating a 
quit >different
>system when you turn off constraints. Also Gromacs does not optimize 
>based

>on names, since the name might not say anything about the molecule.
>I don't know what effect of what optimizations you want to test,
>but setting the environment variable GMX_NO_SOLV_OPT will turn off
>the special inner-loops for water.
>
>Berk

> Date: Fri, 5 Mar 2010 11:31:50 +0100
> From: schlesi at uni-mainz.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Turn-off water optimisation
>
> Dear all,
> I simulated water (spc) with the ffG53a5 force field. For testing
> propose i want to turn of the water optimisation. How do i do this?
> So far i have tried:
> * contraints = none
> * define = -DFLEXIBLE
> * took the spc.itp file and deleted all the stuff for settle and the
> other force fields, changed resname from SOL to WAT (also spc.itp ->
> wat.itp)
>
> But all the time i the log file there is this line:
> Enabling SPC water optimization for 1184 molecules.
>
> Espically with the last option (change of the spc.itp) i don't how
> GROMACS recorgnises that i simulate SPC water, because i has a different
> name and so.
>
> Thanks for your help in advance.
> Greetings
> Thomas
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[gmx-users] Re: diffusion coefficient of oxygen molecule

[Vitaly V. Chaban]

> Respected experts
> I want to calculate the self diffusion cofficient of an oxygen molecule in 
> water. The experimental value in the literature is found to be 2.5 x 10-9 
> nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off 
> Lennard Jones interaction between water and oxygen. I want to reproduce this 
> value. In your experience, which model of water would give the closer value. 
> I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 
> 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding 
> potential has been taken to be harmonic. Any knowledge of related literature 
> would be helpful because I could not find by googling.
>
> Your idea will really help me.
> Neal

Many guys enjoy SPCE. Its diffusion constant is lower than those of
the models you mentioned, if I'm not mistaken.


-- 
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http://www-rmn.univer.kharkov.ua/chaban.html
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RE: [gmx-users] Turn-off water optimisation

[Berk Hess]

Hi,

You don't want to mess with the topology, you will be simulating a quit 
different
system when you turn off constraints. Also Gromacs does not optimize based
on names, since the name might not say anything about the molecule.
I don't know what effect of what optimizations you want to test,
but setting the environment variable GMX_NO_SOLV_OPT will turn off
the special inner-loops for water.

Berk

> Date: Fri, 5 Mar 2010 11:31:50 +0100
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Turn-off water optimisation
> 
> Dear all,
> I simulated water (spc) with the ffG53a5 force field. For testing 
> propose i want to turn of the water optimisation. How do i do this?
> So far i have tried:
> * contraints = none
> * define = -DFLEXIBLE
> * took the spc.itp file and deleted all the stuff for settle and the 
> other force fields, changed resname from SOL to WAT (also spc.itp -> 
> wat.itp)
> 
> But all the time i the log file there is this line:
> Enabling SPC water optimization for 1184 molecules.
> 
> Espically with the last option (change of the spc.itp) i don't how 
> GROMACS recorgnises that i simulate SPC water, because i has a different 
> name and so.
> 
> Thanks for your help in advance.
> Greetings
> Thomas
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] Turn-off water optimisation

[Thomas Schlesier]

Dear all,
I simulated water (spc) with the ffG53a5 force field. For testing 
propose i want to turn of the water optimisation. How do i do this?

So far i have tried:
* contraints = none
* define = -DFLEXIBLE
* took the spc.itp file and deleted all the stuff for settle and the 
other force fields, changed resname from SOL to WAT (also spc.itp -> 
wat.itp)


But all the time i the log file there is this line:
Enabling SPC water optimization for 1184 molecules.

Espically with the last option (change of the spc.itp) i don't how 
GROMACS recorgnises that i simulate SPC water, because i has a different 
name and so.


Thanks for your help in advance.
Greetings
Thomas
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Re: [gmx-users] diffusion coefficient of oxygen molecule

[Amit Choubey]

Hi,

If i remember correctly SPC/E water might be worth trying. There is plenty
of research paper in this field. Try this paper

http://pubs.acs.org/doi/abs/10.1021/jp003020w

Also P,T coupling have effects on Diffusion Coeff.


amit

On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa  wrote:

> Respected experts
> I want to calculate the self diffusion cofficient of an oxygen molecule in
> water. The experimental value in the literature is found to be 2.5 x 10-9
> nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off
> Lennard Jones interaction between water and oxygen. I want to reproduce this
> value. In your experience, which model of water would give the closer value.
> I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units
> and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding
> potential has been taken to be harmonic. Any knowledge of related literature
> would be helpful because I could not find by googling.
>
> Your idea will really help me.
> Neal
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] diffusion coefficient of oxygen molecule

[Erik Marklund]

Sunil Thapa skrev:

Respected experts
I want to calculate the self diffusion cofficient of an oxygen 
molecule in water. The experimental value in the literature is found 
to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have 
considered cut-off Lennard Jones interaction between water and oxygen. 
I want to reproduce this value. In your experience, which model of 
water would give the closer value. I have seen that the self diffusion 
of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual 
value is 2.4 unit. For oxygen the bonding potential has been taken to 
be harmonic. Any knowledge of related literature would be helpful 
because I could not find by googling.
 
Your idea will really help me.

Neal



Hi,

I do know that there are finite size effects that affects the diffusion 
coefficient, so you should make sure you use a big enough box. 
Furthermore, for water polarizability has an impact on the diffusion 
coefficient, so if you want to reproduce experimental values, consider 
using a polarizable model.


--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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[gmx-users] diffusion coefficient of oxygen molecule

[Sunil Thapa]

Respected experts
I want to calculate the self diffusion cofficient of an oxygen molecule in 
water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s 
at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones 
interaction between water and oxygen. I want to reproduce this value. In your 
experience, which model of water would give the closer value. I have seen that 
the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas 
the actual value is 2.4 unit. For oxygen the bonding potential has been taken 
to be harmonic. Any knowledge of related literature would be helpful because I 
could not find by googling.
 
Your idea will really help me.
Neal


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