Re: [gmx-users] Matching atom name and types in OPLS-aa FF

[tree]

Dear Justin:


Thank you for your email!

Thanks to your help and explanation, I am feeling more comfortable with 
OPLS topology modification.
Before this work, I have used Gromacs without modifying FF paramters for 
simulating 'water' in general systems, which can easily obtained from PDB 
sites.
So, it was not too easy to generate a sort of new topology even I've 
learned MD.


I understand what you meant here. :)
I did not mean the selection "1" (Harmonic potential function) is a sort 
of OPLS-aa FF functions.
My question is actually if I can use the Forth power potential when I 
choose "2" in bond streching section.
Since this funtion has different from from "1" (Harmonic potential 
function), I thought that it may need other paramters that may (may not) 
be different from the given parameters in OPLS-aa FF.

So, my question here is
   [can I use the Forth power potential for bond strech using the given
   OPLS-aa paramters?]
I assume this would be same to others, angle, dihedral, and etc.

Thank you again.


Sincerely,

Kim

On Mon, 16 Mar 2009, Justin A. Lemkul wrote:




Tree wrote:

Dear Dr. Periole:


Thank you for your answer.

You meant that the types of potential functions do not have any relations 
with OPLS-aa (except first ("1") case).

Those (from "2"...) are defined as written the Gromacs manual.



Table 5.4 defines the different types of intramolecular interactions.  You 
should specify the proper terms based on what corresponds to the force field 
functional form.  That is harmonic potential does not necessarily imply OPLS, 
but OPLS might imply that you have to use a harmonic potential (because, in 
fact, many force fields use a harmonic potential for bonds, not just OPLS!)


You should refer to the primary literature for the force field, how it was 
derived, and any subsequent references regarding modifications to the force 
field.


Another option (in addition to doing the background reading!) is to run 
through some tutorial material with a simple protein under OPLS to get a feel 
for how an OPLS topology is automatically created by pdb2gmx.


-Justin



Thank you again.


Sincerely,

Kim

On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole > wrote:



On Mar 16, 2009, at 9:34 AM, tree wrote:

Dear Justin and All:


I truly appreciate your clear answer.
Since my questions are solved by your explanations, I do not
know how I can express my grateful heart.

Now I have to ask second step questions. :)
It is related to the OPLS-aa "bon.itp" file.
Each section (bonds, angle, diherdal, and etc.) has its "type".
I am wondering if this "type" (of course, in OPLS-aa case) has
the same meaning in the Gromos potentials.
As we know, those types for each kind of bonded interactions are
well described in the Gromacs manual with clear equations.
So, my question is (as I mentioned just above) if this is the
same as the OPLS-aa case.

Yes, the bond, angle, dihedral types are independent to the
underlying force field
and correspond to the description in the manual.


To make my question clear, I want to give an example.

[ bonds ]
...
CT  HC  1   0.10900 284512.0; CHARMM 22 
paramter

...

I know the number "1" here means type, which describes what kind
of the bonds (strech) between two bonds is used.
If this is Gromos potential, I am sure this "1" means "harmonic"
potential according to the Chap. 4 of the Gromacs manual.
Is this also applied to OPLS-aa FF?

Thank you for your care, again.


Sincerely yours,

Kim

On Fri, 13 Mar 2009, Justin A. Lemkul wrote:



Tree wrote:

Dear All:
I appreciate your answer always.
Right now, I am trying to add/modify some values in
OPLS-aa FF.
I am confused atom type (opls_xxx) and atom name (e.g.,
C) in "atp", "bon.itp", and "nb.itp" files.
Please let me try the situation by an example, first.
In "atp" file,
 ...
 opls_058   12.01100  ; C  in COOR ester JPC3315(91)
 opls_059   15.99940  ; O= in COOR ester
 ...
In "bon.itp" file,
 ...
 C CA  10.14900   334720.0   ; wlj 8/97
 C_2   CA  10.14900   334720.0   ; wlj 8/97
 ...
In "nb.itp" file,
 ...
 opls_009   C2  7  14.02700 0.000   A 
3.90500e-01 4.93712e-01 ; SIG
 opls_010   C3  6  15.03500 0.000   A 
3.90500e-01 7.32200e-01 ; SIG

 ...
I hope you can sense what my question is here.
When I define a residue in "rtp" 

Re: [gmx-users] g_dipoles

[David van der Spoel]

rams rams wrote:

Dear Users,

I am trying to obtain the dipole moment of a 40 amino acid residue 
peptide using g_dipoles. I am getting a huge number (about 700 Debye). I 
expect it to be around 150 Debye (based on other studies). To make sure 
it I extracted a shapshot of the structure and obtained the dipolemoment 
using the following command:


g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg  -n prot_dip.ndx

I am giving the last few lines of the output below:

Dipole moment (Debye)
-
Average  = 516.7213  Std. Dev. =   0.  Error =   0.

The following averages for the complete trajectory have been calculated:

 Total < M_x > = -54.3459 Debye
 Total < M_y > = 12.8373 Debye
 Total < M_z > = 513.695 Debye

 Total < M_x^2 > = 2953.47 Debye^2
 Total < M_y^2 > = 164.796 Debye^2
 Total < M_z^2 > = 263883 Debye^2

 Total < |M|^2 > = 267001 Debye^2
 Total < |M| >^2 = 267001 Debye^2

 < |M|^2 > - < |M| >^2 = 0 Debye^2

Finite system Kirkwood g factor G_k = 0
Infinite system Kirkwood g factor g_k = 0

Epsilon = 1

The same structure (i.e., what i have used in the above command) if I 
open and check for the dipole moment using YASARA suite of program it is 
showing as 173 Debye. Which is reasonable. Am I making any mistake while 
obtaining the dipole moment using g_dipoles or I am looking at the wrong 
file ??


Is the peptide neutral? Otherwise the result might be orientation 
dependent.





Thanks.

Ram.




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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] how to save grace out put to jpeg or grafifal pic

[Homa Azizian]

hi
my ques. dose not exactly relate to the gromacs while it is about how I can 
save the resulting plot from grace in to the jpeg or other picture file.
thanks 
--
Tehran University of Medical Sciences
www.tums.ac.ir


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RE: [gmx-users] no ngmx?

[Abu Naser]

Hi Barbara,

 

Possibly header files of x-windows  not in the path and therefore, ngmx was not 
compiled during compilation.

 

Abu










 


 

> Date: Mon, 16 Mar 2009 17:46:06 +0100
> From: gioffr...@uni-duesseldorf.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] no ngmx?
> 
> Hello to all,
> 
> I have installed the latest version of gromacs (4.04) to my new Linux 
> (suse 10,3) and I wanted to start working with it. Everything works 
> well, but I cannot start the ngmx . I looked into the directory 
> /usr/local/gromacs/bin and even there is no gmx
> 
> By installation I followed the online installation manual and everything 
> works fine. What can I do to get the ngmx back?
> 
> Greetings
> Barbara
> ___
> gmx-users mailing list gmx-users@gromacs.org
> http://www.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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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View your Twitter and Flickr updates from one place – Learn more!
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Re: [gmx-users] how to save grace out put to jpeg or grafifal pic

[David van der Spoel]

Homa Azizian wrote:

hi
my ques. dose not exactly relate to the gromacs while it is about how I can 
save the resulting plot from grace in to the jpeg or other picture file.
thanks 
--

Tehran University of Medical Sciences
www.tums.ac.ir



within xmgrace use print setup.

--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
___
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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-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] how to save grace out put to jpeg or grafical pic

[Homa Azizian]

hi
my ques. dose not exactly relate to the gromacs while it is about how I can 
save the resulting plot from grace in to the jpeg or other picture file.
thanks 
--
Tehran University of Medical Sciences
www.tums.ac.ir


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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Re: [gmx-users] Matching atom name and types in OPLS-aa FF

[XAvier Periole]

On Mar 17, 2009, at 8:45 AM, tree wrote:


Dear Justin:


Thank you for your email!

Thanks to your help and explanation, I am feeling more comfortable  
with OPLS topology modification.
Before this work, I have used Gromacs without modifying FF paramters  
for simulating 'water' in general systems, which can easily obtained  
from PDB sites.
So, it was not too easy to generate a sort of new topology even I've  
learned MD.


I understand what you meant here. :)
I did not mean the selection "1" (Harmonic potential function) is a  
sort of OPLS-aa FF functions.
My question is actually if I can use the Forth power potential when  
I choose "2" in bond streching section.
Since this funtion has different from from "1" (Harmonic potential  
function), I thought that it may need other paramters that may (may  
not) be different from the given parameters in OPLS-aa FF.

So, my question here is
  [can I use the Forth power potential for bond strech using the given
  OPLS-aa paramters?]
To that the answer is no! If you change the potential to describe a  
bond, angle ...

the parameters will be different! Have a look a the manual chapter 4.

I assume this would be same to others, angle, dihedral, and etc.

Thank you again.


Sincerely,

Kim

On Mon, 16 Mar 2009, Justin A. Lemkul wrote:




Tree wrote:

Dear Dr. Periole:
Thank you for your answer.
You meant that the types of potential functions do not have any  
relations with OPLS-aa (except first ("1") case).

Those (from "2"...) are defined as written the Gromacs manual.


Table 5.4 defines the different types of intramolecular  
interactions.  You should specify the proper terms based on what  
corresponds to the force field functional form.  That is harmonic  
potential does not necessarily imply OPLS, but OPLS might imply  
that you have to use a harmonic potential (because, in fact, many  
force fields use a harmonic potential for bonds, not just OPLS!)


You should refer to the primary literature for the force field, how  
it was derived, and any subsequent references regarding  
modifications to the force field.


Another option (in addition to doing the background reading!) is to  
run through some tutorial material with a simple protein under OPLS  
to get a feel for how an OPLS topology is automatically created by  
pdb2gmx.


-Justin


Thank you again.
Sincerely,
Kim
On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole mailto:x.peri...@rug.nl 
>> wrote:


   On Mar 16, 2009, at 9:34 AM, tree wrote:

   Dear Justin and All:

   I truly appreciate your clear answer.
   Since my questions are solved by your explanations, I do not
   know how I can express my grateful heart.

   Now I have to ask second step questions. :)
   It is related to the OPLS-aa "bon.itp" file.
   Each section (bonds, angle, diherdal, and etc.) has its  
"type".
   I am wondering if this "type" (of course, in OPLS-aa case)  
has

   the same meaning in the Gromos potentials.
   As we know, those types for each kind of bonded  
interactions are

   well described in the Gromacs manual with clear equations.
   So, my question is (as I mentioned just above) if this is the
   same as the OPLS-aa case.

   Yes, the bond, angle, dihedral types are independent to the
   underlying force field
   and correspond to the description in the manual.

   To make my question clear, I want to give an example.

   [ bonds ]
   ...
   CT  HC  1   0.10900 284512.0; CHARMM 22  
paramter

   ...

   I know the number "1" here means type, which describes what  
kind

   of the bonds (strech) between two bonds is used.
   If this is Gromos potential, I am sure this "1" means  
"harmonic"

   potential according to the Chap. 4 of the Gromacs manual.
   Is this also applied to OPLS-aa FF?

   Thank you for your care, again.

   Sincerely yours,

   Kim

   On Fri, 13 Mar 2009, Justin A. Lemkul wrote:

   Tree wrote:

   Dear All:
   I appreciate your answer always.
   Right now, I am trying to add/modify some values in
   OPLS-aa FF.
   I am confused atom type (opls_xxx) and atom name  
(e.g.,

   C) in "atp", "bon.itp", and "nb.itp" files.
   Please let me try the situation by an example, first.
   In "atp" file,
...
opls_058   12.01100  ; C  in COOR ester JPC3315(91)
opls_059   15.99940  ; O= in COOR ester
...
   In "bon.itp" file,
...
C CA  10.14900   334720.0   ; wlj 8/97
C_2   CA  10.14900   334720.0   ; wlj 8/97
...
   In "nb.itp" file,
...
opls_009   C2  7  14.02700 0.000   A  
3.90500e-01 4.93712e-01 ; SIG
opls_010   C3  6  15.03500 0.000 

Re: [gmx-users] gromacs 4 mpi weirdness

[Ran Friedman]

Hi Tsjerk,

I've encountered problem #2 with GMX 4.0.2 before. I'm not exactly sure
what went wrong, but it may have been due to mpi. With lammpi things work.

Hope that helps,

Ran.

Tsjerk Wassenaar wrote:
> Hi,
>
> I'm running in trouble trying to compile gromacs 4.0.x on our national
> Intel Xeon Linux cluster (Lisa/Sara). The same problem pops up with
> different compilers (GNU GCC 3.4, 4.1 (default on the cluster :p),
> Intel). I'm using fftw-3.2.1 and mpich/gnu c.q. mpich/intel. mdrun
> compiles, but when I try to run it, it 1. starts running in the
> gromacs installation directory and 2. starts the same job for every
> processor rather than one job on all of them. Trying to run mdrun in
> an interactive PBS job shows that it's really a problem with mdrun
> itself. I must be overlooking something. Anyone have an idea?
>
> Neither ./configure nor make report any problems. The former I include
> below for completeness. Of course I'd be happy to supply more
> information on request or do some additional tests.
>
> I'll also contact the support team of the facility and report back if
> they come up with a solution.
>
> Cheers,
>
> Tsjerk
>
> tsj...@login-ng1:~/gromacs-4.0.4$ ./configure
> --prefix=/home/tsjerk/GMX404/ --enable-mpi --program-suffix="_mpi"
> --disable-nice
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a ustar tar archive... gnutar
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc-3.4 accepts -g... yes
> checking for gcc-3.4 option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of gcc-3.4... gcc3
> checking dependency style of gcc-3.4... gcc3
> checking for mpxlc... no
> checking for mpicc... mpicc
> checking whether the MPI cc command works... yes
> checking for catamount... no
> checking how to run the C preprocessor... mpicc -E
> checking whether mpicc accepts -O3... yes
> checking whether mpicc accepts -funroll-all-loops... yes
> checking whether mpicc accepts  -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -funroll-all-loops... yes
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking whether byte ordering is bigendian... no
> checking for int... yes
> checking size of int... 4
> checking for long int... yes
> checking size of long int... 4
> checking for long long int... yes
> checking size of long long int... 8
> checking for off_t... yes
> checking size of off_t... 4
> checking that size_t can hold pointers... yes
> checking floating-point format... IEEE754 (little-endian byte and word order)
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for a sed that does not truncate output... /bin/sed
> checking for ld used by mpicc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -B
> checking how to recognise dependent libraries... pass_all
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc3
> checking the maximum length of command line arguments... 32768
> checking command to parse /usr/bin/nm -B output from mpicc object... ok
> checking for objdir... .libs
> checking for ar... ar
> checking for ranlib... ranlib
> checking for strip... strip
> checking if mpicc supports -fno-rtti -fno-exceptions... no
> checking for mpicc option to produce PIC... -fPIC
> checking if mpicc PIC flag -fPIC works... yes
> checking if mpicc static flag -static works... yes
> checking if mpicc supports -c -o file.o... yes
> checking whether the mpicc linker (/usr/bin/ld) supports shared libraries... 
> yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into pr

[gmx-users] do_dssp fatal error

[Homa Azizian]

Hi
thanks Dr. van der Spoel my previous problem fixed.
I have another question.
I download DSSP from http://swift.cmbi.ru.nl/gv/dssp/ from the part 
Distribution in the left partition of the page. it was the zip file and I 
unzip it and positioned it in my /usr/local/bin and adjust the .bashrc. 
when I execut it the error appear:

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro
/dev/null 2> /dev/null


How can I fix the problem?
Than's.


Tehran University of Medical Sciences
www.tums.ac.ir


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[gmx-users] gromacs 4 mpi weirdness

[Tsjerk Wassenaar]

Hi,

I'm running in trouble trying to compile gromacs 4.0.x on our national
Intel Xeon Linux cluster (Lisa/Sara). The same problem pops up with
different compilers (GNU GCC 3.4, 4.1 (default on the cluster :p),
Intel). I'm using fftw-3.2.1 and mpich/gnu c.q. mpich/intel. mdrun
compiles, but when I try to run it, it 1. starts running in the
gromacs installation directory and 2. starts the same job for every
processor rather than one job on all of them. Trying to run mdrun in
an interactive PBS job shows that it's really a problem with mdrun
itself. I must be overlooking something. Anyone have an idea?

Neither ./configure nor make report any problems. The former I include
below for completeness. Of course I'd be happy to supply more
information on request or do some additional tests.

I'll also contact the support team of the facility and report back if
they come up with a solution.

Cheers,

Tsjerk

tsj...@login-ng1:~/gromacs-4.0.4$ ./configure
--prefix=/home/tsjerk/GMX404/ --enable-mpi --program-suffix="_mpi"
--disable-nice
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-3.4 accepts -g... yes
checking for gcc-3.4 option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc-3.4... gcc3
checking dependency style of gcc-3.4... gcc3
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the MPI cc command works... yes
checking for catamount... no
checking how to run the C preprocessor... mpicc -E
checking whether mpicc accepts -O3... yes
checking whether mpicc accepts -funroll-all-loops... yes
checking whether mpicc accepts  -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking for int... yes
checking size of int... 4
checking for long int... yes
checking size of long int... 4
checking for long long int... yes
checking size of long long int... 8
checking for off_t... yes
checking size of off_t... 4
checking that size_t can hold pointers... yes
checking floating-point format... IEEE754 (little-endian byte and word order)
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... yes
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
appending configuration tag "F77" to libtool
checking for special C compiler options needed for large files... no
chec

Re: [gmx-users] do_dssp fatal error

[Justin A. Lemkul]

Homa Azizian wrote:

Hi
thanks Dr. van der Spoel my previous problem fixed.
I have another question.
I download DSSP from http://swift.cmbi.ru.nl/gv/dssp/ from the part 
Distribution in the left partition of the page. it was the zip file and I 
unzip it and positioned it in my /usr/local/bin and adjust the .bashrc. 
when I execut it the error appear:


Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro
/dev/null 2> /dev/null



The executable itself must be in /usr/local/bin.  If you placed the unzipped 
archive in /usr/local/bin, then dssp is a directory.  Furthermore, the 
executable produced from that source code will be call dsspcbmi, and will have 
to be re-named.


-Justin



How can I fix the problem?
Than's.


Tehran University of Medical Sciences
www.tums.ac.ir




--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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 mpi weirdness

[Tsjerk Wassenaar]

Hi,

Okay, after some communication with the administrators, it appeared
that this arose from some misloaded (mpi) libraries both at
compiletime and at runtime. My mistake, obviously. Let's see if I get
it right this time.

Cheers,

Tsjerk

On Tue, Mar 17, 2009 at 10:53 AM, Ran Friedman  wrote:
> Hi Tsjerk,
>
> I've encountered problem #2 with GMX 4.0.2 before. I'm not exactly sure
> what went wrong, but it may have been due to mpi. With lammpi things work.
>
> Hope that helps,
>
> Ran.
>
> Tsjerk Wassenaar wrote:
>> Hi,
>>
>> I'm running in trouble trying to compile gromacs 4.0.x on our national
>> Intel Xeon Linux cluster (Lisa/Sara). The same problem pops up with
>> different compilers (GNU GCC 3.4, 4.1 (default on the cluster :p),
>> Intel). I'm using fftw-3.2.1 and mpich/gnu c.q. mpich/intel. mdrun
>> compiles, but when I try to run it, it 1. starts running in the
>> gromacs installation directory and 2. starts the same job for every
>> processor rather than one job on all of them. Trying to run mdrun in
>> an interactive PBS job shows that it's really a problem with mdrun
>> itself. I must be overlooking something. Anyone have an idea?
>>
>> Neither ./configure nor make report any problems. The former I include
>> below for completeness. Of course I'd be happy to supply more
>> information on request or do some additional tests.
>>
>> I'll also contact the support team of the facility and report back if
>> they come up with a solution.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> tsj...@login-ng1:~/gromacs-4.0.4$ ./configure
>> --prefix=/home/tsjerk/GMX404/ --enable-mpi --program-suffix="_mpi"
>> --disable-nice
>> checking build system type... i686-pc-linux-gnu
>> checking host system type... i686-pc-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking whether build environment is sane... yes
>> checking for a thread-safe mkdir -p... /bin/mkdir -p
>> checking for gawk... gawk
>> checking whether make sets $(MAKE)... yes
>> checking how to create a ustar tar archive... gnutar
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc-3.4 accepts -g... yes
>> checking for gcc-3.4 option to accept ISO C89... none needed
>> checking for style of include used by make... GNU
>> checking dependency style of gcc-3.4... gcc3
>> checking dependency style of gcc-3.4... gcc3
>> checking for mpxlc... no
>> checking for mpicc... mpicc
>> checking whether the MPI cc command works... yes
>> checking for catamount... no
>> checking how to run the C preprocessor... mpicc -E
>> checking whether mpicc accepts -O3... yes
>> checking whether mpicc accepts -funroll-all-loops... yes
>> checking whether mpicc accepts  -O3 -fomit-frame-pointer
>> -finline-functions -Wall -Wno-unused -funroll-all-loops... yes
>> checking for grep that handles long lines and -e... /bin/grep
>> checking for egrep... /bin/grep -E
>> checking for ANSI C header files... yes
>> checking for sys/types.h... yes
>> checking for sys/stat.h... yes
>> checking for stdlib.h... yes
>> checking for string.h... yes
>> checking for memory.h... yes
>> checking for strings.h... yes
>> checking for inttypes.h... yes
>> checking for stdint.h... yes
>> checking for unistd.h... yes
>> checking whether byte ordering is bigendian... no
>> checking for int... yes
>> checking size of int... 4
>> checking for long int... yes
>> checking size of long int... 4
>> checking for long long int... yes
>> checking size of long long int... 8
>> checking for off_t... yes
>> checking size of off_t... 4
>> checking that size_t can hold pointers... yes
>> checking floating-point format... IEEE754 (little-endian byte and word order)
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking whether ln -s works... yes
>> checking whether make sets $(MAKE)... (cached) yes
>> checking for a sed that does not truncate output... /bin/sed
>> checking for ld used by mpicc... /usr/bin/ld
>> checking if the linker (/usr/bin/ld) is GNU ld... yes
>> checking for /usr/bin/ld option to reload object files... -r
>> checking for BSD-compatible nm... /usr/bin/nm -B
>> checking how to recognise dependent libraries... pass_all
>> checking dlfcn.h usability... yes
>> checking dlfcn.h presence... yes
>> checking for dlfcn.h... yes
>> checking for g++... g++
>> checking whether we are using the GNU C++ compiler... yes
>> checking whether g++ accepts -g... yes
>> checking dependency style of g++... gcc3
>> checking the maximum length of command line arguments... 32768
>> checking command to parse /usr/bin/nm -B output from mpicc object... ok
>> checking for objdir... .libs
>> checking for ar... ar
>> checking for ranlib... ranlib
>> checking for strip... strip
>> checking if mpicc supports -fno-rtti -fno-ex

[gmx-users] OS - Compiler - GROMACS compatibility

[alkasrivastava]

Hi,

Since the following warning is given in the GROMACS home page,


WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
compilers come with recent Linux distrubutions like Fedora 5/6 etc.


is the problem only with the 4.1.x series or with compilers of higher
series also? Can we use the latest 4.3.2 series of compilers which come
with fedora core 10?

Also is it possible that we install 4.0 series of compiler in the
operating system with higher series of compilers and use gromacs then.

We bought a new system but that is not supporting fedora core 4 so we are
wondering which operating system should be used or if any alternative is
there.

Please help me.

Thanks in advance
ALKA
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Re: [gmx-users] OS - Compiler - GROMACS compatibility

[Alexey Shvetsov]

For me gentoo and gcc 4.3.x works fine =)
And yes gcc 4.1.x is broken 

On Вторник 17 марта 2009 12:44:43 alkasrivast...@iitb.ac.in wrote:
> Hi,
>
> Since the following warning is given in the GROMACS home page,
>
> 
> WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
> compilers come with recent Linux distrubutions like Fedora 5/6 etc.
> 
>
> is the problem only with the 4.1.x series or with compilers of higher
> series also? Can we use the latest 4.3.2 series of compilers which come
> with fedora core 10?
>
> Also is it possible that we install 4.0 series of compiler in the
> operating system with higher series of compilers and use gromacs then.
>
> We bought a new system but that is not supporting fedora core 4 so we are
> wondering which operating system should be used or if any alternative is
> there.
>
> Please help me.
>
> Thanks in advance
> ALKA
> ___
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-- 
Alexey 'Alexxy' Shvetsov
Gentoo Dev


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[gmx-users] Softcores: sc-power = 1 ou 2 ?

[Eudes Fileti]

Hello,
I have a doubt regarding the use of soft-core.
When the use of sc-power = 2 is more recommended than sc-power = 1?
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
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[gmx-users] Equilibration

[Emanuel Peter]

Dear Gromacs users,

I have read about an equilibration procedure for proteins.
It has the following sequence:

- cool down to 20 K an let this run for about 1 ps.
- heat the system up with 10 K every 500 steps until you get 300 K.
- do a run for 4 ps at 300 K.

Is this kind of equilibration really necessary ?
At the moment I do not know for what reason one should equilibrate in
this way.

One told me that he removed stepwisely constraints while equilibrating.
Could anyone tell me why one should equilibrate with this scheme ?

Thanks in advance.

Emanuel


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[gmx-users] mdrun hangs with the pull option

[Manik Mayur]

Hi,
I am trying to simulate a case where I am pulling a set of atoms with
constant velocity with respect to another set of atoms, like:

XXX --> U (velocity, moving wall, pull group)
ooo
ooo  -> fluid
ooo
XXX --> fixed wall (reference group)

but while running mdrun for the case, it simply becomes unresponsive after
300 steps (no output message even with the -v option). Can somebody suggest
what I might be missing. I am appending the md.log and .mdp file for
reference however, for quick reference the excerpts are->

*) eql.mdp:

; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = constraint
pull_geometry = direction
pull_start = yes
pull_init =
pull_nstxout = 10
pull_ngroups = 1
pull_group0 = WD
pull_group1 = WU
pull_vec1 = 1 0 0
pull_rate1 = 1

*) md.log:

pull = constraint
   pull_geometry= direction
   pull_dim (3):
  pull_dim[0]=1
  pull_dim[1]=1
  pull_dim[2]=1
   pull_r1  = 1
   pull_r0  = 1.5
   pull_constr_tol  = 1e-06
   pull_nstxout = 10
   pull_nstfout = 1
   pull_ngrp= 1
   pull_group 0:
 atom (672):
atom[0,...,671] = {672,...,1343}
 weight: not available
 pbcatom  = 1007
 vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
 init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
 rate = 0
 k= 0
 kB   = 0
   pull_group 1:
 atom (672):
atom[0,...,671] = {0,...,671}
 weight: not available
 pbcatom  = 335
 vec (3):
vec[0]= 1.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
 init (3):
init[0]= 2.08088e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
 rate = 1
 k= 0
 kB   = 0

The other useful data might be:
OS- Ubuntu 8.04
Gromacs- 4.0.2

Thanks,
Manik Mayur
-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur


md.log
Description: Binary data


eql.mdp
Description: Binary data
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Re: [gmx-users] Equilibration

[Justin A. Lemkul]

Emanuel Peter wrote:

Dear Gromacs users,

I have read about an equilibration procedure for proteins.
It has the following sequence:

- cool down to 20 K an let this run for about 1 ps.
- heat the system up with 10 K every 500 steps until you get 300 K.
- do a run for 4 ps at 300 K.

Is this kind of equilibration really necessary ?
At the moment I do not know for what reason one should equilibrate in
this way.



IMHO, it's unnecessary.  Warming up a system slowly is not unreasonable, but 
I've always done straight equilibration at the desired temperature and/or 
pressure and achieved reasonable results.



One told me that he removed stepwisely constraints while equilibrating.
Could anyone tell me why one should equilibrate with this scheme ?



Constraints or restraints?  These are separate concepts in Gromacs.  Removing 
constraints seems pointless, unless you want to start using a smaller timestep! 
 Slowly removing restraints (like position restraints) might be necessary for a 
very sensitive system, but for a standard protein in water, it's probably excessive.


-Justin


Thanks in advance.

Emanuel


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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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] g_dipoles

[rams rams]

Dear David,

The peptide is having a -ve charge of 3. Though the components might
dependent upon the orientation but the average might be the same
irrespective of the orientation I suppose.

Ram.

On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel
wrote:

> rams rams wrote:
>
>> Dear Users,
>>
>> I am trying to obtain the dipole moment of a 40 amino acid residue peptide
>> using g_dipoles. I am getting a huge number (about 700 Debye). I expect it
>> to be around 150 Debye (based on other studies). To make sure it I extracted
>> a shapshot of the structure and obtained the dipolemoment using the
>> following command:
>>
>> g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg  -n prot_dip.ndx
>>
>> I am giving the last few lines of the output below:
>>
>> Dipole moment (Debye)
>> -
>> Average  = 516.7213  Std. Dev. =   0.  Error =   0.
>>
>> The following averages for the complete trajectory have been calculated:
>>
>>  Total < M_x > = -54.3459 Debye
>>  Total < M_y > = 12.8373 Debye
>>  Total < M_z > = 513.695 Debye
>>
>>  Total < M_x^2 > = 2953.47 Debye^2
>>  Total < M_y^2 > = 164.796 Debye^2
>>  Total < M_z^2 > = 263883 Debye^2
>>
>>  Total < |M|^2 > = 267001 Debye^2
>>  Total < |M| >^2 = 267001 Debye^2
>>
>>  < |M|^2 > - < |M| >^2 = 0 Debye^2
>>
>> Finite system Kirkwood g factor G_k = 0
>> Infinite system Kirkwood g factor g_k = 0
>>
>> Epsilon = 1
>>
>> The same structure (i.e., what i have used in the above command) if I open
>> and check for the dipole moment using YASARA suite of program it is showing
>> as 173 Debye. Which is reasonable. Am I making any mistake while obtaining
>> the dipole moment using g_dipoles or I am looking at the wrong file ??
>>
>
> Is the peptide neutral? Otherwise the result might be orientation
> dependent.
>
>
>
>> Thanks.
>>
>> Ram.
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>> interface or send it to gmx-users-requ...@gromacs.org.
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>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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RE: [gmx-users] Softcores: sc-power = 1 ou 2 ?

[Berk Hess]

Hi,

Never (unless you want to reproduce old simulations).

Berk

Date: Tue, 17 Mar 2009 10:50:48 -0300
From: fil...@ufabc.edu.br
To: gmx-users@gromacs.org
Subject: [gmx-users] Softcores: sc-power = 1 ou 2 ?

Hello, I have a doubt regarding the use of soft-core. When the use of sc-power 
= 2 is more recommended than sc-power = 
1?eef___
Eudes Eterno Fileti

Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/

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RE: [gmx-users] mdrun hangs with the pull option

[Berk Hess]

Hi,

You pull rate is ridiculously high (1 nm/ps).

Berk
 

Date: Tue, 17 Mar 2009 19:54:50 +0530
From: manik.ma...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] mdrun hangs with the pull option

Hi,
I am trying to simulate a case where I am pulling a set of atoms with constant 
velocity with respect to another set of atoms, like:

XXX --> U (velocity, moving wall, pull group)

ooo
ooo  -> fluid
ooo
XXX --> fixed wall (reference group)

but while running mdrun for the case, it simply becomes unresponsive after 300 
steps (no output message even with the -v option). Can somebody suggest what I 
might be missing. I am appending the md.log and .mdp file for reference 
however, for quick reference the excerpts are->


*) eql.mdp:

; COM PULLING  
; Pull type: no, umbrella, constraint or constant_force
pull = constraint
pull_geometry = direction
pull_start = yes
pull_init = 

pull_nstxout = 10
pull_ngroups = 1
pull_group0 = WD
pull_group1 = WU
pull_vec1 = 1 0 0
pull_rate1 = 1

*) md.log:

pull = constraint

   pull_geometry= direction
   pull_dim (3):
  pull_dim[0]=1
  pull_dim[1]=1
  pull_dim[2]=1
   pull_r1  = 1
   pull_r0  = 1.5
   pull_constr_tol  = 1e-06

   pull_nstxout = 10
   pull_nstfout = 1
   pull_ngrp= 1
   pull_group 0:
 atom (672):
atom[0,...,671] = {672,...,1343}
 weight: not available
 pbcatom  = 1007

 vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
 init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00

 rate = 0
 k= 0
 kB   = 0
   pull_group 1:
 atom (672):
atom[0,...,671] = {0,...,671}
 weight: not available
 pbcatom  = 335

 vec (3):
vec[0]= 1.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
 init (3):
init[0]= 2.08088e+00
init[1]= 0.0e+00
init[2]= 0.0e+00

 rate = 1
 k= 0
 kB   = 0

The other useful data might be:
OS- Ubuntu 8.04
Gromacs- 4.0.2
Thanks,
Manik Mayur
-- 

Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur

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RE: [gmx-users] g_dipoles

[Berk Hess]

Hi,

I don't think orientation is an issue.

I guess the numbers could be correct.
g_dipoles subtracts the net charge of a molecules at its center of mass.
If your charge a located somewhat to one side of the molecule,
this could result in a quite large dipole.

But different definitions are possible for the dipole of a charged molecule.

Berk

Date: Tue, 17 Mar 2009 10:44:47 -0400
Subject: Re: [gmx-users] g_dipoles
From: rams.c...@gmail.com
To: gmx-users@gromacs.org

Dear David,

The peptide is having a -ve charge of 3. Though the components might dependent 
upon the orientation but the average might be the same irrespective of the 
orientation I suppose.

Ram.


On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel  
wrote:

rams rams wrote:


Dear Users,



I am trying to obtain the dipole moment of a 40 amino acid residue peptide 
using g_dipoles. I am getting a huge number (about 700 Debye). I expect it to 
be around 150 Debye (based on other studies). To make sure it I extracted a 
shapshot of the structure and obtained the dipolemoment using the following 
command:




g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg  -n prot_dip.ndx



I am giving the last few lines of the output below:



Dipole moment (Debye)

-

Average  = 516.7213  Std. Dev. =   0.  Error =   0.



The following averages for the complete trajectory have been calculated:



 Total < M_x > = -54.3459 Debye

 Total < M_y > = 12.8373 Debye

 Total < M_z > = 513.695 Debye



 Total < M_x^2 > = 2953.47 Debye^2

 Total < M_y^2 > = 164.796 Debye^2

 Total < M_z^2 > = 263883 Debye^2



 Total < |M|^2 > = 267001 Debye^2

 Total < |M| >^2 = 267001 Debye^2



 < |M|^2 > - < |M| >^2 = 0 Debye^2



Finite system Kirkwood g factor G_k = 0

Infinite system Kirkwood g factor g_k = 0



Epsilon = 1



The same structure (i.e., what i have used in the above command) if I open and 
check for the dipole moment using YASARA suite of program it is showing as 173 
Debye. Which is reasonable. Am I making any mistake while obtaining the dipole 
moment using g_dipoles or I am looking at the wrong file ??





Is the peptide neutral? Otherwise the result might be orientation dependent.








Thanks.



Ram.









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-- 

David van der Spoel, Ph.D., Professor of Biology

Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.

Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.

sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se


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Re: [gmx-users] g_dipoles

[rams rams]

Thank you Berk.

Is there any way I can draw some reasonable numbers out of it. My main
concern is to see the variation of the dipolemoment along the simulation
time.

Ram.

2009/3/17 Berk Hess 

>  Hi,
>
> I don't think orientation is an issue.
>
> I guess the numbers could be correct.
> g_dipoles subtracts the net charge of a molecules at its center of mass.
> If your charge a located somewhat to one side of the molecule,
> this could result in a quite large dipole.
>
> But different definitions are possible for the dipole of a charged
> molecule.
>
> Berk
>
> --
> Date: Tue, 17 Mar 2009 10:44:47 -0400
> Subject: Re: [gmx-users] g_dipoles
> From: rams.c...@gmail.com
> To: gmx-users@gromacs.org
>
>
> Dear David,
>
> The peptide is having a -ve charge of 3. Though the components might
> dependent upon the orientation but the average might be the same
> irrespective of the orientation I suppose.
>
> Ram.
>
> On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel  > wrote:
>
> rams rams wrote:
>
> Dear Users,
>
> I am trying to obtain the dipole moment of a 40 amino acid residue peptide
> using g_dipoles. I am getting a huge number (about 700 Debye). I expect it
> to be around 150 Debye (based on other studies). To make sure it I extracted
> a shapshot of the structure and obtained the dipolemoment using the
> following command:
>
> g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg  -n prot_dip.ndx
>
> I am giving the last few lines of the output below:
>
> Dipole moment (Debye)
> -
> Average  = 516.7213  Std. Dev. =   0.  Error =   0.
>
> The following averages for the complete trajectory have been calculated:
>
>  Total < M_x > = -54.3459 Debye
>  Total < M_y > = 12.8373 Debye
>  Total < M_z > = 513.695 Debye
>
>  Total < M_x^2 > = 2953.47 Debye^2
>  Total < M_y^2 > = 164.796 Debye^2
>  Total < M_z^2 > = 263883 Debye^2
>
>  Total < |M|^2 > = 267001 Debye^2
>  Total < |M| >^2 = 267001 Debye^2
>
>  < |M|^2 > - < |M| >^2 = 0 Debye^2
>
> Finite system Kirkwood g factor G_k = 0
> Infinite system Kirkwood g factor g_k = 0
>
> Epsilon = 1
>
> The same structure (i.e., what i have used in the above command) if I open
> and check for the dipole moment using YASARA suite of program it is showing
> as 173 Debye. Which is reasonable. Am I making any mistake while obtaining
> the dipole moment using g_dipoles or I am looking at the wrong file ??
>
>
> Is the peptide neutral? Otherwise the result might be orientation
> dependent.
>
>
>
> Thanks.
>
> Ram.
>
>
> 
>
> ___
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>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
> ___
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>
>
>
> --
> What can you do with the new Windows Live? Find 
> out
>
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[gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal

[maria goranovic]

Hello

I am trying to restrain water along the bilayer normal. For this;

1.  I made a posre_solvent.itp using genpr. It look like this:

; position restraints for Solvent

[ position_restraints ]
;  i funct   fcxfcyfcz
340831  0  0   1000
340841  0  0   1000
340851  0  0   1000
... (there are ~ 60,000 water molecules)

2. I include this file in my topology file using:

#ifdef POSRES_SOLVENT
#include posre_solvent.itp
#endif

3. And finally, the mdp file looks like:
..
define  =   -DFLEX_SPC -DPOSRES_SOLVENT
..

Why do I get a segmentation fault on running grompp?

Thank u for helping

-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] mdrun hangs with the pull option

[Manik Mayur]

2009/3/17 Berk Hess 

>  Hi,
>
> You pull rate is ridiculously high (1 nm/ps).
>

Is there any upper limit on the pull rate?
btw are the other parameters consistent with the system I am trying to
simulate?


> Berk
>
>
> --
> Date: Tue, 17 Mar 2009 19:54:50 +0530
> From: manik.ma...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] mdrun hangs with the pull option
>
>
> Hi,
> I am trying to simulate a case where I am pulling a set of atoms with
> constant velocity with respect to another set of atoms, like:
>
> XXX --> U (velocity, moving wall, pull group)
> ooo
> ooo  -> fluid
> ooo
> XXX --> fixed wall (reference group)
>
> but while running mdrun for the case, it simply becomes unresponsive after
> 300 steps (no output message even with the -v option). Can somebody suggest
> what I might be missing. I am appending the md.log and .mdp file for
> reference however, for quick reference the excerpts are->
>
> *) eql.mdp:
>
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant_force
> pull = constraint
> pull_geometry = direction
> pull_start = yes
> pull_init =
> pull_nstxout = 10
> pull_ngroups = 1
> pull_group0 = WD
> pull_group1 = WU
> pull_vec1 = 1 0 0
> pull_rate1 = 1
>
> *) md.log:
>
> pull = constraint
>pull_geometry= direction
>pull_dim (3):
>   pull_dim[0]=1
>   pull_dim[1]=1
>   pull_dim[2]=1
>pull_r1  = 1
>pull_r0  = 1.5
>pull_constr_tol  = 1e-06
>pull_nstxout = 10
>pull_nstfout = 1
>pull_ngrp= 1
>pull_group 0:
>  atom (672):
> atom[0,...,671] = {672,...,1343}
>  weight: not available
>  pbcatom  = 1007
>  vec (3):
> vec[0]= 0.0e+00
> vec[1]= 0.0e+00
> vec[2]= 0.0e+00
>  init (3):
> init[0]= 0.0e+00
> init[1]= 0.0e+00
> init[2]= 0.0e+00
>  rate = 0
>  k= 0
>  kB   = 0
>pull_group 1:
>  atom (672):
> atom[0,...,671] = {0,...,671}
>  weight: not available
>  pbcatom  = 335
>  vec (3):
> vec[0]= 1.0e+00
> vec[1]= 0.0e+00
> vec[2]= 0.0e+00
>  init (3):
> init[0]= 2.08088e+00
> init[1]= 0.0e+00
> init[2]= 0.0e+00
>  rate = 1
>  k= 0
>  kB   = 0
>
> The other useful data might be:
> OS- Ubuntu 8.04
> Gromacs- 4.0.2
>
> Thanks,
> Manik Mayur
> --
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger
>
> ___
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>



-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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Re: [gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal

[XAvier Periole]

You've probably conflicts of restrains and forces in your system.

Note that our definition of the position restraints if applicable to
all solvent molecules should be :

[position_restraints]
1 1 0 0 1000
2 1 0 0 1000
3 1 0 0 1000

if not it will look at the atom of the solvent number 34083 ... etc.  
You basically

do not retrain the atoms you think.

then I would only retrain the oxygen of the water molecules, hydrogens  
might

need to move.

On Mar 17, 2009, at 4:56 PM, maria goranovic wrote:


Hello

I am trying to restrain water along the bilayer normal. For this;

1.  I made a posre_solvent.itp using genpr. It look like this:

; position restraints for Solvent

[ position_restraints ]
;  i funct   fcxfcyfcz
340831  0  0   1000
340841  0  0   1000
340851  0  0   1000
... (there are ~ 60,000 water molecules)

2. I include this file in my topology file using:

#ifdef POSRES_SOLVENT
#include posre_solvent.itp
#endif

3. And finally, the mdp file looks like:
..
define  =   -DFLEX_SPC -DPOSRES_SOLVENT
..

Why do I get a segmentation fault on running grompp?

Thank u for helping

--
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] mdrun hangs with the pull option

[Manik Mayur]

On Tue, Mar 17, 2009 at 9:31 PM, Manik Mayur  wrote:

>
>
> 2009/3/17 Berk Hess 
>
>>  Hi,
>>
>> You pull rate is ridiculously high (1 nm/ps).
>>
>
Also I am simulating in reduced dimentions. I think it is fine then.

Is there any upper limit on the pull rate?
> btw are the other parameters consistent with the system I am trying to
> simulate?
>
>
>> Berk
>>
>>
>> --
>> Date: Tue, 17 Mar 2009 19:54:50 +0530
>> From: manik.ma...@gmail.com
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] mdrun hangs with the pull option
>>
>>
>> Hi,
>> I am trying to simulate a case where I am pulling a set of atoms with
>> constant velocity with respect to another set of atoms, like:
>>
>> XXX --> U (velocity, moving wall, pull group)
>> ooo
>> ooo  -> fluid
>> ooo
>> XXX --> fixed wall (reference group)
>>
>> but while running mdrun for the case, it simply becomes unresponsive after
>> 300 steps (no output message even with the -v option). Can somebody suggest
>> what I might be missing. I am appending the md.log and .mdp file for
>> reference however, for quick reference the excerpts are->
>>
>> *) eql.mdp:
>>
>> ; COM PULLING
>> ; Pull type: no, umbrella, constraint or constant_force
>> pull = constraint
>> pull_geometry = direction
>> pull_start = yes
>> pull_init =
>> pull_nstxout = 10
>> pull_ngroups = 1
>> pull_group0 = WD
>> pull_group1 = WU
>> pull_vec1 = 1 0 0
>> pull_rate1 = 1
>>
>> *) md.log:
>>
>> pull = constraint
>>pull_geometry= direction
>>pull_dim (3):
>>   pull_dim[0]=1
>>   pull_dim[1]=1
>>   pull_dim[2]=1
>>pull_r1  = 1
>>pull_r0  = 1.5
>>pull_constr_tol  = 1e-06
>>pull_nstxout = 10
>>pull_nstfout = 1
>>pull_ngrp= 1
>>pull_group 0:
>>  atom (672):
>> atom[0,...,671] = {672,...,1343}
>>  weight: not available
>>  pbcatom  = 1007
>>  vec (3):
>> vec[0]= 0.0e+00
>> vec[1]= 0.0e+00
>> vec[2]= 0.0e+00
>>  init (3):
>> init[0]= 0.0e+00
>> init[1]= 0.0e+00
>> init[2]= 0.0e+00
>>  rate = 0
>>  k= 0
>>  kB   = 0
>>pull_group 1:
>>  atom (672):
>> atom[0,...,671] = {0,...,671}
>>  weight: not available
>>  pbcatom  = 335
>>  vec (3):
>> vec[0]= 1.0e+00
>> vec[1]= 0.0e+00
>> vec[2]= 0.0e+00
>>  init (3):
>> init[0]= 2.08088e+00
>> init[1]= 0.0e+00
>> init[2]= 0.0e+00
>>  rate = 1
>>  k= 0
>>  kB   = 0
>>
>> The other useful data might be:
>> OS- Ubuntu 8.04
>> Gromacs- 4.0.2
>>
>> Thanks,
>> Manik Mayur
>> --
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>>
>> --
>> Express yourself instantly with MSN Messenger! MSN 
>> Messenger
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.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-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
>



-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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[gmx-users] Range checking error: only on double precision

[Jack Shultz]

Hello,

I just wanted to compare results between single and double precision.
I reused the same parameters. Single works. Double caused errors on
mdrun. Any idea why?

http://hydrogenathome.org/result.php?resultid=1292662

---
Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]



-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
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Re: [gmx-users] Range checking error: only on double precision

[Justin A. Lemkul]

Jack Shultz wrote:

Hello,

I just wanted to compare results between single and double precision.
I reused the same parameters. Single works. Double caused errors on
mdrun. Any idea why?

http://hydrogenathome.org/result.php?resultid=1292662



I don't know why any of that worked at all.  You've got missing atoms and 
inconsistent naming (LYSH should be LYP if you really want a protonated lysine 
under the Amber ports, etc).  Did you give pdb2gmx -missing?  Otherwise, 
topology generation should have failed.


Especially troublesome:

System has non-zero total charge: -2.309866e+01

I would suggest running tests on a physically realistic system that has all 
atoms present and an integer charge.  Maybe single precision somehow overcame 
these topology problems, but I wouldn't trust any of the results.


-Justin


---
Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]





--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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] Range checking error: only on double precision

[Jack Shultz]

Justin,

Can you suggest any pdb files I could use that are more simple? I've
been trying to use files from tutorials but it seems like are always
problematic.

Jack

On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul  wrote:
>
>
> Jack Shultz wrote:
>>
>> Hello,
>>
>> I just wanted to compare results between single and double precision.
>> I reused the same parameters. Single works. Double caused errors on
>> mdrun. Any idea why?
>>
>> http://hydrogenathome.org/result.php?resultid=1292662
>>
>
> I don't know why any of that worked at all.  You've got missing atoms and
> inconsistent naming (LYSH should be LYP if you really want a protonated
> lysine under the Amber ports, etc).  Did you give pdb2gmx -missing?
>  Otherwise, topology generation should have failed.
>
> Especially troublesome:
>
> System has non-zero total charge: -2.309866e+01
>
> I would suggest running tests on a physically realistic system that has all
> atoms present and an integer charge.  Maybe single precision somehow
> overcame these topology problems, but I wouldn't trust any of the results.
>
> -Justin
>
>> ---
>> Program mdrun, VERSION 4.0.3
>> Source code file: nsgrid.c, line: 357
>>
>> Range checking error:
>> Explanation: During neighborsearching, we assign each particle to a grid
>> based on its coordinates. If your system contains collisions or parameter
>> errors that give particles very high velocities you might end up with some
>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>> put these on a grid, so this is usually where we detect those errors.
>> Make sure your system is properly energy-minimized and that the potential
>> energy seems reasonable before trying again.
>>
>> Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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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-- 
Jack

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http://hydrogenathome.org
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Re: [gmx-users] Range checking error: only on double precision

[Justin A. Lemkul]

Well, several tutorials use lysozyme, PDB 1AKI.  I would also recommend not 
using ffamber if you are running automated tests, since there are quirks with 
requiring specific nomenclature (for lysine, histidine, terminal residues, etc).


-Justin

Jack Shultz wrote:

Justin,

Can you suggest any pdb files I could use that are more simple? I've
been trying to use files from tutorials but it seems like are always
problematic.

Jack

On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul  wrote:


Jack Shultz wrote:

Hello,

I just wanted to compare results between single and double precision.
I reused the same parameters. Single works. Double caused errors on
mdrun. Any idea why?

http://hydrogenathome.org/result.php?resultid=1292662


I don't know why any of that worked at all.  You've got missing atoms and
inconsistent naming (LYSH should be LYP if you really want a protonated
lysine under the Amber ports, etc).  Did you give pdb2gmx -missing?
 Otherwise, topology generation should have failed.

Especially troublesome:

System has non-zero total charge: -2.309866e+01

I would suggest running tests on a physically realistic system that has all
atoms present and an integer charge.  Maybe single precision somehow
overcame these topology problems, but I wouldn't trust any of the results.

-Justin


---
Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]




--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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
Graduate Research Assistant
ICTAS Doctoral Scholar
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] Range checking error: only on double precision

[Jack Shultz]

I guess its the amber03 force field I'm having issues with. The
lysozyme tutorial works if I use -ff G43a2
Thanks

Jack

On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul  wrote:
>
> Well, several tutorials use lysozyme, PDB 1AKI.  I would also recommend not
> using ffamber if you are running automated tests, since there are quirks
> with requiring specific nomenclature (for lysine, histidine, terminal
> residues, etc).
>
> -Justin
>
> Jack Shultz wrote:
>>
>> Justin,
>>
>> Can you suggest any pdb files I could use that are more simple? I've
>> been trying to use files from tutorials but it seems like are always
>> problematic.
>>
>> Jack
>>
>> On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul  wrote:
>>>
>>> Jack Shultz wrote:

 Hello,

 I just wanted to compare results between single and double precision.
 I reused the same parameters. Single works. Double caused errors on
 mdrun. Any idea why?

 http://hydrogenathome.org/result.php?resultid=1292662

>>> I don't know why any of that worked at all.  You've got missing atoms and
>>> inconsistent naming (LYSH should be LYP if you really want a protonated
>>> lysine under the Amber ports, etc).  Did you give pdb2gmx -missing?
>>>  Otherwise, topology generation should have failed.
>>>
>>> Especially troublesome:
>>>
>>> System has non-zero total charge: -2.309866e+01
>>>
>>> I would suggest running tests on a physically realistic system that has
>>> all
>>> atoms present and an integer charge.  Maybe single precision somehow
>>> overcame these topology problems, but I wouldn't trust any of the
>>> results.
>>>
>>> -Justin
>>>
 ---
 Program mdrun, VERSION 4.0.3
 Source code file: nsgrid.c, line: 357

 Range checking error:
 Explanation: During neighborsearching, we assign each particle to a grid
 based on its coordinates. If your system contains collisions or
 parameter
 errors that give particles very high velocities you might end up with
 some
 coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
 put these on a grid, so this is usually where we detect those errors.
 Make sure your system is properly energy-minimized and that the
 potential
 energy seems reasonable before trying again.

 Variable ci has value -2147483648. It should have been within [ 0 .. 300
 ]



>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> 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-us...@gromacs.org
>>> http://www.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-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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-us...@gromacs.org
> http://www.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-requ...@gromacs.org.
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>



-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
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Re: [gmx-users] Matching atom name and types in OPLS-aa FF

[Tree]

Dear Dr. Periole:


Thank you for your answer.
That was the point which I wanted to double check (of course after reading
the manual...).

Thank you again!


Sincerely,

Kim

On Tue, Mar 17, 2009 at 6:09 PM, XAvier Periole  wrote:

>
> On Mar 17, 2009, at 8:45 AM, tree wrote:
>
> Dear Justin:
>>
>>
>> Thank you for your email!
>>
>> Thanks to your help and explanation, I am feeling more comfortable with
>> OPLS topology modification.
>> Before this work, I have used Gromacs without modifying FF paramters for
>> simulating 'water' in general systems, which can easily obtained from PDB
>> sites.
>> So, it was not too easy to generate a sort of new topology even I've
>> learned MD.
>>
>> I understand what you meant here. :)
>> I did not mean the selection "1" (Harmonic potential function) is a sort
>> of OPLS-aa FF functions.
>> My question is actually if I can use the Forth power potential when I
>> choose "2" in bond streching section.
>> Since this funtion has different from from "1" (Harmonic potential
>> function), I thought that it may need other paramters that may (may not) be
>> different from the given parameters in OPLS-aa FF.
>> So, my question here is
>>  [can I use the Forth power potential for bond strech using the given
>>  OPLS-aa paramters?]
>>
> To that the answer is no! If you change the potential to describe a bond,
> angle ...
> the parameters will be different! Have a look a the manual chapter 4.
>
> I assume this would be same to others, angle, dihedral, and etc.
>>
>> Thank you again.
>>
>>
>> Sincerely,
>>
>> Kim
>>
>> On Mon, 16 Mar 2009, Justin A. Lemkul wrote:
>>
>>
>>>
>>> Tree wrote:
>>>
 Dear Dr. Periole:
 Thank you for your answer.
 You meant that the types of potential functions do not have any
 relations with OPLS-aa (except first ("1") case).
 Those (from "2"...) are defined as written the Gromacs manual.

>>>
>>> Table 5.4 defines the different types of intramolecular interactions.
>>>  You should specify the proper terms based on what corresponds to the force
>>> field functional form.  That is harmonic potential does not necessarily
>>> imply OPLS, but OPLS might imply that you have to use a harmonic potential
>>> (because, in fact, many force fields use a harmonic potential for bonds, not
>>> just OPLS!)
>>>
>>> You should refer to the primary literature for the force field, how it
>>> was derived, and any subsequent references regarding modifications to the
>>> force field.
>>>
>>> Another option (in addition to doing the background reading!) is to run
>>> through some tutorial material with a simple protein under OPLS to get a
>>> feel for how an OPLS topology is automatically created by pdb2gmx.
>>>
>>> -Justin
>>>
>>> Thank you again.
 Sincerely,
 Kim
 On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole >>> x.peri...@rug.nl>> wrote:

   On Mar 16, 2009, at 9:34 AM, tree wrote:

   Dear Justin and All:

   I truly appreciate your clear answer.
   Since my questions are solved by your explanations, I do not
   know how I can express my grateful heart.

   Now I have to ask second step questions. :)
   It is related to the OPLS-aa "bon.itp" file.
   Each section (bonds, angle, diherdal, and etc.) has its "type".
   I am wondering if this "type" (of course, in OPLS-aa case) has
   the same meaning in the Gromos potentials.
   As we know, those types for each kind of bonded interactions are
   well described in the Gromacs manual with clear equations.
   So, my question is (as I mentioned just above) if this is the
   same as the OPLS-aa case.

   Yes, the bond, angle, dihedral types are independent to the
   underlying force field
   and correspond to the description in the manual.

   To make my question clear, I want to give an example.

   [ bonds ]
   ...
   CT  HC  1   0.10900 284512.0; CHARMM 22
 paramter
   ...

   I know the number "1" here means type, which describes what kind
   of the bonds (strech) between two bonds is used.
   If this is Gromos potential, I am sure this "1" means "harmonic"
   potential according to the Chap. 4 of the Gromacs manual.
   Is this also applied to OPLS-aa FF?

   Thank you for your care, again.

   Sincerely yours,

   Kim

   On Fri, 13 Mar 2009, Justin A. Lemkul wrote:

   Tree wrote:

   Dear All:
   I appreciate your answer always.
   Right now, I am trying to add/modify some values in
   OPLS-aa FF.
   I am confused atom type (opls_xxx) and atom name (e.g.,
   C) in "atp", "bon.itp", and "nb.itp" files.
   Please let me try the situation by an example, first.
 

RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again

[Eudes Fileti]

Hello Berk, I have tried to calculate the free energy of transfer
for a polyhydroxylated (from benzene to ethanol).
The Dg/dlambda plot, for both, benzene and ethanol shows a
very high and narrow peak near lambda=0. In the case of ethanol
is worse due to the solute-solvent hydrogen bonds.

I performed two sets of simulations, one for sc-power=1 and another
for sc-power=2. For sc-power=1 I got a peak much higher than for
sc-power=2, and therefore the integration in this case (sc-power=1)
could lead me to a much greater error. (please see figure
http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg)
In both cases (ethanol and benzene) the curves coincide for values of lambda
beyond 0.4.

That is the why of my original question. Not in this case is justified
use sc-power=2? Have you any tips on how to ensure the accuracy of
calculation of Delta_G in this case?

Bests
eef


Message: 3
Date: Tue, 17 Mar 2009 15:49:12 +0100
From: Berk Hess 
Subject: RE: [gmx-users] Softcores: sc-power = 1 ou 2 ?
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"


Hi,

Never (unless you want to reproduce old simulations).

Berk

Date: Tue, 17 Mar 2009 10:50:48 -0300
From: fil...@ufabc.edu.br
To: gmx-users@gromacs.org
Subject: [gmx-users] Softcores: sc-power = 1 ou 2 ?

Hello, I have a doubt regarding the use of soft-core. When the use of
sc-power = 2 is more recommended than sc-power =
1?eef___
Eudes Eterno Fileti

Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
___
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