[gmx-users] conversion of gromacs topology format

[aiswarya pawar]

Hi gromacs users,

Is there a way to convert gromacs topology format to Amber.

Thanks,
Aiswarya
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Re: [gmx-users] conversion of gromacs topology format

[Mark Abraham]

On 8/09/2011 6:06 PM, aiswarya pawar wrote:

Hi gromacs users,

Is there a way to convert gromacs topology format to Amber.


Did you try Googling for such a tool first? :) There probably isn't one, 
because starting from scratch with leap is sufficiently easy that a 
conversion tool is not worth the development and maintenance time.


Mark
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[gmx-users] How to make a CG topology for a modified residue?

[Du Jiangfeng (BIOCH)]

Dear Everyone,

I am going to simulate the interaction of prothrombin's Gla domain with 
membrane in martini force field. Here I encountered a problem: there are 10 
modified GLUs in GLA domain. Martini force field can't recognize them. How 
should I overcome this problem?

What I want to do now is to add this modified residue into martini force field, 
but I do not know whether it is feasible or logical? What's worse, I really 
don't know what is BNLN, BNKB or ANGL? Where can I get some references about 
this story?

Any help will be appreciated,
 


Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
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Re: [gmx-users] How to make a CG topology for a modified residue?

[Mark Abraham]

On 8/09/2011 6:29 PM, Du Jiangfeng (BIOCH) wrote:

Dear Everyone,

I am going to simulate the interaction of prothrombin's Gla domain with 
membrane in martini force field. Here I encountered a problem: there are 10 
modified GLUs in GLA domain. Martini force field can't recognize them. How 
should I overcome this problem?

What I want to do now is to add this modified residue into martini force field, 
but I do not know whether it is feasible or logical? What's worse, I really 
don't know what is BNLN, BNKB or ANGL? Where can I get some references about 
this story?


Depending on the details of the modified GLU, you will need to consider 
the points made at 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, 
http://www.gromacs.org/Documentation/How-tos/Parameterization and in the 
Martini documentation.


Mark
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[gmx-users] Constant-pH simulation

[Emanuel Peter]

Dear Mr. Baptista, and others,

Thank you for your advice.
I was not aware of the constant pH-simulation technique up to now
and I will remember the given remarks in the future.
Would be desirable to have sometimes comments on 
any topic of such quality as that remark of Mr. Baptista.
I was especially thinking about transition states and the 
time-dependent processes of deprotonation and protonation
, but that's not the case in the given schemes (as far as
I have understood now).
Next time, I will not try to involve too much in such a 
discussion with other people, who have much more 
experience in this field. 

Bests,

Emanuel



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[gmx-users] no output in g_dist

[aiswarya pawar]

Hi users,

To get the distance between water and protein i did -

 g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11

from this i should obtain an output file as distance.xvg which i dont get.

and my output is printed on the terminal as-

t: 1  136 SOL 2336 OW  0.772373 (nm)
t: 1  136 SOL 2337 HW1  0.706358 (nm)
t: 1  136 SOL 2338 HW2  0.807787 (nm)
t: 1  139 SOL 2345 OW  0.821094 (nm)
t: 1  139 SOL 2346 HW1  0.810919 (nm)
t: 1  139 SOL 2347 HW2  0.771526 (nm)
t: 1  7237 SOL 23640 HW1  0.997056 (nm)
t: 1  11793 SOL 37307 OW  0.868929 (nm)
t: 1  11793 SOL 37308 HW1  0.927205 (nm)
t: 1  11793 SOL 37309 HW2  0.776699 (nm)
t: 2  125 SOL 2303 OW  0.940527 (nm)

In this

t: 1  136 SOL 2336 OW  0.772373 (nm)

does the 't' states the time frame, 136 SOL states the SOL molecule number
and 2336 OW the residue contact from protein and the 0.772373 nm the
distance between them.

Thanks
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Re: [gmx-users] no output in g_dist

[Justin A. Lemkul]

aiswarya pawar wrote:

Hi users,

To get the distance between water and protein i did -

 g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11

from this i should obtain an output file as distance.xvg which i dont get.



Try without specifying -dist simultaneously.  Also realize that the distance 
between the COM of the protein and the COM of water is probably constant (per 
COM motion removal algorithms) and may actually be zero.



and my output is printed on the terminal as-

t: 1  136 SOL 2336 OW  0.772373 (nm) 
t: 1  136 SOL 2337 HW1  0.706358 (nm)

t: 1  136 SOL 2338 HW2  0.807787 (nm)
t: 1  139 SOL 2345 OW  0.821094 (nm)
t: 1  139 SOL 2346 HW1  0.810919 (nm)
t: 1  139 SOL 2347 HW2  0.771526 (nm)
t: 1  7237 SOL 23640 HW1  0.997056 (nm)
t: 1  11793 SOL 37307 OW  0.868929 (nm)
t: 1  11793 SOL 37308 HW1  0.927205 (nm)
t: 1  11793 SOL 37309 HW2  0.776699 (nm)
t: 2  125 SOL 2303 OW  0.940527 (nm) 


In this

t: 1  136 SOL 2336 OW  0.772373 (nm) 

does the 't' states the time frame, 136 SOL states the SOL molecule 
number and 2336 OW the residue contact from protein and the 0.772373 nm 
the distance between them.




More or less.  OW, HW1, and HW2 are atoms, not residues.  But yes, that's what 
the -dist option does.


-Justin

--


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] g_sas

[Smolin, Nikolai]

Dear All,

I am wondering what kind of volume computed by g_sas?
volume inside SAS or inside contact surface (Connoly volume)?

Best regards,
Thanks

Nikolai

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UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory
P.O.Box 2008 Oak Ridge TN 37831-6164, USA.
Building 6011, room 233,
Tel: (865) 241-5237, (865) 241-5192
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[gmx-users] g_sas of ligands

[Steven Neumann]

Dear Gromacs Users,

I am calculating SAS using g_sas of ligands in my system: protein, 30
ligands in water. The hydrophobic SAS of ligands decrease and reach stable
value. Hydrophilic remains stable over the simulation time. I am wondering
whether it  (the decrease o hydrophobic) is because of binding to protein or
aggregations of my small molecules (They do aggregate) or both? I mean: how
is it caculated? Is binding to protein included in the decrease of the
hydrophobic SAS of lignads or it is impossible and  aggregation will be the
one thing?

Thank you,

Steven
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Re: [gmx-users] no output in g_dist

[lina]

On Thu, Sep 8, 2011 at 8:25 PM, aiswarya pawar  wrote:
> Hi users,
>
> To get the distance between water and protein i did -
>
>  g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11
>
> from this i should obtain an output file as distance.xvg which i dont get.

The -dist option: Print all atoms in group 2 (water) closer than dist to
the center of mass of group 1 (protein in
your case).

As you have seen, it *print* the result on the screen.

To obtain the distance.xvg file, please don't use the -dist option here.

>
> and my output is printed on the terminal as-
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
> t: 1  136 SOL 2337 HW1  0.706358 (nm)
> t: 1  136 SOL 2338 HW2  0.807787 (nm)
> t: 1  139 SOL 2345 OW  0.821094 (nm)
> t: 1  139 SOL 2346 HW1  0.810919 (nm)
> t: 1  139 SOL 2347 HW2  0.771526 (nm)
> t: 1  7237 SOL 23640 HW1  0.997056 (nm)
> t: 1  11793 SOL 37307 OW  0.868929 (nm)
> t: 1  11793 SOL 37308 HW1  0.927205 (nm)
> t: 1  11793 SOL 37309 HW2  0.776699 (nm)
> t: 2  125 SOL 2303 OW  0.940527 (nm)
>
> In this
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
>
> does the 't' states the time frame, 136 SOL states the SOL molecule number
> and 2336 OW the residue contact from protein and the 0.772373 nm the
> distance between them.
>
> Thanks
>
>
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>



-- 
Best Regards,

lina
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[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

[Marcin Zielinski]

Hi there,

I've been having hard times the past days trying to build SP and DP binaries
of GROMACS 4.5.4 on our Power6 system, here at SARA, using IBM XL compilers,
LAPACK, BLAS, GSL and FFTW3.

At the end, I think I've succeeded and had to use two dirty hacks to 
avoid problems.

I'm waiting now for results confirmation from friend of mine.

First thing, small patch to cmake/FindLAPACK.cmake
-set(CMAKE_REQUIRED_LIBRARIES ${_flags} "-Wl,--start-group
${${LIBRARIES}} ${_blas};-Wl,--end-group" ${_threads})
+set(CMAKE_REQUIRED_LIBRARIES ${_flags} "-Wl,--start-group
${${LIBRARIES}} ${_blas} -Wl,--end-group" ${_threads})
(Note the removed semicolon. )

Create Your build directory, I had source dir and build dir in the same 
root dir.


Second thing, before issuing make (and after cmake) modify src/config.h 
inside Your build directory:
line 45: remove ## _ (should look like this: #define F77_FUNC(name,NAME) 
name)
line 48: remove ## _ (should look like this: #define 
F77_FUNC_(name,NAME)name)


After that, cmake command, for sp and tools only:
module load lapack fftw3/3.2.2 gsl/1.15 cmake

cmake \
  -DFFTW3F_INCLUDE_DIR=/include \
  -DFFTW3F_LIBRARIES=/lib/libfftw3f.a \
  -DGMX_EXTERNAL_BLAS=ON \
  -DBLAS_LIBRARIES=/lib/libgslcblas.so \
  -DGMX_EXTERNAL_LAPACK=ON \
  -DLAPACK_LIBRARIES=/lib/liblapack.a \
  -DGMX_GSL=ON \
  -DCMAKE_INSTALL_PREFIX=/gromacs/4.5.4-sp \
  -DGMX_X11=OFF \
  -DCMAKE_CXX_COMPILER=mpCC \
  -DCMAKE_CXX_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
  -DCMAKE_CXX_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \

  -DCMAKE_C_COMPILER=mpcc \
  -DCMAKE_C_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp -qessl" \
  -DCMAKE_C_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \

  -DCMAKE_F77_COMPILER=mpfort \
  -DCMAKE_F77_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
  -DCMAKE_F77_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \
  -DCMAKE_EXE_LINKER_FLAGS="-L/lib -L/usr/lib64 
-L/lib -L/opt/ibmcmp/xlsmp/1.8/lib64 
-L/sara/sw/lapack/3.3.1-xlf12/lib -L/opt/ibmcmp/xlf/12.1/lib64 -llapack 
-lgslcblas -lgsl -lesslsmp -lxlf90_r -lxlsmp -lxlfmath -lxlomp_ser " \
  -DCMAKE_SHARED_LINKER_FLAGS="-L/lib -L/usr/lib64 
-L/lib -L/xlsmp/1.8/lib64 -Llapack>/lib -L/xlf/12.1/lib64 -llapack -lgslcblas -lgsl 
-lesslsmp -lxlf90_r -lxlsmp -lxlfmath -lxlomp_ser" \
  -DCMAKE_MODULE_LINKER_FLAGS="-L/lib -L/usr/lib64 
-L/lib -L/xlsmp/1.8/lib64 -Llapack>/lib -L/xlf/12.1/lib64 -llapack -lgslcblas -lgsl 
-lesslsmp -lxlf90_r -lxlsmp -lxlfmath -lxlomp_ser" \

  -DGMX_MPI=OFF \
  ../gromacs-4.5.4

From here, there's a straight way for a parallel build for mdrun and 
same goes for double precision.

Hope this is going to help to anyone having similar problems as I did.

good luck,
--
Marcin Zielinski
Supercomputing group, OSD
SARA
Science Park 140   mob +31 (0)65 123 5602
1098 XG Amsterdam  tel +31 (0)20 888 4074
www.sara.nlfax +31 (0)20 668 3167
marcin.zielin...@sara.nl
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[gmx-users] compressing waterbox

[madhumita das]

Hi,

   I have genrated a membrane protein system solvated in a water
box.But the water molecules are found as loosly packed. Is there any program
or method to shrink a system in a water box like inflategro for lipids?
  Please help this beginner.
  Thanks.

Madhumita Das
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Re: [gmx-users] compressing waterbox

[Justin A. Lemkul]

madhumita das wrote:

Hi,

   I have genrated a membrane protein system solvated in a water 
box.But the water molecules are found as loosly packed. Is there any 
program or method to shrink a system in a water box like inflategro for 
lipids?


The better solution is to solvate only once you have achieved the desired 
dimensions for the membrane after packing the lipids.  If you solvate too early, 
your system will be unstable or will take a long time to equilibrate, at least.


Some might suggest applying higher pressure to compress the system, but I think 
that will alter the lipid dynamics too much.  The best solution is better 
construction.


-Justin

--


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] X and Y dimensions in nanometers

[Conrado Pedebos]

 
Dear gmx-users,

I am working with a system composed by
20 molecules which are aggregated in water. I want to calculate the
dimensions of this aggregate, but it has an elipsoidal shape, instead
of a globular shape, as follows in this representation: 

          |
 _|__
-( )--X
  |
  |
    Y

Which gromacs tool could I use to
perform this analysis and calculate X and Y (nm) as a function of
time? 

I tried using g_gyrate and observing
the Rx, Ry and Rz components, but I couldn't get it right.

Thanks in advance,

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[gmx-users] dialanine using charmm27 ff

[Sandeep Somani]

Hi

I am trying to set up a simulation for dialanine using charmm27 ff but am
getting errors in pdb2gmx due to missing definitions in rtp file.

I created the pdb file (below) using Charmm for the sequence
ACE-ALA-ALA-CT3.

pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and
CT3.

Does someone have the appropriate definitions for these residues ?
( I have tried http://swissparam.ch/ to generate an itp file for the
molecule, but upon using it in GMX it does not give the same energy as that
from charmm. )

I am using GMX4.5.4.

Thanks
Sandeep

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Post Doc
Wales Research Group
Department of Chemistry
Cambridge

=
REMARK Charmm commands:
REMARK ! CONSTRUCT STRUCTURE FROM SEQUENCE
REMARK READ SEQUence CARD
REMARK *
REMARK 1
REMARK ALA ALA
REMARK GENErate DIALA FIRSt ACE LAST CT3 WARN SETUp
REMARK
ATOM  1  CAY ALA 1  -2.160   0.537   0.930  1.00  0.00  DIAL
ATOM  2  HY1 ALA 1  -2.466   0.003   0.005  1.00  0.00  DIAL
ATOM  3  HY2 ALA 1  -2.562   1.572   0.910  1.00  0.00  DIAL
ATOM  4  HY3 ALA 1  -2.562   0.001   1.816  1.00  0.00  DIAL
ATOM  5  CY  ALA 1  -0.672   0.582   1.009  1.00  0.00  DIAL
ATOM  6  OY  ALA 1  -0.105   1.128   1.954  1.00  0.00  DIAL
ATOM  7  N   ALA 1   0.000   0.000   0.000  1.00  0.00  DIAL
ATOM  8  HN  ALA 1  -0.453  -0.444  -0.769  1.00  0.00  DIAL
ATOM  9  CA  ALA 1   1.459   0.000   0.000  1.00  0.00  DIAL
ATOM 10  HA  ALA 1   1.812  -0.497   0.897  1.00  0.00  DIAL
ATOM 11  CB  ALA 1   1.949  -0.834  -1.207  1.00  0.00  DIAL
ATOM 12  HB1 ALA 1   1.514  -1.854  -1.155  1.00  0.00  DIAL
ATOM 13  HB2 ALA 1   1.628  -0.373  -2.167  1.00  0.00  DIAL
ATOM 14  HB3 ALA 1   3.056  -0.932  -1.214  1.00  0.00  DIAL
ATOM 15  C   ALA 1   2.096   1.401   0.000  1.00  0.00  DIAL
ATOM 16  O   ALA 1   1.425   2.432   0.000  1.00  0.00  DIAL
ATOM 17  N   ALA 2   3.451   1.458   0.000  1.00  0.00  DIAL
ATOM 18  HN  ALA 2   3.954   0.594   0.000  1.00  0.00  DIAL
ATOM 19  CA  ALA 2   4.276   2.664   0.000  1.00  0.00  DIAL
ATOM 20  HA  ALA 2   4.065   3.236  -0.897  1.00  0.00  DIAL
ATOM 21  CB  ALA 2   3.864   3.539   1.207  1.00  0.00  DIAL
ATOM 22  HB1 ALA 2   2.776   3.756   1.155  1.00  0.00  DIAL
ATOM 23  HB2 ALA 2   4.063   3.014   2.167  1.00  0.00  DIAL
ATOM 24  HB3 ALA 2   4.407   4.508   1.214  1.00  0.00  DIAL
ATOM 25  C   ALA 2   5.791   2.399   0.000  1.00  0.00  DIAL
ATOM 26  O   ALA 2   6.597   3.328   0.000  1.00  0.00  DIAL
ATOM 27  NT  ALA 2   6.175   1.110   0.000  1.00  0.00  DIAL
ATOM 28  HNT ALA 2   5.528   0.351   0.000  1.00  0.00  DIAL
ATOM 29  CAT ALA 2   7.566   0.777   0.000  1.00  0.00  DIAL
ATOM 30  HT1 ALA 2   8.048   1.201   0.907  1.00  0.00  DIAL
ATOM 31  HT2 ALA 2   7.683  -0.327   0.000  1.00  0.00  DIAL
ATOM 32  HT3 ALA 2   8.048   1.201  -0.907  1.00  0.00  DIAL
TER  33  ALA  2
END
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Re: [gmx-users] dialanine using charmm27 ff

[Mark Abraham]

On 9/09/2011 8:05 AM, Sandeep Somani wrote:

Hi

I am trying to set up a simulation for dialanine using charmm27 ff but 
am getting errors in pdb2gmx due to missing definitions in rtp file.


I created the pdb file (below) using Charmm for the sequence 
ACE-ALA-ALA-CT3.


pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE 
and CT3.


Yes, CHARMM in GROMACS has lacked these for some time. I asked over a 
year ago for them to be added, but that hasn't happened. You can add


[ ACE ]
 [ atoms ]
CT3 CT3 -0.270  0
HT1 HA  0.090   1
HT2 HA  0.090   2
HT3 HA  0.090   3
C   C   0.510   4
O   O   -0.510  5
 [ bonds ]
C   CT3
C   +N
CT3 HT31
CT3 HT32
CT3 HT33
O   C
 [ impropers ]
C   CT3 +N  O

[ CT3 ]
; this can also be done with the .c.tdb, but the atom naming is different
; and this can matter
 [ atoms ]
N   NH1 -0.470  0
HN  H   0.310   1
CT  CT3 -0.110  2
HT1 HA  0.090   3
HT2 HA  0.090   4
HT3 HA  0.090   5
 [ bonds ]
-C  N
N   HN
N   CAT
CT  HT1
CT  HT2
CT  HT3

 [ impropers ]
N   -C  CAT HN
-C  CAT N   -O

to the end of aminoacids.rtp in a local copy of the charmm27.ff folder 
to make this work.




Does someone have the appropriate definitions for these residues ?
( I have tried http://swissparam.ch/ to generate an itp file for the 
molecule, but upon using it in GMX it does not give the same energy as 
that from charmm. )


That will likely be a separate issue.

Mark
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Re: [gmx-users] X and Y dimensions in nanometers

[Mark Abraham]

On 9/09/2011 4:12 AM, Conrado Pedebos wrote:

Dear gmx-users,

I am working with a system composed by 20 molecules which are 
aggregated in water. I want to calculate the dimensions of this 
aggregate, but it has an elipsoidal shape, instead of a globular 
shape, as follows in this representation:


   |
 _|__
-( )--X
   |
   |
  Y

Which gromacs tool could I use to perform this analysis and calculate 
X and Y (nm) as a function of time?




I don't think there is anything to do X, but g_mindist -max can do Y. 
Aligning your principal axes with the coordinate axes and looking at the 
distribution of the coordinates found with g_traj and then g_analyze is 
probably the best you can do.


Mark
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RE: [gmx-users] X and Y dimensions in nanometers

[Dallas Warren]

What was the issue you had with g_gyrate?  As that is the best tool for this 
job.  Do you have pbc issues?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Conrado Pedebos
Sent: Friday, 9 September 2011 4:13 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] X and Y dimensions in nanometers

Dear gmx-users,

I am working with a system composed by 20 molecules which are aggregated in 
water. I want to calculate the dimensions of this aggregate, but it has an 
elipsoidal shape, instead of a globular shape, as follows in this 
representation:

   |
 _|__
-( )--X
   |
   |
  Y

Which gromacs tool could I use to perform this analysis and calculate X and Y 
(nm) as a function of time?

I tried using g_gyrate and observing the Rx, Ry and Rz components, but I 
couldn't get it right.

Thanks in advance,

Conrado Pedebos.
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[gmx-users] Re: no output in g_dist

[aiswarya pawar]

Thanks Lina and Justin.

Is this data good for finding the distance of protein and water as function
of time.


On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar wrote:

> Hi users,
>
> To get the distance between water and protein i did -
>
>  g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11
>
> from this i should obtain an output file as distance.xvg which i dont get.
>
> and my output is printed on the terminal as-
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
> t: 1  136 SOL 2337 HW1  0.706358 (nm)
> t: 1  136 SOL 2338 HW2  0.807787 (nm)
> t: 1  139 SOL 2345 OW  0.821094 (nm)
> t: 1  139 SOL 2346 HW1  0.810919 (nm)
> t: 1  139 SOL 2347 HW2  0.771526 (nm)
> t: 1  7237 SOL 23640 HW1  0.997056 (nm)
> t: 1  11793 SOL 37307 OW  0.868929 (nm)
> t: 1  11793 SOL 37308 HW1  0.927205 (nm)
> t: 1  11793 SOL 37309 HW2  0.776699 (nm)
> t: 2  125 SOL 2303 OW  0.940527 (nm)
>
> In this
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
>
> does the 't' states the time frame, 136 SOL states the SOL molecule number
> and 2336 OW the residue contact from protein and the 0.772373 nm the
> distance between them.
>
> Thanks
>
>
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Re: [gmx-users] Re: no output in g_dist

[Mark Abraham]

On 9/09/2011 3:29 PM, aiswarya pawar wrote:


Thanks Lina and Justin.

Is this data good for finding the distance of protein and water as 
function of time.


If the protein and water are in contact, what do you hope to learn?

Mark
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[gmx-users] amb2gmx.pl to convert GLYCAM topology

[Yun Shi]

Hi all,

I understand this problem has been discussed before, but it seems no
conclusion has been drawn.

GLYCAM force field assigns negative force constants to some dihedrals, and
when amb2gmx.pl was used to convert prmtop file to gromacs top file, these
negative values seem to be ignored. Some people proposed that we change the
code in amb2gmx.pl, that is:

...

  # get all force constants for each line of a dihedral #
  my $lines = $i -1 +$numijkl;
  for(my $j=$i;$j<=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}>0) {
  $V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}

...

the "$pk{$j}>0" is modified to "$pk{$j}!=0".

Others suggest to modify the original prmtop file, that is, to remove the
negative signs, and correspondingly, change the phase shift from 0 to 180.
Then amb2gmx.pl could be used to correctly convert the topology.

I am wondering if the first approach has been validated, since the second
one seems complicated and laborious to carry out.

Thanks for any advice,

Yun
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Re: [gmx-users] amb2gmx.pl to convert GLYCAM topology

[Mark Abraham]

On 9/09/2011 4:21 PM, Yun Shi wrote:

Hi all,

I understand this problem has been discussed before, but it seems no 
conclusion has been drawn.


Someone needs to do some work and report back :-)



GLYCAM force field assigns negative force constants to some dihedrals, 
and when amb2gmx.pl  was used to convert prmtop 
file to gromacs top file, these negative values seem to be ignored. 
Some people proposed that we change the code in amb2gmx.pl 
, that is:


...

  # get all force constants for each line of a dihedral #
  my $lines = $i -1 +$numijkl;
  for(my $j=$i;$j<=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}>0) {
  $V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}

...

the "$pk{$j}>0" is modified to "$pk{$j}!=0".

Others suggest to modify the original prmtop file, that is, to remove 
the negative signs, and correspondingly, change the phase shift from 0 
to 180. Then amb2gmx.pl  could be used to correctly 
convert the topology.


I am wondering if the first approach has been validated, since the 
second one seems complicated and laborious to carry out.


Seems like a straightforward job for regular expression replacement 
using sed/perl/python/whatever. It might even be a one-liner.


Mark
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Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

[Mark Abraham]

On 9/09/2011 1:46 AM, Marcin Zielinski wrote:

Hi there,

I've been having hard times the past days trying to build SP and DP 
binaries
of GROMACS 4.5.4 on our Power6 system, here at SARA, using IBM XL 
compilers,

LAPACK, BLAS, GSL and FFTW3.

At the end, I think I've succeeded and had to use two dirty hacks to 
avoid problems.

I'm waiting now for results confirmation from friend of mine.

First thing, small patch to cmake/FindLAPACK.cmake
-set(CMAKE_REQUIRED_LIBRARIES ${_flags} "-Wl,--start-group
${${LIBRARIES}} ${_blas};-Wl,--end-group" ${_threads})
+set(CMAKE_REQUIRED_LIBRARIES ${_flags} "-Wl,--start-group
${${LIBRARIES}} ${_blas} -Wl,--end-group" ${_threads})
(Note the removed semicolon. )


Thanks. Fixed for next version.



Create Your build directory, I had source dir and build dir in the 
same root dir.


Second thing, before issuing make (and after cmake) modify 
src/config.h inside Your build directory:
line 45: remove ## _ (should look like this: #define 
F77_FUNC(name,NAME) name)
line 48: remove ## _ (should look like this: #define 
F77_FUNC_(name,NAME)name)


If you set GMX_ACCELERATION=POWER6 this (and a few other things) should 
happen automatically.


Mark



After that, cmake command, for sp and tools only:
module load lapack fftw3/3.2.2 gsl/1.15 cmake

cmake \
  -DFFTW3F_INCLUDE_DIR=/include \
  -DFFTW3F_LIBRARIES=/lib/libfftw3f.a \
  -DGMX_EXTERNAL_BLAS=ON \
  -DBLAS_LIBRARIES=/lib/libgslcblas.so \
  -DGMX_EXTERNAL_LAPACK=ON \
  -DLAPACK_LIBRARIES=/lib/liblapack.a \
  -DGMX_GSL=ON \
  -DCMAKE_INSTALL_PREFIX=/gromacs/4.5.4-sp \
  -DGMX_X11=OFF \
  -DCMAKE_CXX_COMPILER=mpCC \
  -DCMAKE_CXX_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
  -DCMAKE_CXX_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \

  -DCMAKE_C_COMPILER=mpcc \
  -DCMAKE_C_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
  -DCMAKE_C_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \

  -DCMAKE_F77_COMPILER=mpfort \
  -DCMAKE_F77_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
  -DCMAKE_F77_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \
  -DCMAKE_EXE_LINKER_FLAGS="-L/lib -L/usr/lib64 
-L/lib -L/opt/ibmcmp/xlsmp/1.8/lib64 
-L/sara/sw/lapack/3.3.1-xlf12/lib -L/opt/ibmcmp/xlf/12.1/lib64 
-llapack -lgslcblas -lgsl -lesslsmp -lxlf90_r -lxlsmp -lxlfmath 
-lxlomp_ser " \
  -DCMAKE_SHARED_LINKER_FLAGS="-L/lib -L/usr/lib64 
-L/lib -L/xlsmp/1.8/lib64 -Llapack>/lib -L/xlf/12.1/lib64 -llapack -lgslcblas -lgsl 
-lesslsmp -lxlf90_r -lxlsmp -lxlfmath -lxlomp_ser" \
  -DCMAKE_MODULE_LINKER_FLAGS="-L/lib -L/usr/lib64 
-L/lib -L/xlsmp/1.8/lib64 -Llapack>/lib -L/xlf/12.1/lib64 -llapack -lgslcblas -lgsl 
-lesslsmp -lxlf90_r -lxlsmp -lxlfmath -lxlomp_ser" \

  -DGMX_MPI=OFF \
  ../gromacs-4.5.4

From here, there's a straight way for a parallel build for mdrun and 
same goes for double precision.

Hope this is going to help to anyone having similar problems as I did.

good luck,


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