[gmx-users] pbc interference with g_dist

[Suman Chakrabarty]

Hi,

after spending a long time with a seemingly wrong result with g_dist,
I discovered that g_dist actually uses pbc and nearest image
convention to calculate the distance.

As a result, the end-to-end distance of my polymer chain is calculated
as 1.5 nm, while actually it should be 12.44 nm (box length = 13.9422
nm). Since I am interested in the end-to-end distance of the single
polymer chain irrespective of the position of the two ends, I would
like to know what would be the best way to go about it.

I hope I could explain my problem.


Thanks and regards,
Suman.
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Re: Re: Re: [gmx-users] How to break a disulfide bond ???

[Venkat Reddy]

Thanks Sharada madam n justin sir for ur kind attention.I followed ur
command "pdb2gmx -ss".its asking like

Link CYS-37 SG-306 and CYS-59 SG-453 (y/n) ?n
Link CYS-44 SG-358 and CYS-50 SG-390 (y/n) ?y
Link CYS-72 SG-560 and CYS-101 SG-764 (y/n) ?y
Link CYS-82 SG-628 and CYS-93 SG-707 (y/n) ?y
Link CYS-150 SG-1137 and CYS-156 SG-1173 (y/n) ?y
Link CYS-203 SG-1546 and CYS-258 SG-1984 (y/n) ?y
Link CYS-210 SG-1603 and CYS-231 SG-1767 (y/n) ?y

actually i want to break the s-s bond between CYS37 n CYS59 . so i've given
the options like as shown above. When i again visualized the pdb in
pymol,its showing the disulfides as it is (no break between CYS37 n CYS59).
Can u suggest me wat to do 
Thanks for giving reply.
On Fri, Mar 6, 2009 at 7:24 PM, sharada  wrote:

> Do you intend to protonate a pair of cysteins and not make a SS bond?
> Then pdb2gmx -ss should do the job.
>
> Sharada
>
>
> *-- Original Message --*
> From: sharada 
> To: Discussion list for GROMACS users 
> Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST)
> Subject: Re: Re: [gmx-users] How to break a disulfide bond ???
>
> If you donot make it, it is as good as breaking it...
>
> Sharada
>
> *-- Original Message --*
> From: Venkat Reddy 
> To: Discussion list for GROMACS users 
> Date: Fri, 6 Mar 2009 11:31:57 +0530
> Subject: Re: [gmx-users] How to break a disulfide bond ???
>
> Hai !
>
> with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break
> a particular ss bond (not all).
> Thank you
>
>
> On Fri, Mar 6, 2009 at 11:01 AM, sharada  wrote:
>
>>
>> pdb2gmx -h
>>
>> sharada
>>
>>
>>
>> *-- Original Message --*
>> From: Venkat Reddy 
>> To: Discussion list for GROMACS users 
>> Date: Fri, 6 Mar 2009 10:50:24 +0530
>> Subject: [gmx-users] How to break a disulfide bond ???
>>
>> Hai Every one ! Is it possible to break a disulfide bridge using gromacs
>> ?If so,Can anybody suggest me, how to do it???
>>
>> Thanks for ur valuable time
>>
>> With best wishes
>> Venkat Reddy Chirasani
>> M.Tech Bioinformatics
>> UNIVERSITY OF HYDERABAD
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>
>
>
> --
> Venkat Reddy Chirasani
> M.Tech Bioinformatics
> UNIVERSITY OF HYDERABAD
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-- 
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
Laboratory of Computational Biology
Centre for DNA Fingerprinting and Diagnostics
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[gmx-users] A Question About gmxtest

[Reza Salari]

Hi everyone!

Thanks to GROMACS developers, version 4.0.4 has been released along with 
gmxtest 4.0.4. However, I have encountered some problems in passing all tests. 
I have installed GROMACS on different machines (64 bit AMD and Intel quad 
cores) using diffrent configure flags (based on instructions in the INSTALL 
file) and used fftw3 with double and float types, but still tests always fail 
in COMPLEX (field, tip4p, water) and KERNEL (~16 tests) on all machines. I 
looked into the test output files and noticed that those failed kernel tests 
almost always failed in the first step [I think that the test output files only 
include the steps that failed].

I don't know how much I must be worried about the test results. Has anybody 
been able to successfully run all tests on a x86_64 machine? If so, could you 
point out where I could have possibly gone wrong?

Thank you in advance,___
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[gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory

[nam kim]

I have experienced OS (RedHat Enterprise) for a hour or 3 hours
whiling using gromacs 4.0.4 g-utilities such as g_vanhove.

My log error messages are:

Out of Memory  g_vanhove_mpi
Out of Memory g_anaeig_mpi

Are g-utilites of Gromacs 4.0.4 buggy?

Thanks
-Nam
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Re: [gmx-users] .gro files problems

[Justin A. Lemkul]

Andrew Voronkov wrote:

Dear GROMACS users,
I'm trying to do this tutorial



It's always best to post a link to the tutorial you're using.  There are dozens 
of Gromacs tutorials out there.



with 1ijy structure from rcsb.org
All .gro files on different step raise questions.
1) conf.gro - by VMD I see some strange groups which are not linked with the 
protein.


This may or may not be an artefact of VMD's efforts to guess where bonds should 
be.  Sometimes it's smart, sometimes it's not.



2) After solvatation step in solvated.gro the protein is not in the middle of 
solution but somewhere in the edge, how to solve this?


editconf -c


3) After energy minimization protein even goes out of the solution. Looks like 
I am doing everything according to the tutorial (except the structure) but 
there are still problems...



Use editconf -c and try again.


The .gro files are in the attachment.


The listserv ate them, but they probably won't aid much in diagnosis, anyway.


On minimization step I also get:
Steepest Descents converged to machine precision in 73 steps,
but did not reach the requested Fmax


Depending on what your target Fmax was, this may not be a problem.  Fmax < 1000 
is generally adequate for a simple protein in water.



On equilibration step I also get an error(with such .gro file it very 
proabable):



Or you could have an error in your .mdp file (inappropriate parameters, etc), so 
if things continue to fail, post the .mdp file (not as an attachment, just embed 
the text).


-Justin


Warning: 1-4 interaction between 2 and 19 at distance 2.795 which is larger 
than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.000 ps: Water molecule starting at atom 33175 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
step 0Segmentation fault


Best regards,
Andrew
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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] using pdb2gmx

[Justin A. Lemkul]

oguz gurbulak wrote:

Dear All,


I'm trying to create gro and .top files using pdb2gmx. I created 
n-dodecane.pdb using Chem3D and got 100 molecules using packmol. I added 
TER cards between each seperate molecules.  Then I tried to get gro and 
.top files using the commands in below :



pdb2gmx –ff G43a2 –f n-dodecane.pdb –o n-dodecane.gro –p n-dodecane.top


pdb2gmx –ff G43a2 –f n-dodecane.packmol100.pdb –o n-dodecane.gro –p 
n-dodecane.top ( added TER cards )



pdb2gmx –ff G43a2 –f n-dodecane.packmol100.pdb –o n-dodecane.gro –p 
n-dodecane.top



I couldn't get gro and .top files. Could you please help me to get gro 
and .top files successfuly ? I also need some information about using 
packmol pdb file in Gromacs. I want to run md for 100 n-dodecane molecules.





You will not be able to use pdb2gmx to generate a topology unless the relevant 
molecules/residues are defined in your force field's .rtp file.


When posting questions, it is best to include the actual error message instead 
of "it didn't work" or some such equivalent.


You could probably use the PRODRG server to generate a topology for a simple 
molecule like n-dodecane.


If you have a .pdb file from Packmol, it can be used within Gromacs without any 
further modification (.gro is not necessary).  You just need an appropriate 
topology for the system.


-Justin


Thank you very much for your attention.



Sincerely





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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] Error in pdb2gmx

[Justin A. Lemkul]

Robert Kretschmer wrote:

Dear all,
 
i have a problem while running pdb2gmx. I want to run a md simulation 
with HIV-ReverseTranscriptase (PDB: 1TVR & 1HNV). But in pdb2gmx i get 
the following error:
 
"Fatal error:

Incomplete ring in HIS221"
 
I checked HIS221 and found, that it should be an alanine.
 


The .pdb file probably has the name HIS, but some of the atoms are missing.  If 
it is indeed supposed to be an alanine, change the residue name in the .pdb 
file.  If it is supposed to be HIS, however, then you need to re-build the 
residue using some kind of modeling software.



What kann I do?
 


Check for "MISSING" comments in the header of the .pdb file to be sure of what 
you are doing.


-Justin


kind regards
 
robert





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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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[gmx-users] Re: OXY not found

[Andy Torres]

Thanks Justin and Chris for the fast answer! I follow the Chris instructions
but modifying the molecule name '[ OTWO ]' for   '[ OTW ]' because
otherwise gromacs error appears (there are other names with 4 letters code,
I don't know why these is not valid). But it's working now!
Andy

2009/3/5 

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> Today's Topics:
>
>   1. problem in running grompp (victor doss)
>   2. problem running grompp -  error message here (victor doss)
>   3. Re: problem running grompp -  error message here
>  (Justin A. Lemkul)
>   4. OXY not found (Andy Torres)
>   5. Re: OXY not found (Justin A. Lemkul)
>   6. distance restraints for alpha helix (abhigna polavarapu)
>   7. OXY not found (Chris Neale)
>
>
> --
>
> Message: 1
> Date: Thu, 5 Mar 2009 17:32:12 +
> From: victor doss 
> Subject: [gmx-users] problem in running grompp
> To: 
> Message-ID: 
> Content-Type: text/plain; charset="windows-1252"
>
>
> Hello,
>
> when I run grompp  I get the following error message always. Whoever has  a
> correct fix to get rid of this error message and get the actual result,
>  Please suggest.
>
> Thanking you
>
>
> Dr. Victor A. Doss
>
>
> _
> The new Windows Live Messenger. You don’t want to miss this.
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> Message: 2
> Date: Thu, 5 Mar 2009 17:34:59 +
> From: victor doss 
> Subject: [gmx-users] problem running grompp -  error message here
> To: 
> Message-ID: 
> Content-Type: text/plain; charset="windows-1252"
>
>
> Hello,
>
> when I run grompp  I get the following error message
> always. Whoever has  a correct fix to get rid of this error message and
> get the actual result,  Please suggest.
>
> Thanking you
>
>
> Dr. Victor A. Doss
>
>
> processing topology...
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 2 bonded neighbours for SOL 82
> Excluding 2 bonded neighbours for SOL 9514
> NOTE:
>  System has non-zero total charge: 8.00e+00
>
> processing coordinates...
> double-checking input for internal consistency...
>
> ---
> Program grompp, VERSION 3.3.3
> Source code file: ../../../../src/kernel/grompp.c, line: 1134
>
> Fatal error:
> There were 3 error(s) processing your input
> ---
>
> "Can't You Make This Thing Go Faster ?" (Black Crowes)
>
> d...@dv-laptop:~/g
>
>
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> Message: 3
> Date: Thu, 05 Mar 2009 13:02:29 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] problem running grompp -  error message here
> To: Discussion list for GROMACS users 
> Message-ID: <49b013b5.6030...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> victor doss wrote:
> > Hello,
> >
> > when I run grompp  I get the following error message always. Whoever
> > has  a correct fix to get rid of this error message and get the actual
> > result,  Please suggest.
> >
> > Thanking you
> >
> >
> > Dr. Victor A. Doss
> >
> >
> > processing topology...
> > Generated 332520 of the 332520 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 332520 of the 332520 1-4 parameter combinations
> > Excluding 3 bonded neighbours for Protein_A 1
> > Excluding 2 bonded neighbours for SOL 82
> > Excluding 2 bonded neighbours for SOL 9514
> > NOTE:
> >   System has non-zero total charge: 8.00e+00
> >
> > processing coordinates...
> > double-checking input for internal consistency...
> >
> > ---
> > Program grompp, VERSI

[gmx-users] .gro files problems

[Andrew Voronkov]

Dear GROMACS users,
I'm trying to do this tutorial

with 1ijy structure from rcsb.org
All .gro files on different step raise questions.
1) conf.gro - by VMD I see some strange groups which are not linked with the 
protein.
2) After solvatation step in solvated.gro the protein is not in the middle of 
solution but somewhere in the edge, how to solve this?
3) After energy minimization protein even goes out of the solution. Looks like 
I am doing everything according to the tutorial (except the structure) but 
there are still problems...

The .gro files are in the attachment.
On minimization step I also get:
Steepest Descents converged to machine precision in 73 steps,
but did not reach the requested Fmax
On equilibration step I also get an error(with such .gro file it very 
proabable):

Warning: 1-4 interaction between 2 and 19 at distance 2.795 which is larger 
than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.000 ps: Water molecule starting at atom 33175 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
step 0Segmentation fault


Best regards,
Andrew
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[gmx-users] using pdb2gmx

[oguz gurbulak]

Dear All,



I'm trying to create gro and .top files
using pdb2gmx. I
created  n-dodecane.pdb using Chem3D and  got 100 molecules using
packmol.  I added TER cards between each seperate molecules.  Then I tried to 
get gro
and .top files using the commands in below :



pdb2gmx
 –ff G43a2
–f 
n-dodecane.pdb  –o n-dodecane.gro –p n-dodecane.top



pdb2gmx
 –ff G43a2
–f 
n-dodecane.packmol100.pdb  –o n-dodecane.gro –p n-dodecane.top (
added TER cards )



pdb2gmx
 –ff G43a2
–f 
n-dodecane.packmol100.pdb  –o n-dodecane.gro –p n-dodecane.top



I
couldn't get  gro and .top files. Could you please help me to get 
gro and .top files successfuly ? I also need some information about
using packmol pdb file in Gromacs. I want to run md for 100 
n-dodecane molecules. 




Thank
you very much for your attention.




Sincerely


  ___
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[gmx-users] Error in pdb2gmx

[Robert Kretschmer]

Dear all,

i have a problem while running pdb2gmx. I want to run a md simulation with 
HIV-ReverseTranscriptase (PDB: 1TVR & 1HNV). But in pdb2gmx i get the following 
error:

"Fatal error:
Incomplete ring in HIS221"

I checked HIS221 and found, that it should be an alanine.

What kann I do?

kind regards

robert___
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Re: Re: Re: [gmx-users] How to break a disulfide bond ???

[sharada]

Do you intend to protonate a pair of cysteins and not make a SS bond?  
Then pdb2gmx -ss should do the job. 
Sharada
-- Original Message --
From: sharada  
To: Discussion list for GROMACS users 
Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST)
Subject: Re:  Re: [gmx-users] How to break a disulfide bond ???
If you donot make it, it is as good as breaking it...
Sharada
-- Original Message --
From: Venkat Reddy 
To: Discussion list for GROMACS users 
Date: Fri, 6 Mar 2009 11:31:57 +0530
Subject: Re: [gmx-users] How to break a disulfide bond ???
Hai !
with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break a 
particular ss bond (not all).
Thank you
On Fri, Mar 6, 2009 at 11:01 AM, sharada 
 wrote:
pdb2gmx -h
sharada
 
-- Original Message --
From: Venkat Reddy 
To: Discussion list for GROMACS users 

Date: Fri, 6 Mar 2009 10:50:24 +0530
Subject: [gmx-users] How to break a disulfide bond ???
Hai Every one ! Is it possible to break a disulfide bridge using gromacs 
?If so,Can anybody suggest me, how to do it???
Thanks for ur valuable time
With best wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
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-- 
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
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Re: [gmx-users] Installing topolbuild

[Bruce D. Ray]

From: vivek sharma 
To: Discussion list for GROMACS users 
Sent: 
Subject: Re: [gmx-users] Installing topolbuild

On Friday, March 6, 2009 2:29:32 AM,
vivek sharma  wrote:
> Thanks for your reply. I am workin on RHEL with architecture x86_64. 
> when i searched for libm.* I got a few location, I tried "make: again after
> exporting these location in LD_LIBRARY_PATH. but i am getting the
> same error again.

I am not familiar with RHEL nor with x86_64 bit architecture.  I believe
that 64 bit *nixes have both 32 bit and 64 bit libraries.  Thus, one needs
to select the correct libm.* for the compilation options.  It is probably best
to use 32 bit compilation options for topolbuild, but I don't know what
those would be for the compiler you are using.

> I think, i didn't downloaded the appropriate files for
> installation. Can you tell me the appropriate location to download the
> topolbuild.

topolbuild 1.2.1 (does gromacs ua and amber forcefields) is at:


topolbuild 1.1.2 (does amber forcefields only) is at:


> And some precise installation instruction can help me more, as I am not
> comfortable with linux env. 

Because I do not know every system and in particular have absolutely
no knowledge of RHEL in general or RHEL with architecture x86_64
in particular, the only instructions I can give you are:

1. Set appropriate environmental parameters for your system.
2. Edit one of the two Makefiles (Makefile and Makefile.G4OsX) 
   supplied to set such parameters as compiler, compilation options,
   library selections, and needed libraries appropriate for your system.
3. make -f 

Both Makefile and Makefile.G4OsX specify the compiler with
the line
  CC = cc
This might need to be changed either by passing the option
when invoking make or by editing the appropriate file.

Compiler options are the only line that differs between Makefile
and Makefile.G4OsX and are specified on a line that reads for
Makefile:
  CFLAGS = -O
or for Makefile.G4OsX:
  CFLAGS = -O2 -mcpu=7450 -mtune=970

The compilation instruction reads:
\t$(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm
where I am denoting the tab at the start of the line with "\t"
because this composer seems to replace the tab with spaces
and I want this to be absolutely clear.  Pointers to special
libraries can be added to this line as -L/.
Libraries are selected with -l.

All of the systems to which I have ever had access have always
had exp and sqrt functions located in /usr/lib/libm.so (SUN),
/usr/lib32/libm.so (SGI), or /usr/lib/libm.dylib (Os X).  You should
check your systems documentation to be sure that the correct library
and correct library options are selected.

I do not have access to very many systems.  This has compiled on Mac
G4 ppc simply by typing -f Makefile.G4OsX
I am told that it compiles on intel based Mac's running OsX and on at
least some versions of 32 bit Linux.

As I look at your error message, it appears to me as if there might have
been some prior warning messages that could shed more light on this.
In particular, where is math.h located?


> 2009/3/5 Bruce D. Ray 
> On Thursday, March 5, 2009 1:47:28 AM,

> vivek sharma  wrote:
 
>> I am trying to Install topolbuild on my system, while doing so with
>> the make file given in the topolbuild folder. but I end up with a list
>> of error mentioned below:
>> ..
>> .
>> .
>> .
>> .compare_FF.c:(.text+0x1285): undefined reference to `exp'
>> 
compare_FF.c:(.text+0x12cc): undefined reference to `sqrt'
>> collect2: ld returned 1 exit status
>> make: *** [topolbuild] Error 1
>> 
>> If somebody has tried this. please help me in figuring out the problem.
> 
> The errors mean that ld cannot locate the math library ( the -lm in the
> compilation instruction in Makefile which tells it to link against libm.*
> that is usually found in /usr/lib .  On most *nix's, this is libm.so but
> 
its libm.dylib on Mac OS X.)  If libm.* is not present in either the
> standard location, or in someplace pointed to by LD_LIBRARY_PATH
> then it will not be found.
> 
> What is the system on which you are trying to build, where is libm.*
> 
located, and what is LD_LIBRARY_PATH set to?  If libm.* is in
> some unusual place, then the easiest way to go is to add that location
> to LD_LIBRARY_PATH 
> 
> As a side note, an early version of topolbuild was missing the -lm
> 
in the compilation instruction in Makefile.  I checked what I've
> submitted since then and the makefiles all have the -lm as the last
> item in the compilation instruction.

Sincerely,

 -- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



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Re: [gmx-users] gromacs in parallel version

[Justin A. Lemkul]

ANINDITA GAYEN wrote:

Dear all,

Sorry for the former post without any subject.
I want to install gromacs in parallel version. I already 
have the normal version of gromacs and i want an MPI version of mdrun. 
The commands i have used are as followed.

*make distclean*
*./configure --enable-float --enable-mpi --prefix=/home/x 
--program-suffix=_mpi*

*make mdrun -j 4*
*make install-mdrun*
[ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc 
include ...

   export CPPFLAGS=-I/home/x/fftw-3.2.1/include
   export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
grmmacs installation run successfully.
But when i run
mdrun_mpi ..i got the message  "Can't read MPIRUN_MPD" 
and the mdrun_mpi program does not run.


What command are you actually issuing to run mdrun_mpi?  This sounds like more 
of an MPI environment problem, not a Gromacs problem.


-Justin


Any suggestion regarding this problem will be highly acceptable.
thanks in advance,

Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Kolkata-700 009
India



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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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[gmx-users] gromacs in parallel version

[ANINDITA GAYEN]

Dear all,
    Sorry for the former post without any subject.
    I want to install gromacs in parallel version. I already have the 
normal version of gromacs and i want an MPI version of mdrun. The commands i 
have used are as followed.
make distclean
../configure --enable-float --enable-mpi --prefix=/home/x --program-suffix=_mpi
make mdrun -j 4
make install-mdrun
[ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc include 
...
   export CPPFLAGS=-I/home/x/fftw-3.2.1/include
   export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
grmmacs installation run successfully.
But when i run 
mdrun_mpi ..i got the message  "Can't read MPIRUN_MPD" and the 
mdrun_mpi program does not run.
Any suggestion regarding this problem will be highly acceptable.
thanks in advance,

Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Kolkata-700 009
India


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[gmx-users] (no subject)

[ANINDITA GAYEN]

Dear all,
   
I want to install gromacs in parallel version. I already have the
normal version of gromacs and i want an MPI version of mdrun. The
commands i have used are as followed.
make
distclean
../configure --enable-float --enable-mpi
--prefix=/home/x --program-suffix=_mpi
make mdrun -j 4
make
install-mdrun
[ i have installed fftw with
--prefix=/home/x/fftw-3.2.1 and in .bashrc include ...
  
export CPPFLAGS=-I/home/x/fftw-3.2.1/include
   export
LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
grmmacs installation run
successfully.
But when i run 
mdrun_mpi ..i got
the message  "Can't read MPIRUN_MPD" and the mdrun_mpi
program does not run.
Any suggestion regarding this problem will
be highly acceptable.
thanks in advance,



Ms. Anindita Gayen

C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow

Department of Chemistry

University of Calcutta

92, A. P. C. Road

Kolkata-700 009

India


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[gmx-users] Re: g_vellac

[Florian Dommert]

On 06.03.2009, at 13:11, "Vitaly V. Chaban"  wrote:


It's like looking for a black cat in a dark room. If to multiply the
result by 1000 (derived from units) and divide it by 3 - the resulting
value seems to be close to the correct one.


Perfect, isn't it ?

Hope it's true. I will try to describe this tricky procedure in the
gromacs wiki now.


So I have no concern and thanks for putting this into the wiki.
Flo

Vitaly

On Fri, Mar 6, 2009 at 12:56 PM, Florian Dommert
 wrote:


Hi,


On 06.03.2009, at 12:37, "Vitaly V. Chaban"   
wrote:



Hi,

I checked the VACF calculation with the results obtained with my
utility, it's completely correct with
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
where an.ndx contains all the number of atoms of the needed  
molecule.


sounds very good. In my opinion it is a question of units. After  
using

g_analyze you end up with nm^2 / ps very uncommon for a diffusion
coefficient. So if you convert this to more convenient units you  
should

obtain the expected value.
Cheers
Flo


The problem is evidently in the integration. I suspect it's  
something

with units there.

Does
g_analyze -integrate
give a pure integral of the function supplied? '*1/3' is not  
performed

(at least there is nothing about it in the manual)...

Vitaly


Hi Flo,



Yes, I remember our talk about this problem about a year ago.

So what should be the correct notation now?

I just tried
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx
or
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
and then g_analyze -integrate -f vac.xvg

but they give me a value close to 0...







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[gmx-users] Re: g_vellac

[Vitaly V. Chaban]

It's like looking for a black cat in a dark room. If to multiply the
result by 1000 (derived from units) and divide it by 3 - the resulting
value seems to be close to the correct one.

Hope it's true. I will try to describe this tricky procedure in the
gromacs wiki now.

Vitaly

On Fri, Mar 6, 2009 at 12:56 PM, Florian Dommert
 wrote:
>
> Hi,
>
>
> On 06.03.2009, at 12:37, "Vitaly V. Chaban"  wrote:
>
>> Hi,
>>
>> I checked the VACF calculation with the results obtained with my
>> utility, it's completely correct with
>> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
>> where an.ndx contains all the number of atoms of the needed molecule.
>>
> sounds very good. In my opinion it is a question of units. After using
> g_analyze you end up with nm^2 / ps very uncommon for a diffusion
> coefficient. So if you convert this to more convenient units you should
> obtain the expected value.
> Cheers
> Flo
>>
>> The problem is evidently in the integration. I suspect it's something
>> with units there.
>>
>> Does
>> g_analyze -integrate
>> give a pure integral of the function supplied? '*1/3' is not performed
>> (at least there is nothing about it in the manual)...
>>
>> Vitaly
>>
>>> Hi Flo,
>>
>>> Yes, I remember our talk about this problem about a year ago.
>>>
>>> So what should be the correct notation now?
>>>
>>> I just tried
>>> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx
>>> or
>>> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
>>> and then g_analyze -integrate -f vac.xvg
>>>
>>> but they give me a value close to 0...
>>
>
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Re: [gmx-users] How to break a disulfide bond ???

[Justin A. Lemkul]

Venkat Reddy wrote:

Hai !
 
with "pdb2gmx -ss", i can select the ss bonds. But after that, how to 
break a particular ss bond (not all).


You cannot break or re-form bonds under classical mechanics (standard MD).

-Justin


 Thank you
 

On Fri, Mar 6, 2009 at 11:01 AM, sharada > wrote:



pdb2gmx -h 


sharada


*/-- Original Message --/*
From: Venkat Reddy mailto:venkat...@gmail.com>>
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Date: Fri, 6 Mar 2009 10:50:24 +0530
Subject: [gmx-users] How to break a disulfide bond ???

Hai Every one ! Is it possible to break a disulfide bridge using
gromacs ?If so,Can anybody suggest me, how to do it???

Thanks for ur valuable time

With best wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
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--
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD




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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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[gmx-users] Re: g_vellac

[Florian Dommert]

Hi,


On 06.03.2009, at 12:37, "Vitaly V. Chaban"  wrote:


Hi,

I checked the VACF calculation with the results obtained with my
utility, it's completely correct with
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
where an.ndx contains all the number of atoms of the needed molecule.

sounds very good. In my opinion it is a question of units. After using  
g_analyze you end up with nm^2 / ps very uncommon for a diffusion  
coefficient. So if you convert this to more convenient units you  
should obtain the expected value.

Cheers
Flo

The problem is evidently in the integration. I suspect it's something
with units there.

Does
g_analyze -integrate
give a pure integral of the function supplied? '*1/3' is not performed
(at least there is nothing about it in the manual)...

Vitaly


Hi Flo,



Yes, I remember our talk about this problem about a year ago.

So what should be the correct notation now?

I just tried
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx
or
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
and then g_analyze -integrate -f vac.xvg

but they give me a value close to 0...



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[gmx-users] RE: g_vellac

[Vitaly V. Chaban]

Hi,

I checked the VACF calculation with the results obtained with my
utility, it's completely correct with
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
where an.ndx contains all the number of atoms of the needed molecule.

The problem is evidently in the integration. I suspect it's something
with units there.

Does
g_analyze -integrate
give a pure integral of the function supplied? '*1/3' is not performed
(at least there is nothing about it in the manual)...

Vitaly

>Hi Flo,

>Yes, I remember our talk about this problem about a year ago.
>
>So what should be the correct notation now?
>
>I just tried
>g_velacc_402f -acflen 1001 -nonormalize -n an.ndx
>or
>g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
>and then g_analyze -integrate -f vac.xvg
>
>but they give me a value close to 0...
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[gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)

[Gerrit Groenhof]

Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each 
other. The bonds prevent these atoms to get apart too far, so 1-4 won't 
destabilize the overall structure. The SR part is negative, thus keeping 
your protein together.


Gerrit




Message: 3
Date: Fri, 6 Mar 2009 19:43:19 +0900
From: Seungpyo Hong 
Subject: [gmx-users] Positive energy for Coulumb term. Does this mean
Coulumb interaction destabilizes protein?
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Dear GMX-Users,

As I analyze energy terms of proteins, I found something looks weird.
I thought that fullly folded proteins are stabilized by Coulomb interaction
(such as hydrogen bonds).
However, what I found embarasses me.

The Coulomb interaction seems to destabilize the protein structure as its
energy is positive.

Coul-SR + Coul-14 = 32 > 0
Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0


Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
Coul-SR:Protein-Protein-11.6253365.244357.507  -0.735925
-259.047
LJ-SR:Protein-Protein  -6.51389204.554203.627   0.191426
67.3824
Coul-14:Protein-Protein 38.58481212.261196.751.90253
669.696
LJ-14:Protein-Protein   3.58465112.688112.645 -0.0303438
-10.6811
Coul-SR:Protein-Non-Protein   -14.1247443.927437.195   -0.75795
-266.8
LJ-SR:Protein-Non-Protein   -1.5147147.692446.2568   -0.11429
-40.2302


I thought of the total charge of the protein; but it is only +2.
And, the structure is quite stable through the simulation. (RMSD: 0.17)

I am quite confusing about the effect of Coulumb interaction on the
stability of the protein.
I feel like I am missing very important concept about the stability of
protein or the energy term used here.
Can anyone help me to understand the effect of Coulumb interaction in the
stability of the protein?

Any opinion or comment would be great help for me.

Thank you very much!

Sincerely,
Seungpyo Hong

  


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[gmx-users] Positive energy for Coulumb term. Does this mean Coulumb interaction destabilizes protein?

[Seungpyo Hong]

Dear GMX-Users,

As I analyze energy terms of proteins, I found something looks weird.
I thought that fullly folded proteins are stabilized by Coulomb interaction
(such as hydrogen bonds).
However, what I found embarasses me.

The Coulomb interaction seems to destabilize the protein structure as its
energy is positive.

Coul-SR + Coul-14 = 32 > 0
Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0


Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
Coul-SR:Protein-Protein-11.6253365.244357.507  -0.735925
-259.047
LJ-SR:Protein-Protein  -6.51389204.554203.627   0.191426
67.3824
Coul-14:Protein-Protein 38.58481212.261196.751.90253
669.696
LJ-14:Protein-Protein   3.58465112.688112.645 -0.0303438
-10.6811
Coul-SR:Protein-Non-Protein   -14.1247443.927437.195   -0.75795
-266.8
LJ-SR:Protein-Non-Protein   -1.5147147.692446.2568   -0.11429
-40.2302


I thought of the total charge of the protein; but it is only +2.
And, the structure is quite stable through the simulation. (RMSD: 0.17)

I am quite confusing about the effect of Coulumb interaction on the
stability of the protein.
I feel like I am missing very important concept about the stability of
protein or the energy term used here.
Can anyone help me to understand the effect of Coulumb interaction in the
stability of the protein?

Any opinion or comment would be great help for me.

Thank you very much!

Sincerely,
Seungpyo Hong

-- 
--
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'At the same time, he allowed interaction among objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
spho...@kaist.ac.kr
sp1...@gmail.com
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Re: [gmx-users] running GROMACS-MPI on Rocks cluster- strange results

[Diego Enry Gomes]

These results are not strange.
Performance results really depend on the size/setup of your system.  
Next time use gmxbench so we can have a better reference.


Are you using gromacs 4.0.4 ? It scales much better than gromacs-3.x.x  
versions. Anyway, this very bad scaling is normal over gigabit  
ethernet even with cat6 cables and some tricks like using two network  
interfaces per node. (also two switches or with two VPNs)


If you can't afford an infiniband interfaces there is a solution. You  
can try installing the GAMMA drivers for your ethernet interface and  
MPI/GAMMA as MPI. However I'm not quite sure if GAMMA is stable. Also  
you will need two network interfaces, one of them must be Intel.


http://www.disi.unige.it/project/gamma/mpigamma/index.html


On Mar 6, 2009, at 12:34 AM, kala wrote:

i have ran a particular MD of protein in water for 100ps (50,000  
steps) in a variety of combinations


1. on a single processor( non-mpi) intel core2duo 2.2Ghz 2 GB ram  
time taken : 1hr 30 min
2. 2 processors on a single machine (MPI) similar specs time taken :  
35 min
3 .2 processors on different machines (mpi) similar specs time  
taken : 1hr 5 min
4 .5 processors on 5 different machines (mpi) similar specs time  
taken: 38 min
5.10 processors on 5 different machines(mpi) similar specs time  
taken: 45 min


OS
for 1- open discovery ( fedora 9)
for 2-5 Rocks cluster 5.1

network connectivity Gigabit on cat6
Are the above specified time intervals normal or i am making big big  
mistakes.

comments are invited.
kala bharath
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[gmx-users] running GROMACS-MPI on Rocks cluster- strange results

[kala]

i have ran a particular MD of protein in water for 100ps (50,000 steps) in a
variety of combinations

1. on a single processor( non-mpi) intel core2duo 2.2Ghz 2 GB ram time taken
: 1hr 30 min
2. 2 processors on a single machine (MPI) similar specs time taken : 35 min
3 .2 processors on different machines (mpi) similar specs time taken : 1hr 5
min
4 .5 processors on 5 different machines (mpi) similar specs time taken: 38
min
5.10 processors on 5 different machines(mpi) similar specs time taken: 45
min

OS
for 1- open discovery ( fedora 9)
for 2-5 Rocks cluster 5.1

network connectivity Gigabit on cat6
Are the above specified time intervals normal or i am making big big
mistakes.
comments are invited.
kala bharath
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[gmx-users] Change only one atom pair VdW interaction

[Gaurav Chopra]

Hello,

I wanted to know if one can change the VdW epsilon for just one atom pair.
If suppose my system has only carbons, hydrogen and oxygen and if I just
want to change the epsilon for C-O interaction for VdW without effecting
anything else, i.e. not changing C-C interaction for the oplsaa forcefield,
is there a way to do this without modifying the code? As epsilon_H = 0, the
only thing which will be effected by changing epsilon_C would be C-O and C-C
interaction, but I do not want to change C-C interaction but only C-O
interaction.

Thanks,
Gaurav
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