Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

[Tsjerk Wassenaar]

Hi,

Pymol is sort of semi commercial. You can install it easily on Ubuntu,
using apt-get install pymol (free!), you can install from source (also
free!). You can obtain an educational build (also free!, though
requiring registration). Any will do for the building of sequences,
which on linux is as simple as running:

for i in Y W F A; do for j in Y W F A; do for k in Y W F A; do for l
in Y W F A; do
PEP=H$i$j$k$lPAS
pymol -qcd "editor.build_peptide('${PEP}');cmd.save('$PEP.pdb')"
done; done; done; done

Hope it helps,

Tsjerk


2011/4/20 Terry :
>
> Hi Chuan,
> Leap is a part of Ambertools which is free.
> See http://ambermd.org/#AmberTools
> Good luck.
> Terry
>
> 2011/4/20 Liao Chuan 
>>
>> HI, Itamer and Mark, thanks for your prompt replies.
>>
>> Pymol, Amber and Sybyl are commercial software. Any free software/scripts?
>>
>>
>>
>> - Chuan
>>
>>
>>
>> 
>>
>> 发件人: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
>> 代表 Mark Abraham
>> 发送时间: 2011年4月20日 13:31
>> 收件人: Discussion list for GROMACS users
>> 主题: Re: [gmx-users] any software which could convert a polypeptidesequence
>> to a pdb file?
>>
>>
>>
>> On 4/20/2011 2:36 PM, Liao Chuan wrote:
>>
>> Dear gmx-users,
>>
>> I want to conduct simulations of a protein and its ligand, a heptapeptide
>> HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine.
>> Thus, I will have to conduct a total number of 4*4*4=64 runs. I've got the
>> pdb file of the protein, but I have no idea how to prepare the pdb files of
>> those 64 heptapeptides with sequences already known. Is there any
>> software/script which could convert a polypeptide sequence to a pdb file?
>>  Any comment is appreciated!
>>
>> Leap in the AmberTools package is good for this.
>>
>> Mark
>>
>> --
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] dhfr-impl-1nm.bench run keeps failing

[Miah Wadud Dr (ITCS)]

Hello,

I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I 
am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both 
builds fail with the error message:

MPI Application rank 1 exited before MPI_Finalize() with status 0

The rank and the status value vary. Any idea what could be wrong?

Thanks in advance,

--
Wadud Miah, High Performance Computing Systems Developer
Research Computing Services, University of East Anglia
Web: http://www.uea.ac.uk/~xca10fju/
Telephone: 01603 593856

Information Services
--


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Re: [gmx-users] dhfr-impl-1nm.bench run keeps failing

[Mark Abraham]

On 4/20/2011 6:57 PM, Miah Wadud Dr (ITCS) wrote:

Hello,

I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I 
am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both 
builds fail with the error message:

MPI Application rank 1 exited before MPI_Finalize() with status 0

The rank and the status value vary. Any idea what could be wrong?


No idea. That's just a generic advisory from the MPI library. Only the 
mdrun stdout or .log file could have a GROMACS-specific diagnostic 
message. You need to be sure that you can run other MPI programs, too.


Mark



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Re: [gmx-users] pdb2gmx segmentation fault

[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/

***
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Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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 >
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/

***



--


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


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Re: [gmx-users] pdb2gmx segmentation fault

[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/

***
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[gmx-users] Microporous simulation

[Hernan Ahumada]

 Hi everyone

I am trying to run a simulation of Alpo (aluminophosphates) microporous
material,  the topology of the material was build using x2top (it had been
checked).  I got all the bonding and nonbonding parameters, when I run the
energy minimization of this system, Iget this :

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
There were 420 inconsistent shifts. Check your topology
Step=0, Dmax= 1.0e-02 nm, Epot=  3.25885e+04 Fmax= 0.0e+00, atom= 0

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 10 in 1 steps
Potential Energy  =  3.2588531e+04
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

gcq#152: "I Smell Smoke From a Gun Named Extinction" (Pixies)

When I look my finally PDB the structure of microporus material,  some atoms
appear outside the box. I don't know how to fix the atoms inside the box? and
avoid this inconsistent shift. who can help me with this?

Thanks


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RE: [gmx-users] dhfr-impl-1nm.bench run keeps failing

[Miah Wadud Dr (ITCS)]

The MPI library is able to run other MPI jobs as well as other parallel Gromacs 
runs, and it just seems like this run causes this difficulty. I am using 
Platform MPI 8.1.

Regards,
Wadud.

>-Original Message-
>From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
>Behalf Of Mark Abraham
>Sent: Wednesday, April 20, 2011 12:46 PM
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] dhfr-impl-1nm.bench run keeps failing
>
>On 4/20/2011 6:57 PM, Miah Wadud Dr (ITCS) wrote:
>> Hello,
>>
>> I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing.
>I am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both
>builds fail with the error message:
>>
>> MPI Application rank 1 exited before MPI_Finalize() with status 0
>>
>> The rank and the status value vary. Any idea what could be wrong?
>
>No idea. That's just a generic advisory from the MPI library. Only the
>mdrun stdout or .log file could have a GROMACS-specific diagnostic
>message. You need to be sure that you can run other MPI programs, too.
>
>Mark
>
>
>
>--
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Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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 > 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> >>
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/

***


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--

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)

Re: [gmx-users] Microporous simulation

[Justin A. Lemkul]

Hernan Ahumada wrote:

 Hi everyone

I am trying to run a simulation of Alpo (aluminophosphates) microporous
material,  the topology of the material was build using x2top (it had been
checked).  I got all the bonding and nonbonding parameters, when I run the
energy minimization of this system, Iget this :

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
There were 420 inconsistent shifts. Check your topology
Step=0, Dmax= 1.0e-02 nm, Epot=  3.25885e+04 Fmax= 0.0e+00, atom= 0

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 10 in 1 steps
Potential Energy  =  3.2588531e+04
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

gcq#152: "I Smell Smoke From a Gun Named Extinction" (Pixies)

When I look my finally PDB the structure of microporus material,  some atoms
appear outside the box. I don't know how to fix the atoms inside the box? and
avoid this inconsistent shift. who can help me with this?



The inconsistent shifts and high potential energy indicate that the system has 
blown up due to instability.  There is no way to simply "fix" the atoms in the 
box aside from preparing a system that can actually be energy-minimized.


It is odd to me that the force is zero.  Which Gromacs version is this?  What 
hardware are you running it on, and how did you install it (exact commands, 
please)?  I ran into this problem a long time ago due to an as-yet unresolved 
bug, but I am hesitant to suggest that without knowing a whole lot more about 
your setup.


-Justin


Thanks


This message was sent using IMP, the Internet Messaging Program.


--


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


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Re: [gmx-users] pdb2gmx segmentation fault

[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 > >
>>>>
>>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/
>>
>>***
>>
>>
>>-- 
>>
>>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
>>
>>=

Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

[ZHAO Lina]

There is another free tool (Avogadro) which is pretty easy to handle this
also.

Try

http://avogadro.openmolecules.net/wiki/Get_Avogadro

in Build --> Inert ---> Peptides,

Which is very easy to use. you can choose Straight line, beta sheet or alpha
helix or other.

and save as .pdb

lina
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Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

[ZHAO Lina]

apt-get install avogadro

http://avogadro.openmolecules.net/wiki/Distribution_Packages


On Wed, Apr 20, 2011 at 10:34 PM, ZHAO Lina  wrote:

> There is another free tool (Avogadro) which is pretty easy to handle this
> also.
>
> Try
>
> http://avogadro.openmolecules.net/wiki/Get_Avogadro
>
> in Build --> Inert ---> Peptides,
>
> Which is very easy to use. you can choose Straight line, beta sheet or
> alpha helix or other.
>
> and save as .pdb
>
> lina
>
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Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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.



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 > 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>
>> 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>
   > 

   
   >
   
    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, Develop

Re: [gmx-users] pdb2gmx segmentation fault

[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>
>>>> 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>
>>   >> >
>>
>>
>>   >>   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.
>>>

Re: [gmx-users] pdb2gmx segmentation fault

[Matthew Zwier]

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.
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[gmx-users] g_velacc -mol

[Luis Martins]

I'm a recent gromacs user and right now I'm starting to calculate velocity 
autocorrelation functions for a pure compound, using g_velacc.
I'd like to know something more about the properties and consequences of the 
option -mol and what exactly the program does if the option is not included. 
I'm trying to obtain velocity autocorrelation functions for pure water for 
testing purposes and when the option -mol is included the system returns the 
message "core dumped".

Thanks

Luis Martins
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Re: [gmx-users] g_velacc -mol

[David van der Spoel]

On 2011-04-20 18.30, Luis Martins wrote:

I'm a recent gromacs user and right now I'm starting to calculate
velocity autocorrelation functions for a pure compound, using g_velacc.
I'd like to know something more about the properties and consequences of
the option -mol and what exactly the program does if the option is not
included. I'm trying to obtain velocity autocorrelation functions for
pure water for testing purposes and when the option -mol is included the
system returns the message "core dumped".
Thanks
Luis Martins


Even if you have a correct index file?
Try g_velacc -h


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

[Juliette N.]

Hello,

I am trying to obtain the density for my system that is exactly identical to
experimental value but whatever pressure I apply density is still off by 3%.

Is this issue common?
-- 
Thanks,
Jennifer N.
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Re: [gmx-users] density off

[David van der Spoel]

On 2011-04-20 19.40, Juliette N. wrote:

Hello,

I am trying to obtain the density for my system that is exactly
identical to experimental value but whatever pressure I apply density is
still off by 3%.
Is this issue common?
--
Thanks,
Jennifer N.


Yes, force fields are not perfect.
How about running NVT at the experimental density and measuring the 
pressure?


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

[Juliette N.]

Hi David,

I used to apply NPT to fix the density, how can I get the denisty using NVT?

On 20 April 2011 13:46, David van der Spoel  wrote:

> On 2011-04-20 19.40, Juliette N. wrote:
>
>> Hello,
>>
>> I am trying to obtain the density for my system that is exactly
>> identical to experimental value but whatever pressure I apply density is
>> still off by 3%.
>> Is this issue common?
>> --
>> Thanks,
>> Jennifer N.
>>
>>  Yes, force fields are not perfect.
> How about running NVT at the experimental density and measuring the
> pressure?
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Thanks,
Jennifer N.
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Re: [gmx-users] density off

[David van der Spoel]

On 2011-04-20 20.10, Juliette N. wrote:

Hi David,

I used to apply NPT to fix the density, how can I get the denisty using NVT?


You turn off P coupling and fix the right density by scaling using editconf.


On 20 April 2011 13:46, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote:

On 2011-04-20 19.40, Juliette N. wrote:

Hello,

I am trying to obtain the density for my system that is exactly
identical to experimental value but whatever pressure I apply
density is
still off by 3%.
Is this issue common?
--
Thanks,
Jennifer N.

Yes, force fields are not perfect.
How about running NVT at the experimental density and measuring the
pressure?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
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.
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--
Thanks,
Jennifer N.




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

[majid hasan]

Dear All,

I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure 
it 
works) using l-bfgs integrator. When I run in the .trr output file, ends of dna 
only move slightly towards cnt, but it doesn't wrap around it. Could anyone 
please guide me what can be the possible issues here, and how can I improve it?

Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for 
md simulations.

Thank You,
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Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

[Justin A. Lemkul]

majid hasan wrote:

Dear All,

I tried to minimize the energy of CNT-DNA system in vacuum (just to make 
sure it works) using l-bfgs integrator. When I run in the .trr output 
file, ends of dna only move slightly towards cnt, but it doesn't wrap 
around it. Could anyone please guide me what can be the possible issues 
here, and how can I improve it?




Energy minimization and dynamics are independent processes.  You should not 
expect large structural changes during EM with any of the methods.


Moreover, what is the right value of nstlist for amber99sb-ildn 
forcefield for md simulations.




Always start with the primary literature:

dx.doi.org/10.1002/prot.22711

-Justin


Thank You,
Majid



--


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


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Re: [gmx-users] pdb2gmx segmentation fault

[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!
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> 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/
>
> ***
>
>
>
>
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Re: [gmx-users] pdb2gmx segmentation fault

[Matthew Zwier]

Thanks.  I'm no Sun expert, so I'd have to echo Justin's request for
the precise sequence of commands you used to install GROMACS and all
dependencies.

On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli
 wrote:
> 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 list    gmx-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/
>>
>> ***
>>
>>
>>
>
> --
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Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

[majid hasan]

Okay, thanks. But then does it make any big difference on mdrun if we don't 
minimize energy first?

And one more thing, any idea how long it may take to run md for 367 atoms on a 
laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it 
is possible to get any results from mdrun on laptop?

Thanks again,
Majid




From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Wed, April 20, 2011 11:47:09 AM
Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of 
dna around cnt



majid hasan wrote:
> Dear All,
> 
> I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure 
>it works) using l-bfgs integrator. When I run in the .trr output file, ends of 
>dna only move slightly towards cnt, but it doesn't wrap around it. Could 
>anyone 
>please guide me what can be the possible issues here, and how can I improve it?
> 

Energy minimization and dynamics are independent processes.  You should not 
expect large structural changes during EM with any of the methods.

> Moreover, what is the right value of nstlist for amber99sb-ildn forcefield 
> for 
>md simulations.
> 

Always start with the primary literature:

dx.doi.org/10.1002/prot.22711

-Justin

> Thank You,
> Majid
> 

-- 

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


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Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

[Justin A. Lemkul]

majid hasan wrote:
Okay, thanks. But then does it make any big difference on mdrun if we 
don't minimize energy first?




You should always run energy minimization.  What I'm saying is that you should 
not expect to see any major changes or important phenomena evolve when simply 
running EM.


And one more thing, any idea how long it may take to run md for 367 
atoms on a laptop with 2GB ram, and dual core 1.4GHz processor. I am 
just wondering if it is possible to get any results from mdrun on laptop?




You can get results, but that depends entirely upon how much of the processor is 
being used to do other things at the same time.  For a small system, running 
locally may be an option, but for anything larger than a few hundred atoms 
you're better off running on a real cluster to avoid performance loss.  It will 
certainly "work," but probably not as fast as you might need for very long 
simulations.


-Justin


Thanks again,
Majid


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Wed, April 20, 2011 11:47:09 AM
*Subject:* Re: [gmx-users] L-BFGS energy minimization not leading to 
wrapping of dna around cnt




majid hasan wrote:
 > Dear All,
 >
 > I tried to minimize the energy of CNT-DNA system in vacuum (just to 
make sure it works) using l-bfgs integrator. When I run in the .trr 
output file, ends of dna only move slightly towards cnt, but it doesn't 
wrap around it. Could anyone please guide me what can be the possible 
issues here, and how can I improve it?

 >

Energy minimization and dynamics are independent processes.  You should 
not expect large structural changes during EM with any of the methods.


 > Moreover, what is the right value of nstlist for amber99sb-ildn 
forcefield for md simulations.

 >

Always start with the primary literature:

dx.doi.org/10.1002/prot.22711

-Justin

 > Thank You,
 > Majid
 >

-- 

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 


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--


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


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Re: [gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

Matthew Zwier wrote:

Thanks.  I'm no Sun expert, so I'd have to echo Justin's request for
the precise sequence of commands you used to install GROMACS and all
dependencies.



In addition, you can add -g to your CFLAGS to get debugging symbols, then 
execute pdb2gmx via a debugger like gdb.  This should show where the problem is 
coming from.  I have also never used Sun, so I won't be able to comment directly 
on that, either.


-Justin


On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli
 wrote:

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.
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--

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/

***




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--


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


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[gmx-users] time of dynamic

[Víctor Bahamonde]

Hello gmx-users
I have 2 dynamic, one is the continuation of the other. The problem is that 
both start at time 0.Is there any way to change the dynamic time in order to 
concatenate
both?
Thanks in advance.
Víctor E. Bahamonde Padilla
Laboratorio de Fisicoquímica Molecular
Departamento de Química
Facultad de Ciencias
Universidad de Chile
Phone: 562-978-7443
vedua...@ug.uchile.cl


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Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

[majid hasan]

Okay, thanks a lot.

Majid




From: Justin A. Lemkul 
To: Gromacs Users' List 
Sent: Wed, April 20, 2011 12:01:33 PM
Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of 
dna around cnt



majid hasan wrote:
> Okay, thanks. But then does it make any big difference on mdrun if we don't 
>minimize energy first?
> 

You should always run energy minimization.  What I'm saying is that you should 
not expect to see any major changes or important phenomena evolve when simply 
running EM.

> And one more thing, any idea how long it may take to run md for 367 atoms on 
> a 
>laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it 
>is possible to get any results from mdrun on laptop?
> 

You can get results, but that depends entirely upon how much of the processor 
is 
being used to do other things at the same time.  For a small system, running 
locally may be an option, but for anything larger than a few hundred atoms 
you're better off running on a real cluster to avoid performance loss.  It will 
certainly "work," but probably not as fast as you might need for very long 
simulations.

-Justin

> Thanks again,
> Majid
> 
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Wed, April 20, 2011 11:47:09 AM
> *Subject:* Re: [gmx-users] L-BFGS energy minimization not leading to wrapping 
>of dna around cnt
> 
> 
> 
> majid hasan wrote:
>  > Dear All,
>  >
>  > I tried to minimize the energy of CNT-DNA system in vacuum (just to make 
>sure it works) using l-bfgs integrator. When I run in the .trr output file, 
>ends 
>of dna only move slightly towards cnt, but it doesn't wrap around it. Could 
>anyone please guide me what can be the possible issues here, and how can I 
>improve it?
>  >
> 
> Energy minimization and dynamics are independent processes.  You should not 
>expect large structural changes during EM with any of the methods.
> 
>  > Moreover, what is the right value of nstlist for amber99sb-ildn forcefield 
>for md simulations.
>  >
> 
> Always start with the primary literature:
> 
> dx.doi.org/10.1002/prot.22711
> 
> -Justin
> 
>  > Thank You,
>  > Majid
>  >
> 
> -- 
> 
> 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

-- 

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


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Re: [gmx-users] time of dynamic

[Justin A. Lemkul]

Víctor Bahamonde wrote:

Hello gmx-users

I have 2 dynamic, one is the continuation of the other. The problem is 
that both start at time 0.

Is there any way to change the dynamic time in order to concatenate
both?


trjcat -settime.

-Justin


Thanks in advance.

/Víctor E. Bahamonde Padilla
Laboratorio de Fisicoquímica Molecular
Departamento de Química
Facultad de Ciencias
Universidad de Chile
Phone: 562-978-7443
vedua...@ug.uchile.cl/




--


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


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[gmx-users] restarting from cpt and binary identical

[Peter C. Lai]

I have a fairly stupid question about restart from a checkpoint and binary
identical messages, probably because I can't understand the doco.

When I restart (or extend) a double-precision run from a checkpoint involving 
either dlb or even a different decomposition count (say I changed the number of 
parallel threads), I get a message that says it restarted but the 
trajectory is not binary identical.

My question is: I assume this trajectory will continue from the last set of 
double-precision coordinates and velocities in the cpt file? What is the 
loss in precision/error propagation of the resulting trajectory as compared 
to if I started the entire run from the begining? (say I am extending my
trajectory from 1ns to 10ns). I guess I understand that both trajectories 
would be "equally valid" but not binary identical, but what does this mean
in terms of things like ultimate RMSD measurements and so forth? I don't
necessarily care that the two concatenated trajectory files will not cmp to
zero.

-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] restarting from cpt and binary identical

[Mark Abraham]

On 4/21/2011 8:00 AM, Peter C. Lai wrote:

I have a fairly stupid question about restart from a checkpoint and binary
identical messages, probably because I can't understand the doco.

When I restart (or extend) a double-precision run from a checkpoint involving
either dlb or even a different decomposition count (say I changed the number of
parallel threads), I get a message that says it restarted but the
trajectory is not binary identical.

My question is: I assume this trajectory will continue from the last set of
double-precision coordinates and velocities in the cpt file? What is the
loss in precision/error propagation of the resulting trajectory as compared
to if I started the entire run from the begining? (say I am extending my
trajectory from 1ns to 10ns). I guess I understand that both trajectories
would be "equally valid" but not binary identical, but what does this mean
in terms of things like ultimate RMSD measurements and so forth? I don't
necessarily care that the two concatenated trajectory files will not cmp to
zero.


These issues are discussed here 
http://www.gromacs.org/Documentation/Terminology/Reproducibility


There's no *loss* upon continuation with a new DD, it's just that it is 
almost guaranteed to be different from what would have resulted from 
continuing with the old DD. In the limit of an infinite situation, both 
would converge to the same ensembles.


Makr



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Re: [gmx-users] pdb2gmx segmentation fault

[Peter C. Lai]

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

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)?

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...

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?

On 2011-04-20 10:23:25AM -0500, Ragothaman Yennamalli wrote:
> 
> 
> On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul 
> mailto:jalem...@vt.edu>> 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 
> mailto: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> 
> >
> 
>  
> 
> 
>   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> 
> >
>   
>>> 
> 
> 
>

Re: [gmx-users] dhfr-impl-1nm.bench run keeps failing

[Mark Abraham]

On 4/20/2011 11:17 PM, Miah Wadud Dr (ITCS) wrote:

The MPI library is able to run other MPI jobs as well as other parallel Gromacs 
runs, and it just seems like this run causes this difficulty. I am using 
Platform MPI 8.1.


OK. That covers just one of the points I raised...

Mark


-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Mark Abraham
Sent: Wednesday, April 20, 2011 12:46 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dhfr-impl-1nm.bench run keeps failing

On 4/20/2011 6:57 PM, Miah Wadud Dr (ITCS) wrote:

Hello,

I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing.

I am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both
builds fail with the error message:

MPI Application rank 1 exited before MPI_Finalize() with status 0

The rank and the status value vary. Any idea what could be wrong?

No idea. That's just a generic advisory from the MPI library. Only the
mdrun stdout or .log file could have a GROMACS-specific diagnostic
message. You need to be sure that you can run other MPI programs, too.

Mark



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[gmx-users] g_dipoles and index file

[Sanku M]

Hi,
  I was trying to calculate the dipole moment of part of my peptide. In other 
words, if I have a 10-residue peptide, I was interested in calculating the 
dipole-moment contribution of the backbone. So, I made an index file which have 
a group containing backbone atoms. But, if I try to use g_dipoles to get the 
dipole moment contribution from the backbone atoms, using following command:
g_dipoles  -s  -f  traj -n index.ndx
I get an error :
---
Program g_dipoles_mod_4mpi, VERSION 4.0.5
Source code file: gmx_dipoles.c, line: 1173

Fatal error:
index[1]=197 does not correspond to the first atom of a molecule
---

Any help how to get around this will be appreciated.

Sanku-- 
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[gmx-users] PYP chromophore force field

[Ramachandran G]

Hi gromacs users,
 I am working on Photo active yellow protein.

Although i successfully build the force field and patched the
chromophore to the protein.
After energy minimizing the protein, the chromophore flies away separately.
I don't know whether i am missing anything?
Please help.
Rama
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Re: [gmx-users] PYP chromophore force field

[Peter C. Lai]

Isn't the chromophore supposed to be covalently bonded to the protein?
My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al
1994 and van Beeumen et al 1993: "This small 125-residue protein contains a
p-coumaric acid chromophore that is covalently bound to the protein backbone
via a thiol-ester cysteine linkage Cys-69"...

Maybe you forgot to specify a covalent bond in your topology...

On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> Hi gromacs users,
>  I am working on Photo active yellow protein.
> 
> Although i successfully build the force field and patched the chromophore 
> to the protein.
> After energy minimizing the protein, the chromophore flies away separately. I 
> don't know whether i am missing anything?
> Please help.
> Rama
> 
> 

> -- 
> 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!
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-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] PYP chromophore force field

[Ramachandran G]

Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to
the Sulphur(S) atom of the Cys-69 residue.
But I specified the covalent bond in my topology.

[ bonds]
 C   +SG

[ angles ]
  OC   +SG
 CA1   C   +SG
  C  +SG   +CB

[ dihedrals ]
  O C  +SG+CB
 CA1C  +SG+CB
 HA2   CA1   C   +SG
 CA2   CA1   C   +SG
  C   +SG  +CB   +CA
  C   +SG  +CB   +HB1
  C   +SG  +CB   +HB2

After doing pdb2gmx, i got the right structure. But the chromophore flies
away after minimising.


Thanks
Rama

On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai  wrote:

> Isn't the chromophore supposed to be covalently bonded to the protein?
> My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al
> 1994 and van Beeumen et al 1993: "This small 125-residue protein contains a
> p-coumaric acid chromophore that is covalently bound to the protein
> backbone
> via a thiol-ester cysteine linkage Cys-69"...
>
> Maybe you forgot to specify a covalent bond in your topology...
>
> On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> > Hi gromacs users,
> >  I am working on Photo active yellow protein.
> >
> > Although i successfully build the force field and patched the
> chromophore to the protein.
> > After energy minimizing the protein, the chromophore flies away
> separately. I don't know whether i am missing anything?
> > Please help.
> > Rama
> >
> >
>
> > --
> > 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
>
>
> --
> ===
> Peter C. Lai | University of Alabama-Birmingham
> Programmer/Analyst   | BEC 257
> Genetics, Div. of Research   | 1150 10th Avenue South
> p...@uab.edu  | Birmingham AL 35294-4461
> (205) 690-0808   |
> ===
>
>
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[gmx-users] problem with g_dipoles and index file

[Sanku M]

Hi,
  I was trying to calculate the dipole moment of part of my peptide. In other 
words, if I have a 10-residue peptide, I was interested in calculating the 
dipole-moment contribution of the backbone. So, I made an index file which have 
a group containing backbone atoms. But, if I try to use g_dipoles to get the 
dipole moment contribution from the backbone atoms, using following command:
g_dipoles  -s  -f  traj -n index.ndx
I get an error :
---
Program g_dipoles_mod_4mpi, VERSION 4.0.5
Source code file: gmx_dipoles.c, line: 1173

Fatal error:
index[1]=197 does not correspond to the first atom of a molecule
---

Any help how to get around this will be appreciated.

Sanku-- 
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Re: [gmx-users] PYP chromophore force field

[Mark Abraham]

On 4/21/2011 10:12 AM, Ramachandran G wrote:


Yes, you are right, the chromophore(p-coumaric acid) is covalently 
bonded to the Sulphur(S) atom of the Cys-69 residue.

But I specified the covalent bond in my topology.

[ bonds]
 C   +SG


That's your .rtp entry. What's in your [molecules] section of your topology?

Mark



[ angles ]
  OC   +SG
 CA1   C   +SG
  C  +SG   +CB

[ dihedrals ]
  O C  +SG+CB
 CA1C  +SG+CB
 HA2   CA1   C   +SG
 CA2   CA1   C   +SG
  C   +SG  +CB   +CA
  C   +SG  +CB   +HB1
  C   +SG  +CB   +HB2

After doing pdb2gmx, i got the right structure. But the chromophore 
flies away after minimising.



Thanks
Rama

On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai > wrote:


Isn't the chromophore supposed to be covalently bonded to the protein?
My cursory search shows Vengris et al 2004 in Biophys. J. citing
Baca et al
1994 and van Beeumen et al 1993: "This small 125-residue protein
contains a
p-coumaric acid chromophore that is covalently bound to the
protein backbone
via a thiol-ester cysteine linkage Cys-69"...

Maybe you forgot to specify a covalent bond in your topology...

On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> Hi gromacs users,
>  I am working on Photo active yellow protein.
>
> Although i successfully build the force field and patched
the chromophore to the protein.
> After energy minimizing the protein, the chromophore flies away
separately. I don't know whether i am missing anything?
> Please help.
> Rama
>
>

> --
> gmx-users mailing list gmx-users@gromacs.org

> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/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


--
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu   | Birmingham AL
35294-4461
(205) 690-0808|
===










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Re: [gmx-users] problem with g_dipoles and index file

[Mark Abraham]

On 4/21/2011 10:17 AM, Sanku M wrote:

Hi,
  I was trying to calculate the dipole moment of part of my peptide. 
In other words, if I have a 10-residue peptide, I was interested in 
calculating the dipole-moment contribution of the backbone. So, I made 
an index file which have a group containing backbone atoms. But, if I 
try to use g_dipoles to get the dipole moment contribution from the 
backbone atoms, using following command:

g_dipoles  -s  -f  traj -n index.ndx
I get an error :
---
Program g_dipoles_mod_4mpi, VERSION 4.0.5
Source code file: gmx_dipoles.c, line: 1173

Fatal error:
index[1]=197 does not correspond to the first atom of a molecule
---


Calculating a dipole moment of a possibly-charged species requires that 
there be a reference point, which is conventionally the center of mass 
of the molecule. This means all the atoms of the molecule have to be 
known, and g_dipoles assumes the index group consists of whole molecules.


So to do the partition you want, you will need to provide the same 
molecules, but with zero charges on the non-backbone atoms. That will 
mean making a copy of your .top and hacking those charges to zero to 
generate a new such .tpr.


Mark



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Re: [gmx-users] problem with g_dipoles and index file

[Mark Abraham]

On 4/21/2011 10:33 AM, Mark Abraham wrote:

On 4/21/2011 10:17 AM, Sanku M wrote:

Hi,
  I was trying to calculate the dipole moment of part of my peptide. 
In other words, if I have a 10-residue peptide, I was interested in 
calculating the dipole-moment contribution of the backbone. So, I 
made an index file which have a group containing backbone atoms. But, 
if I try to use g_dipoles to get the dipole moment contribution from 
the backbone atoms, using following command:

g_dipoles  -s  -f  traj -n index.ndx
I get an error :
---
Program g_dipoles_mod_4mpi, VERSION 4.0.5
Source code file: gmx_dipoles.c, line: 1173

Fatal error:
index[1]=197 does not correspond to the first atom of a molecule
---


Calculating a dipole moment of a possibly-charged species requires 
that there be a reference point, which is conventionally the center of 
mass of the molecule. This means all the atoms of the molecule have to 
be known, and g_dipoles assumes the index group consists of whole 
molecules.


So to do the partition you want, you will need to provide the same 
molecules, but with zero charges on the non-backbone atoms. That will 
mean making a copy of your .top and hacking those charges to zero to 
generate a new such .tpr.


Actually, tpbconv has the ability to set the charges of a group in a 
.tpr to zero.


Mark



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[gmx-users] dna and cnt get distorted in md simulation

[majid hasan]

Dear All,

I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then 
ran 
the mdrun with integrator = md. I am using a small ssDNA consisting of two 
residues only (66 atoms), and a small CNT of about 80 atoms. 

My commands are:
For energy minimization,

grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20
mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd


and then I ran molecular dyamics,

grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20
mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd

For individual DNA, and CNT alone, both produce reasonable results, where 
molecule stays together and jiggles around. However on combining the two 
molecules, both energy minimization and mdrun lead to distorted structures: 
bond 
lengths don't remain fixed neither for CNT nor for DNA, and atoms of both 
molecules get intertwined and produce a mess. I tried two .mdp files. 

I got the  first .mdp from a colleague who used it for a simple simulation 
of CNT only (without solvent, and any other molecule) . I made few changes in 
this file after going through manual e.g enabled free energy calculations, 
added 
"nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, 
changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" 
values from 0.9 to 1,
 
 Both .mdp files are placed at following addresses:
http://phas.ubc.ca/~majid/md.mdp   (first .mdp file)
http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file)

It seems to me that problem might be related to non-bonded interaction because 
this is the significant difference between one and two molecule system. Any 
help 
would be much appreciated. 

Thanks,
Majid-- 
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