from:"Ragothaman Yennamalli"

[gmx-users] pdb2gmx segmentation fault

2011-04-19 Thread Ragothaman Yennamalli

Hi,
I have installed the latest version of gromacs 4.5.4 and the installation
went fine. When I run pdb2gmx I get Segmentation fault even before I could
select the force field options. I tried with different pdb files and I get
seg fault without any other error messages.
The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top

Please let me know what am I missing.
Thanks and Regards,
Raghu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli

I had the issue of shared libraries while installing which I did
troubleshoot and the installation went without any errors. I tried
converting the pdb file to a new one using editconf and it runs perfectly
fine. So, there is some issue with pdb2gmx, which I am not able to detect.
Any hints will be appreciated.
Thanks and Regards,
Raghu

Subject: Re: [gmx-users] pdb2gmx segmentation fault
To: Discussion list for GROMACS users 
Message-ID: <4dae452b.3090...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:
> Hi,
> I have installed the latest version of gromacs 4.5.4 and the
> installation went fine. When I run pdb2gmx I get Segmentation fault
> even before I could select the force field options. I tried with
> different pdb files and I get seg fault without any other error messages.
> The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top

Probably, no other GROMACS command works either, because of some shared
library issue related to your new installation.

Mark

-- 

Ragothaman M Yennamalli, Ph.D.
Postdoctoral Research Associate
1012 Crop Genome Informatics Laboratory
Department of Genetics, Development and Cell Biology
Iowa State University
Ames, Iowa 50011-3260 USA

+1 515-294-8971 (Office)
+1 515-294-8280 (Fax)
+1 515-851-1016 (Mobile)

"When you can do the common things of life in an uncommon way, you will
command the attention of the world." -George Washington Carver

http://www.public.iastate.edu/~raghu/
http://www.artistrkrishnarao.com/

***
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli

These were the exact commands used to install fftw 3.2.2
./configure  --prefix=/export/home/raghu/fftw --enable-float --enable-shared
CC=cc F77=f77
make -j 48
make install

These were the exact commands used to install gromacs4.5.4
./configure  --prefix=/export/home/raghu/gromacs --with-fft=fftw3
--without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS'
make -j 48
make install

I had installed the gromacs version 4.5.3 earlier and encountered the same
problem with pdb2gmx. Hence installed the latest version.
Thanks and Regards,
Raghu


On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul  wrote:

>
>
> Ragothaman Yennamalli wrote:
>
>> I had the issue of shared libraries while installing which I did
>> troubleshoot and the installation went without any errors. I tried
>> converting the pdb file to a new one using editconf and it runs perfectly
>> fine. So, there is some issue with pdb2gmx, which I am not able to detect.
>> Any hints will be appreciated.
>>
>
> Please provide the exact commands that you used to install Gromacs.  What
> exactly were the issues that you had to circumvent?  Have you installed
> previous versions of Gromacs that have worked, such that this problem is
> specific to 4.5.4?
>
> -Justin
>
>  Thanks and Regards,
>> Raghu
>>
>> Subject: Re: [gmx-users] pdb2gmx segmentation fault
>> To: Discussion list for GROMACS users > gmx-users@gromacs.org>>
>> Message-ID: <4dae452b.3090...@anu.edu.au > 4dae452b.3090...@anu.edu.au>>
>>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:
>>  > Hi,
>>  > I have installed the latest version of gromacs 4.5.4 and the
>>  > installation went fine. When I run pdb2gmx I get Segmentation fault
>>  > even before I could select the force field options. I tried with
>>  > different pdb files and I get seg fault without any other error
>> messages.
>>  > The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top
>>
>> Probably, no other GROMACS command works either, because of some shared
>> library issue related to your new installation.
>>
>> Mark
>>
>>
>>
>>
>> --
>> 
>> Ragothaman M Yennamalli, Ph.D.
>> Postdoctoral Research Associate
>> 1012 Crop Genome Informatics Laboratory
>> Department of Genetics, Development and Cell Biology
>> Iowa State University
>> Ames, Iowa 50011-3260 USA
>>
>> +1 515-294-8971 (Office)
>> +1 515-294-8280 (Fax)
>> +1 515-851-1016 (Mobile)
>>
>> "When you can do the common things of life in an uncommon way, you will
>> command the attention of the world." -George Washington Carver
>>
>> http://www.public.iastate.edu/~raghu/ <
>> http://www.public.iastate.edu/%7Eraghu/>
>> http://www.artistrkrishnarao.com/
>>
>> ***
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 

Ragothaman M Yennamalli, Ph.D.
Postdoctoral Research Associate
1012 Crop Genome Informatics Laboratory
Department of Genetics, Development and Cell Biology
Iowa State University
Ames, Iowa 50011-3260 USA

+1 515-294-8971 (Office)
+1 515-294-8280 (Fax)
+1 515-851-1016 (Mobile)

"When you can do the common things of life in an uncommon way, you will
command the attention of the world." -George Washington Carver

http://www.public.iastate.edu/~raghu/
http://www.artistrkrishnarao.com/

***
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli

Dear Justin,

Thanks for the mail. Yes, without these CFLAGS the "make" was not
successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring
gromacs. Since without it it would have stopped compiling. I want to agree
with you that it is some issue with shared libraries, but i dont think it is
the issue since I have used the flag --enable-shared. Also, if this was the
case then editconf would not have worked as well.

Thanks and Regards,
Raghu

On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul  wrote:

>
>
> Ragothaman Yennamalli wrote:
>
>> These were the exact commands used to install fftw 3.2.2
>> ./configure  --prefix=/export/home/raghu/fftw --enable-float
>> --enable-shared CC=cc F77=f77
>> make -j 48
>> make install
>>
>> These were the exact commands used to install gromacs4.5.4
>> ./configure  --prefix=/export/home/raghu/gromacs --with-fft=fftw3
>> --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3
>> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
>> -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS'
>>
>
> I'm no compiler expert, but is it necessary to set all these CFLAGS here?
>  Does the installation fail for some reason if they're not set?
>
> Also, how is Gromacs finding FFTW?  You haven't set the CPPFLAGS or
> LDFLAGS.
>
>
>  make -j 48
>> make install
>>
>> I had installed the gromacs version 4.5.3 earlier and encountered the same
>> problem with pdb2gmx. Hence installed the latest version.
>>
>
> This would indicate to me that the problem is not necessarily in Gromacs,
> but the way you're installing it, and as Mark suggested, is probably related
> to some static/shared library issue.
>
> -Justin
>
>  Thanks and Regards,
>> Raghu
>>
>>
>>
>> On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Ragothaman Yennamalli wrote:
>>
>>I had the issue of shared libraries while installing which I did
>>troubleshoot and the installation went without any errors. I
>>tried converting the pdb file to a new one using editconf and it
>>runs perfectly fine. So, there is some issue with pdb2gmx, which
>>I am not able to detect.
>>Any hints will be appreciated.
>>
>>
>>Please provide the exact commands that you used to install Gromacs.
>> What exactly were the issues that you had to circumvent?  Have you
>>installed previous versions of Gromacs that have worked, such that
>>this problem is specific to 4.5.4?
>>
>>-Justin
>>
>>Thanks and Regards,
>>Raghu
>>
>>Subject: Re: [gmx-users] pdb2gmx segmentation fault
>>To: Discussion list for GROMACS users ><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
>>
>><mailto:gmx-users@gromacs.org>>>
>>Message-ID: <4dae452b.3090...@anu.edu.au
>><mailto:4dae452b.3090...@anu.edu.au>
>><mailto:4dae452b.3090...@anu.edu.au
>><mailto:4dae452b.3090...@anu.edu.au>>>
>>
>>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:
>> > Hi,
>> > I have installed the latest version of gromacs 4.5.4 and the
>> > installation went fine. When I run pdb2gmx I get Segmentation
>>fault
>> > even before I could select the force field options. I tried with
>> > different pdb files and I get seg fault without any other
>>error messages.
>> > The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top
>>
>>Probably, no other GROMACS command works either, because of some
>>shared
>>library issue related to your new installation.
>>
>>Mark
>>
>>
>>
>>
>>-- 
>>Ragothaman M Yennamalli, Ph.D.
>>Postdoctoral Research Associate
>>1012 Crop Genome Informatics Laboratory
>>Department of Genetics, Development and Cell Biology
>>Iowa State University
>>Ames, Iowa 50011-3260 USA
>>
>>+1 515-294-8971  (Office)
>>+1 515-294-8280  (Fax)
>>+1 515-851-1016  (Mobile)
>>
>>
>>"When you can do the common things of life in an uncommon

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli

On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul  wrote:

>
>
> Ragothaman Yennamalli wrote:
>
>> Dear Justin,
>>
>> Thanks for the mail. Yes, without these CFLAGS the "make" was not
>> successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring
>> gromacs. Since without it it would have stopped compiling. I want to agree
>> with you that it is some issue with shared libraries, but i dont think it is
>> the issue since I have used the flag --enable-shared. Also,
>>
>
> You did --enable-shared for FFTW, but not Gromacs.  Perhaps there is some
> mismatch there.
>
>
Since configure did not have any such option, i did not use it. However, I
tried compiling with --enable-shared to reinstall gromacs. It installed
without any issues. But, the same segmentation fault.


>
>  if this was the case then editconf would not have worked as well.
>>
>>
> I wouldn't rule it out just yet.  If the installation was successful,
> everything would work.
>
> -Justin
>
>  Thanks and Regards,
>> Raghu
>>
>>
>> On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Ragothaman Yennamalli wrote:
>>
>>These were the exact commands used to install fftw 3.2.2
>>./configure  --prefix=/export/home/raghu/fftw --enable-float
>>--enable-shared CC=cc F77=f77
>>make -j 48
>>make install
>>
>>These were the exact commands used to install gromacs4.5.4
>>./configure  --prefix=/export/home/raghu/gromacs
>>--with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2
>>CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer
>>-finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops
>>-std=gnu99 -D_POSIX_PTHREAD_SEMANTICS'
>>
>>
>>I'm no compiler expert, but is it necessary to set all these CFLAGS
>>here?  Does the installation fail for some reason if they're not set?
>>
>>Also, how is Gromacs finding FFTW?  You haven't set the CPPFLAGS or
>>LDFLAGS.
>>
>>
>>make -j 48
>>make install
>>
>>I had installed the gromacs version 4.5.3 earlier and
>>encountered the same problem with pdb2gmx. Hence installed the
>>latest version.
>>
>>
>>This would indicate to me that the problem is not necessarily in
>>    Gromacs, but the way you're installing it, and as Mark suggested, is
>>probably related to some static/shared library issue.
>>
>>-Justin
>>
>>Thanks and Regards,
>>Raghu
>>
>>
>>
>>On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>
>>   Ragothaman Yennamalli wrote:
>>
>>   I had the issue of shared libraries while installing
>>which I did
>>   troubleshoot and the installation went without any errors. I
>>   tried converting the pdb file to a new one using editconf
>>and it
>>   runs perfectly fine. So, there is some issue with
>>pdb2gmx, which
>>   I am not able to detect.
>>   Any hints will be appreciated.
>>
>>
>>   Please provide the exact commands that you used to install
>>Gromacs.
>>What exactly were the issues that you had to circumvent?
>> Have you
>>   installed previous versions of Gromacs that have worked, such
>>that
>>   this problem is specific to 4.5.4?
>>
>>   -Justin
>>
>>   Thanks and Regards,
>>   Raghu
>>
>>   Subject: Re: [gmx-users] pdb2gmx segmentation fault
>>   To: Discussion list for GROMACS users
>>mailto:gmx-users@gromacs.org>
>>   <mailto:gmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>> <mailto:gmx-users@gromacs.org
>>
>><mailto:gmx-users@gromacs.org>
>>
>>   <mailto:gmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>>>>
>>   Message-ID: <4dae452b.3090...@anu.edu.au
>><mailto:4dae452b.3090...@anu.edu.au>
>>   <mailto:4dae452b.3090...@anu.edu.au
>><mailto:4dae452b

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-20 Thread Ragothaman Yennamalli

It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs.

On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier  wrote:

> I've never seen the -D_POSIX_PTHREAD_SEMANTICS before.  What caused
> you to need to define that flag?
>
> Also...what hardware (cpu) and operating system (linux? what distro?
> what version?) are you using?
>
> Matt Z.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> 
> Ragothaman M Yennamalli, Ph.D.
> Postdoctoral Research Associate
> 1012 Crop Genome Informatics Laboratory
> Department of Genetics, Development and Cell Biology
> Iowa State University
> Ames, Iowa 50011-3260 USA
>
> +1 515-294-8971 (Office)
> +1 515-294-8280 (Fax)
> +1 515-851-1016 (Mobile)
>
> "When you can do the common things of life in an uncommon way, you will
> command the attention of the world." -George Washington Carver
>
> 
> http://www.public.iastate.edu/~raghu/
> http://www.artistrkrishnarao.com/
>
> ***
>
>
>
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-22 Thread Ragothaman Yennamalli

Hi all,
With the help of my colleague Nathan Weeks I am able to run pdb2gmx and all
other commands successfully . Here are his responses which he wanted me to
share with you in case someone is trying to install Gromacs in a similar
system.

We set CFLAGS that way due to the following message when running configure:


checking whether gcc-4.3.2 accepts -native -fast -xO5 -fsimple=2
-fnonstd -dalign -O3 -fomit-frame-pointer -finline-functions -Wall
-Wno-unused -msse2 -funroll-
all-loops -std=gnu99... no
***
* Sorry, these optimization settings don't seem to work for   *
* your C compiler. Use make CFLAGS=..., or edit the top Makefile. *
***


The "-native -fast -xO5 -fsimple=2 -fnonstd -dalign" options that get
generated are for Solaris Studio, but we're using GCC.  Also,
"-D_POSIX_PTHREAD_SEMANTICS" is required on Solaris to make use of the POSIX
versions of reentrant functions like ctime_r() and readdir_r() (if the
standard _POSIX_C_SOURCE or _XOPEN_SOURCE feature test macros
are set, _POSIX_PTHREAD_SEMANTICS will automatically be set as well).

The memory fault that occurs when running pdb2gmx is due to a non-portable
use
of readdir_r() in futil.c; specifically, on Linux, the dirent structure
has a "char d_name[256]" member, and on Solaris, it is "char d_name[1]", and
the user is required to allocate memory to store its contents. The Linux
readdir(3) man page gives an example of how to do this portably:

http://www.kernel.org/doc/man-pages/online/pages/man3/readdir.3.html

I applied this method to futil.c, and it fixed the memory fault problem:


--- src/gmxlib/futil.c.orig 2011-03-15 07:44:30.0 -0500
+++ src/gmxlib/futil.c  2011-04-20 13:04:58.388912208 -0500
@@ -37,6 +37,7 @@
 #include 
 #endif

+#include 
 #include 
 #include 
 #include 
@@ -595,22 +596,28 @@

 #ifdef HAVE_DIRENT_H

-struct dirent   tmp_dirent;
+struct dirent * tmp_dirent;
struct dirent * p;
+size_t len;


if(gmxdir!=NULL && gmxdir->dirent_handle!=NULL)
{
-rc = readdir_r(gmxdir->dirent_handle,&tmp_dirent,&p);
+len  = offsetof(struct dirent, d_name)
+   + fpathconf(dirfd(gmxdir->dirent_handle), _PC_NAME_MAX) + 1;
+smalloc(tmp_dirent, len);
+rc = readdir_r(gmxdir->dirent_handle,tmp_dirent,&p);
+
if(p!=NULL && rc==0)
{
-strncpy(name,tmp_dirent.d_name,maxlength_name);
+strncpy(name,tmp_dirent->d_name,maxlength_name);
}
else
{
name[0] = '\0';
rc  = ENOENT;
}
+sfree(tmp_dirent);
}
else
{


> Also why the make -j 48, when you only have 8 cores?

We have 8 6-core CPUs (48 cores total).

> I'm not even sure if the linker is ok with make -jN for building gromacs,
it
> is not listed as compatible for *BSD ports. Also, does your make (I
imagine
> this is Solaris make) have all the same semantics as gnu-make (gmake)?

We are using GNU make.

> And why did you switch your CC between fftw and gromacs configures?
> Solaris 'cc' may or may not be gcc43. Also, do we know if gcc43 is stable
> especially with -O3...Try removing -O3 or move it to -O2 at most...

The Sun Studio 12.1 C compiler worked for fftw, but not for gromacs.

> To rule out a bad fftw library, you can set --with-fft to use the builtin
> (slower) libfft instead of fftw (but fftw should not be affecting pdb2gmx
> I don't think...).
>
> I too have the questions of your CFLAGS, do you not require -m64 either?

With gcc 4.3, there was a compilation error when -m64 was added to CFLAGS:

###
make[5]: Entering directory
`/tmp//gromacs-4.5.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse'
/bin/sh ../../../../libtool   --mode=compile gcc-4.3.2   -m64 -g
-msse2 -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS -D_REENTRANT -pthread
-I./include -c -o nb_kernel010_ia32_sse.lo nb_kernel010_ia32_sse.s
 gcc-4.3.2 -m64 -g -msse2 -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS
-D_REENTRANT -pthread -I./include -c nb_kernel010_ia32_sse.s  -fPIC
-DPIC -o .libs/nb_kernel010_ia32_sse.o
nb_kernel010_ia32_sse.s: Assembler messages:
nb_kernel010_ia32_sse.s:87: Error: suffix or operands invalid for `push'
nb_kernel010_ia32_sse.s:89: Error: suffix or operands invalid for `push'
nb_kernel010_ia32_sse.s:90: Error: suffix or operands invalid for `push'
nb_kernel010_ia32_sse.s:91: Error: suffix or operands invalid for `push'
nb_kernel010_ia32_sse.s:92: Error: suffix or operands invalid for `push'
nb_kernel010_ia32_sse.s:93: Error: suffix or operands invalid for `push'
nb_kernel010_ia32_sse.s:94: Error: suffix or operands invalid for `push'
nb_kernel010_ia32_sse.s:795: Error: suffix or operan

Re: [gmx-users] pdb2gmx segmentation fault

2011-04-22 Thread Ragothaman Yennamalli

Thanks for the link. Have just filed it.
Thanks and Regards,
Raghu

On Fri, Apr 22, 2011 at 1:12 PM, Justin A. Lemkul  wrote:

> Matthew Zwier wrote:
>
>> Nice catch on the readdir_r().  I wonder if the developers would
>> appreciate a bug report and patch for your fix.
>>
>>
> Yes, please file an issue report on redmine.gromacs.org.  If it doesn't
> get put on a to-do list, it probably won't get done :)
>
> -Justin




-- 

Ragothaman M Yennamalli, Ph.D.
Postdoctoral Research Associate
1012 Crop Genome Informatics Laboratory
Department of Genetics, Development and Cell Biology
Iowa State University
Ames, Iowa 50011-3260 USA

+1 515-294-8971 (Office)
+1 515-294-8280 (Fax)
+1 515-851-1016 (Mobile)

"When you can do the common things of life in an uncommon way, you will
command the attention of the world." -George Washington Carver

http://www.public.iastate.edu/~raghu/
http://www.artistrkrishnarao.com/

***
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] error while compiling gromacs 4.0.2

2008-12-04 Thread Ragothaman Yennamalli

Dear all,
While compiling gromacs 4.0.2 in a AMD 64bit dual processor system, I encounter 
the following error while configuring:

checking size of int... configure: error: cannot compute sizeof (int)
See `config.log' for more details.

Please let me know where I have gone wrong. I am pasting the entire messages 
below:


[EMAIL PROTECTED] gromacs-4.0.2]$ ./configure --enable-mpi --enable-float
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-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 cc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... 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... no
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... configure: error: cannot compute sizeof (int)
See `config.log' for more details.


Thanks in advance,

With Kind Regards,

Ragothaman


  Add more friends to your messenger and enjoy! Go to 
http://messenger.yahoo.com/invite/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] error while compiling gromacs 4.0.2

2008-12-04 Thread Ragothaman Yennamalli

Dear all,
I tried installing the new version of gromacs. 


  Add more friends to your messenger and enjoy! Go to 
http://messenger.yahoo.com/invite/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] plz ignore my previous mail

2008-12-04 Thread Ragothaman Yennamalli

Sorry..for sending an incomplete mail. Please ignore my previous mail.
Raghu


  Add more friends to your messenger and enjoy! Go to 
http://messenger.yahoo.com/invite/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] free energy calculations

2011-07-05 Thread Ragothaman Yennamalli

Hi,
I want to run free energy calculations on a particular protein-ligand
complex. I do not have much knowledge on this so I have some questions,
hopefully someone might give me clear answers.
I am following the tutorial given in this link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html

My questions are as follows:
1. I am assuming that I do not need the "protein without the ligand" form
for free energy calculations. Am I right?

2. To use g_bar, I need to run the protein-ligand complex with
a) first with lambda ranging from 0.5 to 1 for vdw coupling and
b) followed by lambda ranging from 0.5 to 1 for coulombic coupling
Adding these would give the deltaG I am looking for. Am I right?

3. Are there any papers that use g_bar function in gromacs to calculate free
energy?

Thanks in advance,
Raghu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: free energy calculations

2011-07-06 Thread Ragothaman Yennamalli

>
>
> Message: 1
> Date: Tue, 05 Jul 2011 19:14:04 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] free energy calculations
> To: Discussion list for GROMACS users 
> Message-ID: <4e139abc.1030...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Ragothaman Yennamalli wrote:
> > Hi,
> > I want to run free energy calculations on a particular protein-ligand
> > complex. I do not have much knowledge on this so I have some questions,
> > hopefully someone might give me clear answers.
> > I am following the tutorial given in this link:
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html
> >
> > My questions are as follows:
> > 1. I am assuming that I do not need the "protein without the ligand"
> > form for free energy calculations. Am I right?
> >
>
> Free energy calculations can be done on a number of systems.  The tutorial
> is
> just one simple example.
>

Thanks for the mail. So, I technically do not need both the un-complexed and
complexed form of the protein with the ligand.

>
> > 2. To use g_bar, I need to run the protein-ligand complex with
> > a) first with lambda ranging from 0.5 to 1 for vdw coupling and
> > b) followed by lambda ranging from 0.5 to 1 for coulombic coupling
> > Adding these would give the deltaG I am looking for. Am I right?
> >
>
> No.  The range for lambda should be 0 to 1.  Using 0.5 to 1 gives only part
> of
> the free energy for the transformation, and not necessarily half.
>

Apologies, I should have mentioned as from 0 to 1. So, the first step is to
do vdw coupling followed by coulombic coupling. Right?

>
> > 3. Are there any papers that use g_bar function in gromacs to calculate
> > free energy?
> >
>
> The g_bar tool is relatively new to Gromacs, so maybe not.  The BAR method
> itself has been around for decades though, so its applications have been
> demonstrated in the literature many times.
>

Thanks for pointing this.
Raghu

>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] free energy

2011-07-10 Thread Ragothaman Yennamalli

Please see this...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
Raghu

On Sun, Jul 10, 2011 at 12:33 PM, balaji nagarajan  wrote:

>  Dear Users !
>
> Is it possible to calculate the free energy for a molecule ,
>
> at the zero step MD , when i see the mail list this question has been
> posted once ,
>
> but i could not find the reply for this !
>
> is there any option for this like g_energy !
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] where is water?

2011-07-11 Thread Ragothaman Yennamalli

Hi Friends,

When I run pdb2gmx, it automatically asks which water topology should be
included. Also, in the .top file the lines included are:

; Include water topology
#include "gromos53a6.ff/spc.itp"

However, I do not see any water molecules in the .gro file. So, was water
included or not?

Thanks and Regards,
Raghu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] where is water?

2011-07-11 Thread Ragothaman Yennamalli

Thanks...Glad to realize the newer version of gromacs makes life easier.
Raghu

On Mon, Jul 11, 2011 at 11:38 AM, Justin A. Lemkul  wrote:

>
>
> Ragothaman Yennamalli wrote:
>
>> Hi Friends,
>>
>> When I run pdb2gmx, it automatically asks which water topology should be
>> included. Also, in the .top file the lines included are:
>>
>> ; Include water topology
>> #include "gromos53a6.ff/spc.itp"
>>
>> However, I do not see any water molecules in the .gro file. So, was water
>> included or not?
>>
>>
> pdb2gmx does not add water.  That's what genbox does.  The water selection
> utility in pdb2gmx is intended to make your life easier when it comes to
> solvation - the water topology is already present (#included in the .top).
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] simulation of oligomers/monomers

2011-07-18 Thread Ragothaman Yennamalli

Look at this paper where the simulation was done on a protein dimer:
http://www.ncbi.nlm.nih.gov/pubmed/17027497

On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham wrote:

> On 18/07/2011 3:08 PM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I am working on a protein which is a dimer (in the crystal structure),
>> predicted according top PISA.
>> and some of the homologous proteins are dimers (covalent /non-covalent)
>> some are monomers.
>> There has not been any literature regarding the fact that the functional
>> unit is a dimer, ie the enzyme
>> is not functional when the dimeric interface is disturbed due to
>> mutations. Also the active sites are not
>> shared among the dimeric partners. In this situation is it meningful to do
>> a simulation of monomers alone
>> and try to get some information.
>>
>
> The dimeric interface might be so hydrophobic the protein would unfold -
> but unlikely given the homology evidence. It could certainly perturb the
> structure significantly, and perhaps such perturbations connect with the
> activity. Only detailed understanding of the structure and function can help
> you decide about this.
>
>
>  In general is it necessary to simulate only the functional oligomers or
>> monomer also can be done ?
>>
>
> Depends on the system, and depends what you wish to learn.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  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/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] simulation of oligomers/monomers

2011-07-18 Thread Ragothaman Yennamalli

With regards to run a monomeric simulation as resonable or not, I would
agree with Mark that it depends what you wish to learn, and depends on what
your hypothesis is.
Ragothaman

On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M  wrote:

> Thank you Sir,
>
> The interface is connected by salt bridges and hydrogen bonding
> interactions and not severely
> hydrophobic. I tried simulating the monomers it stayed quite stable without
> unfolding till 50ns.
> Even the other structure which are reported to be dimer is a reported as a
> trimer in solution.
> Another one is a part of a bifunctional protein which is an octamer. So
> Because of all these
> confusions I through some information could be obtained from a monomeric
> simulation..
> Is it reasonable?
>
>
> Thanking you
> With Regards
> M. Kavyashree
>
> On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli <
> ragotha...@gmail.com> wrote:
>
>> Look at this paper where the simulation was done on a protein dimer:
>> http://www.ncbi.nlm.nih.gov/pubmed/17027497
>>
>> On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham wrote:
>>
>>> On 18/07/2011 3:08 PM, Kavyashree M wrote:
>>>
>>>> Dear users,
>>>>
>>>> I am working on a protein which is a dimer (in the crystal structure),
>>>> predicted according top PISA.
>>>> and some of the homologous proteins are dimers (covalent /non-covalent)
>>>> some are monomers.
>>>> There has not been any literature regarding the fact that the functional
>>>> unit is a dimer, ie the enzyme
>>>> is not functional when the dimeric interface is disturbed due to
>>>> mutations. Also the active sites are not
>>>> shared among the dimeric partners. In this situation is it meningful to
>>>> do a simulation of monomers alone
>>>> and try to get some information.
>>>>
>>>
>>> The dimeric interface might be so hydrophobic the protein would unfold -
>>> but unlikely given the homology evidence. It could certainly perturb the
>>> structure significantly, and perhaps such perturbations connect with the
>>> activity. Only detailed understanding of the structure and function can help
>>> you decide about this.
>>>
>>>
>>>  In general is it necessary to simulate only the functional oligomers or
>>>> monomer also can be done ?
>>>>
>>>
>>> Depends on the system, and depends what you wish to learn.
>>>
>>> Mark
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>
>>
>>
>>
>>
>> --
>>
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] protein ligand

2011-07-31 Thread Ragothaman Yennamalli

Hi,

I know this is off topic. Can someone please suggest independent scoring
functions that can calculate binding energies between protein and ligand?

Thanks and Regards,
Ragothaman
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] running at higher temperatures

2011-08-10 Thread Ragothaman Yennamalli

Hi,
When running simulations at a constant higher temperatures (such as
simulating a thermophile) would changing "ref_t" and "gen_temp" to the
appropriate kelvin is enough?
Thanks and Regards,
Raghu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Trajectory viewing by freeing a part

2011-09-07 Thread Ragothaman Yennamalli

Hi,
While viewing a trajectory I am trying to see how a particular part or group
is behaving, while keeping the rest frozen (I dont want them to move). For
example, in a two domain protein keeping one domain frozen and seeing the
other domain movement or in a protein ligand complex keeing the protein
frozen and seeing the movement of the ligand. I tried -center in trjconv and
selected the group that I need to center. Any other suggestions?
Thanks and Regards,
Raghu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] error while running grompp

2008-01-18 Thread Ragothaman Yennamalli

Dear all,
We are trying running Gromacs in different systems
with different number of processors. In sun opteron
cluster we checked and it ran perectly fine. When,
using the same input files, to run in apple g5 system
with same number of processors. I get the following
message when I run grompp:
 creating statusfile for 4 nodes...

Back Off! I just backed up mdout.mdp to
./#mdout.mdp.9#
checking input for internal consistency...
calling /lib/cpp...
sh: line 1: /lib/cpp: No such file or directory
cpp exit code: 32512
Tried to execute: '/lib/cpp 
-I/Users/swadha/new_gromacs/share/top  master.top >
gromppOC6J5h'
The '/lib/cpp' command is defined in the .mdp file
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file
(confout.gro, 78268)
 does not match topology (master.top, 0)


I made new toplogy files, there is nil difference
between the new and old .top file used in grompp.
Still I get the same error message.

Please let me know where I am going wrong.

Regards,

Raghu

**
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586
**


  Get the freedom to save as many mails as you wish. To know how, go to 
http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] error while running grompp

2008-01-21 Thread Ragothaman Yennamalli

Dear Mark,
Thanks for the mail. I was able to solve the problem,
by changing the path of cpp from /lib/cpp to
/usr/bin/cpp.
With the same system, When I run mdrun calling mpirun
I get the following error message and the program
exits.

mpiexec_bicg5quad.local: mpd_uncaught_except_tb
handling:
  exceptions.IOError: [Errno 9] Bad file descriptor
/Users/deb/mpich2-install/bin/mpirun  1035 
handle_stdin_input
sys.stdin.flush()  # probably does nothing
/Users/deb/mpich2-install/bin/mpdlib.py  527 
handle_active_streams
handler(stream,*args)
/Users/deb/mpich2-install/bin/mpirun  493  mpiexec
rv =
streamHandler.handle_active_streams(timeout=1.0)
/Users/deb/mpich2-install/bin/mpirun  1393  ?
mpiexec()

Please let em know how can I solve this? Just a
reminder that the system is a 4 processor apple G5
system.

Regards,
Raghu

--- Mark Abraham <[EMAIL PROTECTED]> wrote:

> Ragothaman Yennamalli wrote:
> > Dear all,
> > We are trying running Gromacs in different systems
> > with different number of processors. In sun
> opteron
> > cluster we checked and it ran perectly fine. When,
> > using the same input files, to run in apple g5
> system
> > with same number of processors. I get the
> following
> > message when I run grompp:
> >  creating statusfile for 4 nodes...
> > 
> > Back Off! I just backed up mdout.mdp to
> > ./#mdout.mdp.9#
> > checking input for internal consistency...
> > calling /lib/cpp...
> > sh: line 1: /lib/cpp: No such file or directory
> > cpp exit code: 32512
> > Tried to execute: '/lib/cpp 
> > -I/Users/swadha/new_gromacs/share/top  master.top
> >
> > gromppOC6J5h'
> > The '/lib/cpp' command is defined in the .mdp file
> > processing topology...
> > processing coordinates...
> > Fatal error: number of coordinates in coordinate
> file
> > (confout.gro, 78268)
> >  does not match topology (master.top,
> 0)
> > 
> > 
> > I made new toplogy files, there is nil difference
> > between the new and old .top file used in grompp.
> > Still I get the same error message.
> 
> Check out 
>
http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
> 
> Mark
> ___
> 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
> [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 

  Download prohibited? No problem. CHAT from any browser, without download. 
Go to http://in.messenger.yahoo.com/webmessengerpromo.php/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] query related to rerunning MD

2008-01-28 Thread Ragothaman Yennamalli

Hi all,
A query related to rerunning MD. 
For eg: After 5ns run of MD I need to rerun from 3ns
and I take the structure closest to it from the
trajectory files. Taking this 3ns.gro as the starting
structure I redo all the steps for preparation. In
such a case, I am assuming that the velocity will be
taken into account and I need not generate velocity
again. 
Am I right?

Regards,
Raghu



  Forgot the famous last words? Access your message archive online at 
http://in.messenger.yahoo.com/webmessengerpromo.php
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] query about diferent cutoffs

2008-04-09 Thread Ragothaman Yennamalli

Dear all,
In a particular setup of a protein interacting with
ions, the protein needs to be simulated without ions
and after a certain point of time the ions are
introduced to the system, so as to check of the
protein undergoes refolding in the presence ions or
not. Since it is a known fact that in the absence of
ions protein undergoes conformational change and in
the presence of ions the protein remains stable. 

My question is: Can two different distance cutoffs be
defined in gromacs? for eg The distance range for
protein and ions not more than 20Angstroms and for
solvent-solvent not more than 8Angstroms.

Thanks in advance,

Regards,
Ragothaman

**
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586
**


  Explore your hobbies and interests. Go to 
http://in.promos.yahoo.com/groups/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] mpi error

2008-04-11 Thread Ragothaman Yennamalli

Dear all,
I had been running many runs of mdrun in a Sun opteron
cluster with each node having 4 processors.
When I ran my latest mdrun after 15ns run, I get the
following error and mdrun exits without any error
message on other log files. 
***
mpiexec_compute-0-1.local: mpd_uncaught_except_tb
handling:
  exceptions.IOError: [Errno 5] Input/output error
/home/deb/mpich2-install/bin/mpirun  1051 
handle_cli_stderr_input
sys.stderr.write(msg)
/home/deb/mpich2-install/bin/mpdlib.py  762 
handle_active_streams
handler(stream,*args)
/home/deb/mpich2-install/bin/mpirun  515  mpiexec
rv =
streamHandler.handle_active_streams(timeout=1.0)
/home/deb/mpich2-install/bin/mpirun  1423  ?
mpiexec()
***

Please tell me how to troubleshoot this problem as it 
repeated when ran again.

Waiting for your reply,

Regards,

Ragothaman


  Explore your hobbies and interests. Go to 
http://in.promos.yahoo.com/groups/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] trjconv error

2008-04-18 Thread Ragothaman Yennamalli

I wanted to truncate a trajectory file and when I use
trjconv tool, I get an error:
Fatal error:
/media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc
is not a trj file, exiting

The file is able to read by gmxcheck...

What could be the problem?

Thanks in advance.

Regards,

Ragothaman


  Explore your hobbies and interests. Go to 
http://in.promos.yahoo.com/groups/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] trjconv error

2008-04-22 Thread Ragothaman Yennamalli

Hi,
Sorry for not replying immediately.

Gromacs ver 3.2.1
OS is Red hat enterprise 4
Initially I had tried reading the file from an external hard disk and now I 
copied it to another system and tried again. Still the same error.
The reason why I was truncating was due to a magic number error I got while 
reading the trajectory.
"Fatal error: Magic Number Error in XTC file (read 0, should be 1995)"
So, I was truncating it at an earlier time from where I didnt see any errors.

Regards,
Raghu 

--- On Fri, 18/4/08, Mark Abraham <[EMAIL PROTECTED]> wrote:

> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] trjconv error
> To: "Discussion list for GROMACS users" 
> Date: Friday, 18 April, 2008, 8:09 PM
> Ragothaman Yennamalli wrote:
> > I wanted to truncate a trajectory file and when I use
> > trjconv tool, I get an error:
> > Fatal error:
> > /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc
> > is not a trj file, exiting
> > 
> > The file is able to read by gmxcheck...
> > 
> > What could be the problem?
> 
> What GROMACS version? What OS? Have you tried copying the
> file elsewhere 
> and reading from there?
> 
> Mark
> ___
> 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 [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php

  Unlimited freedom, unlimited storage. Get it now, on 
http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] trjconv error

2008-04-23 Thread Ragothaman Yennamalli

Hi,
Thanks for the mail. Well, I am using a old version specifically, even though 
newer versions are available. It is quite confusing since the same file is 
being able to be read by other tools like gmxcheck. And it is while running by 
gmxcheck that I get the Magic number error
Raghu


--- On Wed, 23/4/08, Mark Abraham <[EMAIL PROTECTED]> wrote:

> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] trjconv error
> To: "Gromacs Users" 
> Date: Wednesday, 23 April, 2008, 11:44 AM
> Ragothaman Yennamalli wrote:
> > Hi,
> > Sorry for not replying immediately.
> > 
> > Gromacs ver 3.2.1
> > OS is Red hat enterprise 4
> > Initially I had tried reading the file from an
> external hard disk and now I copied it to another system
> and tried again. Still the same error.
> > The reason why I was truncating was due to a magic
> number error I got while reading the trajectory.
> > "Fatal error: Magic Number Error in XTC file
> (read 0, should be 1995)"
> > So, I was truncating it at an earlier time from where
> I didnt see any errors.
> 
> Dunno. 3.2.1 is a very old version - you should be planning
> your upgrade 
> to version 4 as soon as it's out, unless you need
> compatibility for some 
> reason.
> 
> Otherwise the only reason I can think that gmxdump might
> succeed where 
> trjconv doesn't is that it isn't actually an XTC
> file, but some other 
> format with an .xtc extension.
> 
> Try to replicate your problem with a small simulation. If
> you can, then 
> you probably have a real issue, but this is very unlikely.
> If you can't 
> replicate it, then it seems you've probably mangled
> something and we 
> can't help you.
> 
> Mark
> ___
> 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 [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php


  Bring your gang together. Do your thing. Find your favourite Yahoo! group 
at http://in.promos.yahoo.com/groups/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Error while running starting grompp and mdrun

2008-05-22 Thread Ragothaman Yennamalli

Dear all,
I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 
processors. I am submitting the job via a SGE script.
After, I submit the job by "$qsub test_gromacs", the run terminates with the 
following message in the log file. Please tell me how to troubleshoot this 
problem. The error is repeated if the -np option is changed from 4 to 8.
__
Fatal error: run input file topol.tpr was made for 4 nodes,
 while mdrun expected it to be for 1 nodes.
[compute-1-30.local:24948] [0,0,0] ORTE_ERROR_LOG: Not found in file 
base/pls_base_proxy.c at line 189
__
The script is as follows:
__
#!/bin/bash
#$ -N mpich_gromacs
#$ -S /bin/bash
#$  -cwd
#$ -j yDear all,
I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 
processors. I am submitting the job via a SGE script.
After, I submit the job by "$qsub test_gromacs", the run terminates with the 
following message in the log file. Please tell me how to troubleshoot this 
problem. The error is repeated if the -np option is changed from 4 to 8.

Fatal error: run input file topol.tpr was made for 4 nodes,
 while mdrun expected it to be for 1 nodes.
[compute-1-30.local:24948] [0,0,0] ORTE_ERROR_LOG: Not found in file 
base/pls_base_proxy.c at line 189

The script is as follows:

#!/bin/bash
#$ -N mpich_gromacs
#$ -S /bin/bash
#$  -cwd
#$ -j y
#Set the Parallel Environment and number of procs.
#$ -pe mpich
#Set the Parallel Environment and number of procs.
#$ -pe mpich 4 
#$ -l h_rt=01:00:00

echo Running on host `hostname`
echo Directory is `pwd`
echo This job runs on the following processors:
cat $TMPDIR/machines | tee machinefile
echo This job has allocated $NSLOTS processors

export MDRUN=/home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/mdrun
export MPIRUN=/opt/mpich/gnu/bin/mpirun

##running directory
cd /home/raghu/quad_md/case1

#add -v to create more verbose comments
#-nice 0 needs to be before the -s and other arguments; this corrects the 
default of 19 (lowest priority)

/home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/grompp -f em.mdp -c 
box_sol.gro -p master.top -v -np 4
$MPIRUN -v -np 4  $MDRUN -v -nice 0 -np $NSLOTS -s topol.tpr -o traj.trr -e 
ener.edr -x traj.xtc -g md.log -c confout.gro >&em_run.log


Regards,
Ragothaman


  BMR - a key player in weight issues. Know more - 
http://in.search.yahoo.com/search?&fr=na_onnetwork_mail_taglines&ei=UTF-8&rd=r1&p=basal+metabolic+rate
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Error while running starting grompp and mdrun

2008-05-22 Thread Ragothaman Yennamalli

Dear Mark,
Thanks for the mail.


> 
> Since there's three different usages of -np you'd
> need to be more 
> precise to make a good description of your problem.
>

I was changing the -np option in mdrun and grompp.
 
> The symptoms you observe make sense if $NSLOTS==1. Since
> all three -np 
> flags need the same value after them, you should use the
> same variable 
> each time. You should verify that the "echo" line
> tells you that has 
> $NSLOTS==4 like you need.
> 
Yes. I checked by typing echo $NSLOTS and it says 4. So, I changed all the 
three -np option to -np $NSLOTS..Still the same error. 

Regards,
Ragothaman



  Bollywood, fun, friendship, sports and more. You name it, we have it on 
http://in.promos.yahoo.com/groups/bestofyahoo/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] removing a water molecule

2007-05-27 Thread Ragothaman Yennamalli

Dear all,
I am running a MD simulation, which stops after 6ns
run with an error saying:

t = 6825.932 ps: Water molecule starting at atom 19637
can not be settled.
Check for bad contacts and/or reduce the
timestep.Wrote pdb files with previous and current
coordinates

How does one proceed from here? Is removing the single
water molecule a solution? In that case wouldn't there
be a conflict between the number of atoms of previous
trr file and the new one being made?

Thanks in advance,
Ragothaman




__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] removing a water molecule

2007-05-27 Thread Ragothaman Yennamalli

Thanks.
I do get LINCS warning all the time. I had removed two
water molecule, that seemed too close to where the
LINCS warning came for. And started the simulation
again from the scratch and it stopped as mentioned in
my previous message.
Ragothaman
--- Mark Abraham <[EMAIL PROTECTED]> wrote:

> Ragothaman Yennamalli wrote:
> > Dear all,
> > I am running a MD simulation, which stops after
> 6ns
> > run with an error saying:
> > 
> > t = 6825.932 ps: Water molecule starting at atom
> 19637
> > can not be settled.
> > Check for bad contacts and/or reduce the
> > timestep.Wrote pdb files with previous and current
> > coordinates
> > 
> > How does one proceed from here? Is removing the
> single
> > water molecule a solution? In that case wouldn't
> there
> > be a conflict between the number of atoms of
> previous
> > trr file and the new one being made?
> 
> Yes, you can't continue from where you are. You
> should have a close look 
> at what's been happening and see if there are any
> other problems. 
> Probably you need a more gentle
> minimization-equilibration regime at the 
> start.
> 
> Mark
> ___
> 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
> [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 



  Download prohibited? No problem! To chat from any browser without 
download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.php
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] removing a water molecule

2007-05-28 Thread Ragothaman Yennamalli

Hi,
Thanks for the mail. I checked my input structure. I
dont have any water along with the protein.
Regards,
Ragothaman

--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:

> Hi Ragothaman,
> 
> Also check for isolated water molecules. These can
> be a pain, since
> they are sort of part of the protein, but are
> coupled to the solvent
> outside. One common source for
> LINCS/water-molecule-can't-be-settled
> errors.
> 
> Cheers,
> 
> Tsjerk
> 
> On 5/28/07, Mark Abraham <[EMAIL PROTECTED]>
> wrote:
> > Ragothaman Yennamalli wrote:
> > > Thanks.
> > > I do get LINCS warning all the time. I had
> removed two
> > > water molecule, that seemed too close to where
> the
> > > LINCS warning came for. And started the
> simulation
> > > again from the scratch and it stopped as
> mentioned in
> > > my previous message.
> >
> > Yup. Go and fix your equilibration regime (copy
> something reasonable
> > from a published paper or a tutorial). A normal
> simulation should have
> > no LINCS errors.
> >
> > Mark
> > ___
> > 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
> [EMAIL PROTECTED]
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> ___
> 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
> [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 



  Download prohibited? No problem! To chat from any browser without 
download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.php
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] [Fwd: Problem with Position restrained dynamics]

2007-07-24 Thread Ragothaman Yennamalli

Can you send us the pr.mdp file? 
Regards,
Raghu

--- David van der Spoel <[EMAIL PROTECTED]> wrote:

> 
> 
>  Original Message 
> Subject:  Problem with Position restrained dynamics
> Date: Tue, 24 Jul 2007 19:19:39 +0530
> From: E BHARATHY <[EMAIL PROTECTED]>
> Reply-To: CHANDRIKA RAO
> <[EMAIL PROTECTED]>
> To:   [EMAIL PROTECTED], [EMAIL PROTECTED]
> 
> 
> 
> 
> Dear Dr. David,
> When i prepared my position restrained dynamics
> MD, grompp generated
> /Back Off! I just backed up mdout.mdp to
> ./#mdout.mdp.3#/
> /WARNING 1 [file pr.mdp, line unknown]:/
> /  Unknown left-hand warnings in parameter
> file/
> 
> Ignoring this warning i proceeded with mdrun, but i
> get the following
> LINCS warning and the mdrun stopped after 3 steps,
> 
> /Reading file BHE_pr.tpr, VERSION 3.2.1 (double
> precision)/

  Get the freedom to save as many mails as you wish. To know how, go to 
http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Gromacs version

2008-01-04 Thread Ragothaman Yennamalli

Hi,
Can anyone please tell me how to find which version of
gromacs is installed in a particular system? Since
with the path where it is installed, I am unable to
make out if it 3.2.1 or 3.3.

Thanks in advance,
Raghu 




  Forgot the famous last words? Access your message archive online at 
http://in.messenger.yahoo.com/webmessengerpromo.php
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Gromacs version

2008-01-05 Thread Ragothaman Yennamalli

Hi Tsjerk and Mark,
Thanks a lot. It is 3.2.1 that's installed.
Regards,
Raghu

--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:

> Hi Raghu,
> 
> Try any of the pograms (with the -h flag) and the
> header will tell you which
> version you have...
> 
> Cheers,
> 
> Tsjerk
> 
> On Jan 5, 2008 8:38 AM, Ragothaman Yennamalli
> <[EMAIL PROTECTED]> wrote:
> 
> > Hi,
> > Can anyone please tell me how to find which
> version of
> > gromacs is installed in a particular system? Since
> > with the path where it is installed, I am unable
> to
> > make out if it 3.2.1 or 3.3.
> >
> > Thanks in advance,
> > Raghu
> >
> >
> >
> >
> >  Forgot the famous last words? Access your
> message archive online at
> >
> http://in.messenger.yahoo.com/webmessengerpromo.php
> > ___
> > 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
> [EMAIL PROTECTED]
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> > ___
> 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
> [EMAIL PROTECTED]
> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php



  Chat on a cool, new interface. No download required. Go to 
http://in.messenger.yahoo.com/webmessengerpromo.php
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] LINCS warning

2006-09-08 Thread Ragothaman Yennamalli

Dear all,
I have a query,
1. Are two trajectories comparable if each one of them
has been run in a different version of gromacs? Eg,
v3.2 and v3.3.

Thanks in advance,
Regards,
Raghu

**
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586
**



__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Gromacs version

2006-09-09 Thread Ragothaman Yennamalli

Dear all,
I have a query,
1. Are two trajectories comparable if each one of them
has been run in a different version of gromacs? Eg,
v3.2 and v3.3.

Thanks in advance,
Regards,
Raghu

**
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586
**



__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] MPIRUN error while running position restrained MD

2007-01-18 Thread Ragothaman Yennamalli

Dear all,
I am running gromacs3.2 version. When I am running the
position restraint md for the protein, the process
stops within 100 steps with the following error:
-
One of the processes started by mpirun has exited with
  nonzero exit
code.  This typically indicates that the process
finished in error.
If your process did not finish in error, be sure to
include a "return
0" or "exit(0)" in your C code before exiting the
application.

PID 16200 failed on node n0 (10.10.0.8) due to signal
9.
-

I searched the mailing list and google and understood
that the pressure coupling parameter "tau_p" value in
the .mdp file has to be more than 1.0 and I did the
same. Even otherwise the process gets killed with the
same error.
Please tell me what I am overlooking or making an
error.
Thanks in advance.

Regards,
Raghu

**
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586
**



__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] MPIRUN error while running position restrained MD

2007-01-22 Thread Ragothaman Yennamalli

Hi,
This is the tail of the .log file
new box (3x3):
   new box[0]={-4.13207e+15,  0.0e+00,
-0.0e+00}
   new box[1]={ 0.0e+00, -5.17576e+15,
-0.0e+00}
   new box[2]={ 0.0e+00,  1.51116e+23,
-1.14219e+16}
Correcting invalid box:
old box (3x3):
   old box[0]={-4.13207e+15,  0.0e+00,
-0.0e+00}
   old box[1]={ 0.0e+00, -5.17576e+15,
-0.0e+00}
   old box[2]={ 0.0e+00,  1.51116e+23,
-1.14219e+16}
THe log files have generated as huge files (approx
20GB) which have used all the disk space. 
Raghu
--- Mark Abraham <[EMAIL PROTECTED]> wrote:

> Ragothaman Yennamalli wrote:
> > Dear all,
> > I am running gromacs3.2 version. When I am running
> the
> > position restraint md for the protein, the process
> > stops within 100 steps with the following error:
> >
>
-
> > One of the processes started by mpirun has exited
> with
> >   nonzero exit
> > code.  This typically indicates that the process
> > finished in error.
> > If your process did not finish in error, be sure
> to
> > include a "return
> > 0" or "exit(0)" in your C code before exiting the
> > application.
> > 
> > PID 16200 failed on node n0 (10.10.0.8) due to
> signal
> > 9.
> >
>
-
> > 
> > I searched the mailing list and google and
> understood
> > that the pressure coupling parameter "tau_p" value
> in
> > the .mdp file has to be more than 1.0 and I did
> the
> > same. 
> 
> This is likely irrelevant. What do the ends of the
> .log files say?
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 




__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] MPIRUN error while running position restrained MD

2007-01-22 Thread Ragothaman Yennamalli

HI,
Since the log files and crashed .pdb files had filled
the whole disk space I had to delete them and start
again. 
I am simulating a homodimer protein in a water box. I
have mutated three residues and want to look the
behaviour of the protein. I have four setups for the
same protein without mutation and with mutation and
respective controls. Among the four only one is
crashing at the position restraint stage. The other
three didnt show me this error (except for the one
line LINCS warning). 
I have run the position restrained dynamics again. Yes
as you are saying it starts with LINCS warning. 
This is what it says after the LINCS warning.
*
Back Off! I just backed up step20672.pdb to
./#step20672.pdb.1#
Sorry couldn't backup step20672.pdb to
./#step20672.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673, time 91.346 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 348017441898496.00 (between atoms 7000 and
7002) rms nan
bonds that rotated more than 30 degrees:
**
I am attaching the .mdp file along with this email. 
Thanks in advance.
Raghu

--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:

> Hi Ragu,
> 
> The tail of the .log file is not very informative
> here. Please try to
> find in the log where it first went wrong. It may
> well start out with
> a LINCS warning.
> Besides, please be more specific in what you're
> trying to simulate,
> and what protocol you used.
> 
> Cheers,
> 
> Tsjerk
> 
> On 1/19/07, Ragothaman Yennamalli
> <[EMAIL PROTECTED]> wrote:
> > Hi,
> > This is the tail of the .log file
> > new box (3x3):
> >new box[0]={-4.13207e+15,  0.0e+00,
> > -0.0e+00}
> >new box[1]={ 0.0e+00, -5.17576e+15,
> > -0.0e+00}
> >new box[2]={ 0.0e+00,  1.51116e+23,
> > -1.14219e+16}
> > Correcting invalid box:
> > old box (3x3):
> >old box[0]={-4.13207e+15,  0.0e+00,
> > -0.0e+00}
> >old box[1]={ 0.0e+00, -5.17576e+15,
> > -0.0e+00}
> >old box[2]={ 0.0e+00,  1.51116e+23,
> > -1.14219e+16}
> > THe log files have generated as huge files (approx
> > 20GB) which have used all the disk space.
> > Raghu
> > --- Mark Abraham <[EMAIL PROTECTED]> wrote:
> >
> > > Ragothaman Yennamalli wrote:
> > > > Dear all,
> > > > I am running gromacs3.2 version. When I am
> running
> > > the
> > > > position restraint md for the protein, the
> process
> > > > stops within 100 steps with the following
> error:
> > > >
> > >
> >
>
-
> > > > One of the processes started by mpirun has
> exited
> > > with
> > > >   nonzero exit
> > > > code.  This typically indicates that the
> process
> > > > finished in error.
> > > > If your process did not finish in error, be
> sure
> > > to
> > > > include a "return
> > > > 0" or "exit(0)" in your C code before exiting
> the
> > > > application.
> > > >
> > > > PID 16200 failed on node n0 (10.10.0.8) due to
> > > signal
> > > > 9.
> > > >
> > >
> >
>
-
> > > >
> > > > I searched the mailing list and google and
> > > understood
> > > > that the pressure coupling parameter "tau_p"
> value
> > > in
> > > > the .mdp file has to be more than 1.0 and I
> did
> > > the
> > > > same.
> > >
> > > This is likely irrelevant. What do the ends of
> the
> > > .log files say?
> > >
> > > Mark
> > > ___
> > > gmx-users mailing listgmx-users@gromacs.org
> > >
> http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the
> > > list. Use the
> > > www interface or send it to
> > > [EMAIL PROTECTED]
> > > Can't post? Read
> > > http://

Re: [gmx-users] MPIRUN error while running position restrained MD

2007-01-22 Thread Ragothaman Yennamalli

Hi Mark,
Thanks for the mail. Yes, I solvate the protein and
then do a EM with steepest descent and then I proceed
to do position restrained MD, first restraining the
protein and then the backbone. It is at the backbone
restraint step I got this error. Also I assumed that
if there are any bad contacts they would get resolved
in minimization step, but looks like it hasn't. Please
tell me how to solve this problem. 
Raghu
--- Mark Abraham <[EMAIL PROTECTED]> wrote:

> Ragothaman Yennamalli wrote:
> > HI,
> > Since the log files and crashed .pdb files had
> filled
> > the whole disk space I had to delete them and
> start
> > again. 
> > I am simulating a homodimer protein in a water
> box. I
> > have mutated three residues and want to look the
> > behaviour of the protein. I have four setups for
> the
> > same protein without mutation and with mutation
> and
> > respective controls. Among the four only one is
> > crashing at the position restraint stage. The
> other
> > three didnt show me this error (except for the one
> > line LINCS warning). 
> > I have run the position restrained dynamics again.
> Yes
> > as you are saying it starts with LINCS warning. 
> > This is what it says after the LINCS warning.
> 
> You should be doing some energy minimization before
> attempting MD, else 
> some bad contacts will send badness around the
> system, maybe eventually 
> causing such crashes. Make sure you do EM after
> solvating (and before if 
> you need to!)
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 




__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] MPIRUN error while running position restrained MD

2007-01-25 Thread Ragothaman Yennamalli

Hi,
I increased the tau_p to 2.0 and lincs-iter to 4. Now
the system is running smoothly.
Regards,
Ragothaman

--- Mark Abraham <[EMAIL PROTECTED]> wrote:

> Ragothaman Yennamalli wrote:
> > HI,
> > Since the log files and crashed .pdb files had
> filled
> > the whole disk space I had to delete them and
> start
> > again. 
> > I am simulating a homodimer protein in a water
> box. I
> > have mutated three residues and want to look the
> > behaviour of the protein. I have four setups for
> the
> > same protein without mutation and with mutation
> and
> > respective controls. Among the four only one is
> > crashing at the position restraint stage. The
> other
> > three didnt show me this error (except for the one
> > line LINCS warning). 
> > I have run the position restrained dynamics again.
> Yes
> > as you are saying it starts with LINCS warning. 
> > This is what it says after the LINCS warning.
> 
> You should be doing some energy minimization before
> attempting MD, else 
> some bad contacts will send badness around the
> system, maybe eventually 
> causing such crashes. Make sure you do EM after
> solvating (and before if 
> you need to!)
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 




__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] MPIRUN error while running position restrained MD

2007-01-26 Thread Ragothaman Yennamalli

Hi Tsjerk,
I completely agree with you. I am treating symptoms
rather than the problem. I read your previous comment
on the LINCS warning to Shangwa Han. I dont have any
unnatural amino acids in the protein and EM steps
converged to machine precision. I am attaching the
potential energy .xvg file after EM. I will look into
those atoms and see if I can resolve this problem.
Regards,
Raghu
--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:

> Hi Ragothaman,
> 
> You would do good to try and find out what caused
> the error. You may
> be treating symptoms rather than problems now, and
> simply covering up
> some more severe wrong in your system. Maybe try to
> start a simulation
> after some while, using the same parameters as
> before. This might
> allow your system to relax sufficiently.
> 
> Cheers,
> 
> Tsjerk
> 
> 

__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/

energy.xvg
Description: 1113252116-energy.xvg
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

45 matches

Mail list logo