[gmx-users] Re: Some questions on Tabulated Dihedral Potential

2009-07-21 Thread Johannes Kamp




Hi Cynthia,

I'm also working on including some tabulated functions but I don't have
any simulation yet. Thus I'm not a 'specialist' in this topic, but I
hope I can help you a little.


  Dear
all,
  
  
  I tried to include 2 tabulated dihedral potential functions into
my simulation. But it seems to be not able to generate correct results.
The system just exploded. I defined 3601 points in each table (from
-180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two
warning information:
  
  
  WARNING: For the 3598 non-zero entries for table 0 in
table_d1.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential
  WARNING: For the 3598 non-zero entries for table 0 in
table_d2.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential
  
  Do these two warnings matter very much? I checked the values for
x,f(x),-f'(x) in the tables and don't think there're mistakes. has
anyone of you met with such problems?
  
  
  There're also some other confusions:
  1. Can the constant k before the cubic spline function be
defined arbitrarily, as long as themultiplicationof k and f(x) equals
to the dihedral potential?
  2. The tables do not need to be supplied to mdrun using
'-tableb', right? I found if I omitted -tableb and the following table
files, GROMACS can still go and find the two tables.
  3. how to use '-tableb' if two tables are supplied? '-tableb
table_d1.xvg table_d2.xvg' or '-tableb table_d1.xvg -tableb
table_d2.xvg'? I tried both and error information was given that
GROMACS can not find 'table_d1_d1.xvg'. I then delete '_d1' in both of
the commands and there was no error information any more. It seems that
only one table can be supplied to mdrun by using'-tableb', the second
table can not be recognized all the time.
  
  

If you read the manual page of mdrun (i.e. in the appendix of GROMACS
manual) you find the following:

"When tabulated bonded functions are present in the topology,
interaction functions are read using the -tableb option. For each
different tabulated interaction type the table file name is modified in
a different way: before the file extension an underscore is appended,
then a b for bonds, an a for angles or a d for dihedrals and finally
the table number of the interaction type."

Thus you run mdrun -tableb mytablefilename.xvg and GROMACS
automatically adds _d* before .xvg, where * is the
table number specified in the topology. In your case GROMACS finds your
table files automatically, because you gave them the default names
GROMACS searches for. 
For further informations read chapters 4.2.13, 5.7.1 and D.74 (manpage
mdrun) of the GROMACS manual.

  
  
  Thanks for your help
  CH
  
  

Johannes


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Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential

2009-07-21 Thread Ran Friedman
Hi,

Johannes Kamp wrote:
 Hi Cynthia,

 I'm also working on including some tabulated functions but I don't
 have any simulation yet. Thus I'm not a 'specialist'  in this topic,
 but I hope I can help you a little.

 Dear all, 

 I tried to include 2 tabulated dihedral potential functions into my
 simulation. But it seems to be not able to generate correct results.
 The system just exploded. I defined 3601 points in each table (from
 -180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates
 two warning information:

 WARNING: For the 3598 non-zero entries for table 0 in table_d1.xvg
 the forces deviate on average 193% from minus the numerical
 derivative of the potential
 WARNING: For the 3598 non-zero entries for table 0 in table_d2.xvg
 the forces deviate on average 193% from minus the numerical
 derivative of the potential
  
 Do these two warnings matter very much? I checked the values for
 x,f(x),-f'(x) in the tables and don't think there're mistakes. has
 anyone of you met with such problems?
In the tables you should supply potentials and forces. The forces are
also calculated numerically, and a warning is emitted if the numerical
derivatives deviate too much from the forces supplied by the user. Since
the forces are interpolated, if the numerical derivative is too far from
the input what you'd get will be different then expected. You can
calculate the derivatives yourself and see where there are deviations.

Good luck,
Ran
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[gmx-users] Re: mdrun -nosum still complains that 15 % of the runtime was spent communicating energies

2009-07-21 Thread chris . neale

Thanks mark, I'll respond inline.


Chris Neale wrote:

I have now tested with and without -nosum and it appears that the option
is working (see 51 vs. 501 Number of communications) but that the total
amount of time communicating energies didn't go down by very much. Seems
strange to me. Anybody have any ideas if this is normal?


Seems strange, but perhaps a 45-second test is not sufficiently long to
demonstrate suitable scaling.


Agreed, although I find it a good jumping off point, especially now  
that we need to optimize -npme. If I use quick tests to narrow down  
the range of nodes/npme that is going to scale the best then I fine  
tune it with longer scaling tests.


There's no discussion in the 4.0.5 release

notes of a relevant change to -nosum, but there has been a change:
http://oldwww.gromacs.org/content/view/181/132/.


Thanks, I did see this but don't think that it is related to this  
issue, which I have now confirmed in both 4.0.4 and 4.0.5.





At the very least, I suggest adding an if statement to mdrun so that it
doesn't output the -nosum usage note if the user did in fact use -nosum
in that run.


Without using -nosum:

   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

Computing: Nodes Number G-CyclesSeconds %
---
...
Write traj.  256  2  233.218   93.7 0.5
Update   256501  777.511  312.5 1.7
Constraints  256   1002 1203.894  483.9 2.7
Comm. energies   256501 7397.995 2973.916.5
Rest 256 128.058   51.5 0.3
---
Total384   44897.46818048.0   100.0
---

NOTE: 16 % of the run time was spent communicating energies,
 you might want to use the -nosum option of mdrun


   Parallel run - timing based on wallclock.

  NODE (s)   Real (s)  (%)
  Time: 47.000 47.000100.0
  (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:  13485.788712.634  1.842 13.029
Finished mdrun on node 0 Mon Jul 20 12:53:41 2009

#

And using -nosum:

   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
Computing: Nodes Number G-CyclesSeconds %
---
...
Write traj.  256  2  213.521   83.3 0.5
Update   256501  776.606  303.0 1.8
Constraints  256   1002 1200.285  468.2 2.7
Comm. energies   256 51 6926.667 2702.115.6
Rest 256 127.503   49.7 0.3
---
Total384   44296.67017280.0   100.0
---

NOTE: 16 % of the run time was spent communicating energies,
 you might want to use the -nosum option of mdrun


   Parallel run - timing based on wallclock.

  NODE (s)   Real (s)  (%)
  Time: 45.000 45.000100.0
  (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:  14084.547744.277  1.924 12.475

#

Thanks,
Chris.

Chris Neale wrote:

Hello,

I have been running simulations on a larger number of processors
recently and am confused about the message regarding -nosum that
occurs at the end of the .log file. In this case, I have included the
-nosum option to mdrun and I still get this warning (gromacs 4.0.4).

My command was:
mpirun -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -machinefile
$PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.4/exec/bin/mdrun
-deffnm test -nosum -npme 128


Perhaps assigning the result of this to a variable and printing it
before executing it would help confirm that -nosum really was there.


I am not sure what you mean... the while line as a variable? I'm  
pretty sure that -nosum is there.




Your mdrun output from your first email was...


#

To confirm that I am asking mdrun for -nosum, to stderr I get:
...
Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-deffnm  string testSet the default filename for all file options
-[no]xvgrbool   yes Add specific codes (legends etc.) in the
output
   xvg files for the xmgrace program
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint128 Number of separate nodes to be used for
PME, -1

回复: [gmx-users] Re: Some questions on T abulated Dihedral Potential

2009-07-21 Thread hong bingbing
Hi, Ran,

The potential f(x) and force -f'(x) in the table are calculated by myself 
before constructing the table. The potential can be written in an analytical 
form and the force is calculated as the analytical negative derivative of the 
potential at point x. There should not be so large deviation betw. the value I 
supplied and the value calculated by GROMACS. Wait. Is there something wrong in 
my interpretation? What's  your method to get the force? Is there a way to see 
the numerical derivative generated by GROMACS?

Thanks
CH






发件人: Ran Friedman r.fried...@bioc.uzh.ch
收件人: Discussion list for GROMACS users gmx-users@gromacs.org
已发送: 2009/7/21(周二), 上午8:17:11
主题: Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential

Hi,

Johannes Kamp wrote: 
Hi Cynthia,

I'm also working on including some tabulated functions but I don't have
any simulation yet. Thus I'm not a 'specialist'  in this topic, but I
hope I can help you a little.


Dear
all,  

I tried to include 2 tabulated dihedral potential functions
into
my simulation. But it seems to be not able to generate correct results.
The system just exploded. I defined 3601 points in each table (from
-180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two
warning information:

WARNING: For the 3598 non-zero entries for table 0 in
table_d1.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential
WARNING: For the 3598 non-zero entries for table 0 in
table_d2.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential

 
Do these two warnings matter very much? I checked the values
for
x,f(x),-f'(x) in the tables and don't think there're mistakes. has
anyone of you met with such problems? 

In the tables you should supply potentials and forces. The forces are
also calculated numerically, and a warning is emitted if the numerical
derivatives deviate too much from the forces supplied by the user.
Since the forces are interpolated, if the numerical derivative is too
far from the input what you'd get will be different then expected. You
can calculate the derivatives yourself and see where there are
deviations.

Good luck,
Ran



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Re: 回复: [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential

2009-07-21 Thread Ran Friedman
Hi,

The numerical derivative for the Nth value y[N] is calculated as:
der = y[N+1] - y[N-1] * 0.5 * deltaX
where y is the potential deltaX is the difference between two successive
values in your input (e.g., 1 if you have a table that goes from -180 to
180 with 361 values).

I don't think you can print the number without changing the code, but
it's not difficult to calculate. You can plot your forces and -der and
see where they deviate.

Ran.

hong bingbing wrote:
 Hi, Ran,

 The potential f(x) and force -f'(x) in the table are calculated by
 myself before constructing the table. The potential can be written in
 an analytical form and the force is calculated as the analytical
 negative derivative of the potential at point x. There should not be
 so large deviation betw. the value I supplied and the value calculated
 by GROMACS. Wait. Is there something wrong in my interpretation?
 What's  your method to get the force? Is there a way to see the
 numerical derivative generated by GROMACS?

 Thanks
 CH

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Re: 回复: [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential

2009-07-21 Thread Ran Friedman
Ran Friedman wrote:
 Hi,

 The numerical derivative for the Nth value y[N] is calculated as:
 der = y[N+1] - y[N-1] * 0.5 * deltaX
Correction:
der =  (y[N+1] - y[N-1]) * 0.5 * deltaX
 where y is the potential deltaX is the difference between two
 successive values in your input (e.g., 1 if you have a table that goes
 from -180 to 180 with 361 values).

 I don't think you can print the number without changing the code, but
 it's not difficult to calculate. You can plot your forces and -der and
 see where they deviate.

 Ran.

 hong bingbing wrote:
 Hi, Ran,

 The potential f(x) and force -f'(x) in the table are calculated by
 myself before constructing the table. The potential can be written in
 an analytical form and the force is calculated as the analytical
 negative derivative of the potential at point x. There should not be
 so large deviation betw. the value I supplied and the value
 calculated by GROMACS. Wait. Is there something wrong in my
 interpretation? What's  your method to get the force? Is there a way
 to see the numerical derivative generated by GROMACS?

 Thanks
 CH

 

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-- 
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.unizh.ch
Skype: ran.friedman
--

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[gmx-users] large force on an atom

2009-07-21 Thread Samik Bhattacharya
hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using 
inflategro perl script. just after the first run when i'm running grompp to 
minimize it i have found a large force on a phenylalanin atom which is well 
over 



1015   

 

Now what to do with this one?  I had a view of that particular atom through
pymol which is an Oxygen (CO). Right now I’m a little anxious that if I keep
this and go on it’ll affect the future steps. Any suggestions regarding this
will be very encouraging.
Thank You
Shamik






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Re: [gmx-users] large force on an atom

2009-07-21 Thread Justin A. Lemkul



Samik Bhattacharya wrote:
hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using 
inflategro perl script. just after the first run when i'm running grompp 
to minimize it i have found a large force on a phenylalanin atom which 
is well over 10^15   ^ Now what to do with this one?  I had a view of 
that particular atom through pymol which is an Oxygen (CO). Right now 
I’m a little anxious that if I keep this and go on it’ll affect the 
future steps. Any suggestions regarding this will be very encouraging..


Well, is that atom clashing with something else in your system?  The only way I 
can think to get a force of 10^15 is substantial atomic overlap.


-Justin


Thank You
Shamik



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--


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


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Re: 回复: 回复: [gmx-users] Re: So me questions on Tabulated Dihedral Potential

2009-07-21 Thread Ran Friedman
As I wrote it der is the derivative itself, so you should plot (-1)*der.
Ran.

hong bingbing wrote:
 Thanks Ran. Should there also be a minus sign before (y[N+1]-y[N-1])
 because the third column in the table is -f'(x)?
 CH
  




 
 *发件人:* Ran Friedman r.fried...@bioc.uzh.ch
 *收件人:* Discussion list for GROMACS users gmx-users@gromacs.org
 *已发送:* 2009/7/21(周二), 上午9:41:42
 *主题:* Re: 回复: [gmx-users] Re: Some questions on Tabulated
 Dihedral Potential

 Ran Friedman wrote:
 Hi,

 The numerical derivative for the Nth value y[N] is calculated as:
 der = y[N+1] - y[N-1] * 0.5 * deltaX
 Correction:
 der =聽 (y[N+1] - y[N-1]) * 0.5 * deltaX
 where y is the potential deltaX is the difference between two
 successive values in your input (e.g., 1 if you have a table that
 goes from -180 to 180 with 361 values).

 I don't think you can print the number without changing the code, but
 it's not difficult to calculate. You can plot your forces and -der
 and see where they deviate.

 Ran.

 hong bingbing wrote:
 Hi, Ran,

 The potential f(x) and force -f'(x) in the table are calculated by
 myself before constructing the table. The potential can be written
 in an analytical form and the force is calculated as the analytical
 negative derivative of the potential at point x. There should not be
 so large deviation betw. the value I supplied and the value
 calculated by GROMACS. Wait. Is there something wrong in my
 interpretation? What's 聽your method to get the force? Is there a
 way to see the numerical derivative generated by GROMACS?

 Thanks
 CH

 

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 -- 
 --
 Ran Friedman
 Postdoctoral Fellow
 Computational Structural Biology Group (A. Caflisch)
 Department of Biochemistry
 University of Zurich
 Winterthurerstrasse 190
 CH-8057 Zurich, Switzerland
 Tel. +41-44-639
 Email: r.fried...@bioc.unizh.ch
 Skype: ran.friedman
 --
   

 
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-- 
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.unizh.ch
Skype: ran.friedman
--

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[gmx-users] comparison of gromacs in CENTOS and UBUNTU

2009-07-21 Thread jagannath mondal
Hi,   I was planning to install one of the linux distributions : CENTOS or 
UBUNTU in our xeon 8-core processor.  Can any one suggest which one will be 
better for Gromacs as far as installation and performance is 
concerned?ThanksJagannath


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[gmx-users] PDB and GRO files

2009-07-21 Thread Jamie Seyed
Hi,

I have a basic question (since I am new). For starting any simulation as I
understand, is to find a .pdb or .gor file. Pdb files for proteins are
already there, but for a new system what is the easiest and quick way to
find it (which software etc). What about .gro files?



I appreciate your help for solve my basic problems.

Thanks, Jamie
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Re: [gmx-users] PDB and GRO files

2009-07-21 Thread Rodrigo faccioli
Hi,

If I understood your question, do you want to know how can you start a
simulation? So, if I'm correct I recommend this link
http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link,
there is flowsheet file which is the flowchart to Gromacs simulation.

Answered your question a little more specific, although basically,  after
you get the pdb file, you need to run the pdb2gmx program. The link above
explains more details about it.

I hope that this email helped you.

Cheers,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com wrote:

 Hi,

 I have a basic question (since I am new). For starting any simulation as I
 understand, is to find a .pdb or .gor file. Pdb files for proteins are
 already there, but for a new system what is the easiest and quick way to
 find it (which software etc). What about .gro files?



 I appreciate your help for solve my basic problems.

 Thanks, Jamie

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Re: [gmx-users] PDB and GRO files

2009-07-21 Thread Jamie Seyed
Hi,
Thanks for your comments. But I do not know how to get (or make) the pdb
file if it is not made (let say for a new system). Are you using special
software to do that to make a pdb or gro file, before starting the
simulation?
Another thing: It is not possible for me to open some web-pages that users
are referring to (some of them are crucial to get the answer)!! Did you face
with the same problem or there is new web-address for them??

Thanks for your help,
Jamie

On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli 
rodrigo_facci...@uol.com.br wrote:

 Hi,

 If I understood your question, do you want to know how can you start a
 simulation? So, if I'm correct I recommend this link
 http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this
 link, there is flowsheet file which is the flowchart to Gromacs simulation.

 Answered your question a little more specific, although basically,  after
 you get the pdb file, you need to run the pdb2gmx program. The link above
 explains more details about it.

 I hope that this email helped you.

 Cheers,

 --
 Rodrigo Antonio Faccioli
 Ph.D Student in Electrical Engineering
 University of Sao Paulo - USP
 Engineering School of Sao Carlos - EESC
 Department of Electrical Engineering - SEL
 Intelligent System in Structure Bioinformatics
 http://laips.sel.eesc.usp.br
 Phone: 55 (16) 3373-9366 Ext 229
 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


   On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.comwrote:

   Hi,

 I have a basic question (since I am new). For starting any simulation as I
 understand, is to find a .pdb or .gor file. Pdb files for proteins are
 already there, but for a new system what is the easiest and quick way to
 find it (which software etc). What about .gro files?



 I appreciate your help for solve my basic problems.

 Thanks, Jamie

 ___
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before
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 Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] PDB and GRO files

2009-07-21 Thread Justin A. Lemkul



Jamie Seyed wrote:

Hi,
Thanks for your comments. But I do not know how to get (or make) the pdb 
file if it is not made (let say for a new system). Are you using special 
software to do that to make a pdb or gro file, before starting the 
simulation?


That's going to depend entirely upon what that system is.  Building a protein or 
peptide is not so trivial.  Building a small molecule is fairly straightforward 
using programs like PRODRG (online) or xLeap (part of AmberTools).


That said, if your goal is to simulate some arbitrary small molecules, the 
previous advice of using pdb2gmx will not apply.  You will have to build the 
topologies yourself.


Another thing: It is not possible for me to open some web-pages that 
users are referring to (some of them are crucial to get the answer)!! 
Did you face with the same problem or there is new web-address for them??
 


If you cite some examples, maybe someone can point you in the right direction. 
The Gromacs webpage is currently migrating to a new site; old webpages can be 
accessed by appending old to the URL, i.e. http://oldwww.gromacs.org is the 
old home page.


-Justin


Thanks for your help,
Jamie

On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli 
rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote:


Hi,

If I understood your question, do you want to know how can you start
a simulation? So, if I'm correct I recommend this link
http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In
this link, there is flowsheet file which is the flowchart to Gromacs
simulation.

Answered your question a little more specific, although basically, 
after you get the pdb file, you need to run the pdb2gmx program. The

link above explains more details about it.

I hope that this email helped you.

Cheers,
 
--

Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com
mailto:jamie.se...@gmail.com wrote:

Hi,

I have a basic question (since I am new). For starting any
simulation as I understand, is to find a .pdb or .gor file. Pdb
files for proteins are already there, but for a new system what
is the easiest and quick way to find it (which software etc).
What about .gro files?

 


I appreciate your help for solve my basic problems.

Thanks, Jamie


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--


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


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[gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

2009-07-21 Thread Vitaly V. Chaban


 Hi,   I was planning to install one of the linux distributions : CENTOS or
 UBUNTU in our xeon 8-core processor.  Can any one suggest which one will be
 better for Gromacs as far as installation and performance is
 concerned?ThanksJagannath



Your question is senseless. The linux distribution will not affect gromacs
performance.


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===
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[gmx-users] Re: PDB and GRO files

2009-07-21 Thread Vitaly V. Chaban

 Hi,

 I have a basic question (since I am new). For starting any simulation as I
 understand, is to find a .pdb or .gor file. Pdb files for proteins are
 already there, but for a new system what is the easiest and quick way to
 find it (which software etc). What about .gro files?

 I appreciate your help for solve my basic problems.

 Thanks, Jamie



Jamie,

Please see the help for genbox, genconf and editconf utlities of the gromacs
package. It seems you should be interested in Protein Data Bank as well:
http://www.rcsb.org/pdb/home/home.do


~ Vitaly

-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===
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Re: [gmx-users] PDB and GRO files

2009-07-21 Thread Jamie Seyed
Hi Justin,

On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Jamie Seyed wrote:

 Hi,
 Thanks for your comments. But I do not know how to get (or make) the pdb
 file if it is not made (let say for a new system). Are you using special
 software to do that to make a pdb or gro file, before starting the
 simulation?


 That's going to depend entirely upon what that system is.  Building a
 protein or peptide is not so trivial.  Building a small molecule is fairly
 straightforward using programs like PRODRG (online) or xLeap (part of
 AmberTools).

 That said, if your goal is to simulate some arbitrary small molecules, the
 previous advice of using pdb2gmx will not apply.  You will have to build the
 topologies yourself.


Is the result of using these programs a pdb file or gro.. would you
please explain a little bit?
The systems that I want to simulate are fullerene and CNT. But before that I
will simulate a box of water, spce. In this case is it ok to use
spc216.pdb (??) or I should use the programs you mentioned?
Sorry for these simple questions..



 Another thing: It is not possible for me to open some web-pages that users
 are referring to (some of them are crucial to get the answer)!! Did you face
 with the same problem or there is new web-address for them??



 If you cite some examples, maybe someone can point you in the right
 direction. The Gromacs webpage is currently migrating to a new site; old
 webpages can be accessed by appending old to the URL, i.e.
 http://oldwww.gromacs.org is the old home page.


For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you
mentioned, but I can not open links on the page. All of them (check force
field for example) can not open with like this message Site settings could
not be loaded...
Is it the page I should use to get a pdb file for my system?? I really
appreciate if you let me know the exact web-address to use PRODRG or xLeap
(?).

Thanks a lot,
Jamie




 -Justin

  Thanks for your help,
 Jamie

 On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli 
 rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote:

Hi,

If I understood your question, do you want to know how can you start
a simulation? So, if I'm correct I recommend this link
http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In
this link, there is flowsheet file which is the flowchart to Gromacs
simulation.

Answered your question a little more specific, although basically,
  after you get the pdb file, you need to run the pdb2gmx program. The
link above explains more details about it.

I hope that this email helped you.

Cheers,
--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com
mailto:jamie.se...@gmail.com wrote:

Hi,

I have a basic question (since I am new). For starting any
simulation as I understand, is to find a .pdb or .gor file. Pdb
files for proteins are already there, but for a new system what
is the easiest and quick way to find it (which software etc).
What about .gro files?


I appreciate your help for solve my basic problems.

Thanks, Jamie


___
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Please search the archive at http://www.gromacs.org/search
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 Please search the archive at 

[gmx-users] Re: PDB and GRO files

2009-07-21 Thread Vitaly V. Chaban


 Is the result of using these programs a pdb file or gro.. would you
 please explain a little bit?
 The systems that I want to simulate are fullerene and CNT. But before that
 I
 will simulate a box of water, spce. In this case is it ok to use
 spc216.pdb


 For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you
 mentioned, but I can not open links on the page. All of them (check force
 field for example) can not open with like this message Site settings could
 not be loaded...
 Is it the page I should use to get a pdb file for my system?? I really
 appreciate if you let me know the exact web-address to use PRODRG or xLeap
 (?).


1. spc216.pdb  should contain SPC water, not SPCE.
2. You can convert your coordinates to PDB format using almost any molecular
viewer (like MOLEKEL, VMD, etc).
3. The nanotubes files (coordinates and topologies) as well as a number of
already equilibrated systems were uploaded by me to the topology section of
the old site. I guess they are still accessible. You may also want to look
for Christopher Stiles' wonderful page with many details.


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===
___
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] PDB and GRO files

2009-07-21 Thread Justin A. Lemkul



Jamie Seyed wrote:

Hi Justin,
 
On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Jamie Seyed wrote:

Hi,
Thanks for your comments. But I do not know how to get (or make)
the pdb file if it is not made (let say for a new system). Are
you using special software to do that to make a pdb or gro file,
before starting the simulation?


That's going to depend entirely upon what that system is.  Building
a protein or peptide is not so trivial.  Building a small molecule
is fairly straightforward using programs like PRODRG (online) or
xLeap (part of AmberTools).

That said, if your goal is to simulate some arbitrary small
molecules, the previous advice of using pdb2gmx will not apply.  You
will have to build the topologies yourself. 

 
Is the result of using these programs a pdb file or gro.. would you 
please explain a little bit?


The documentation of each program will explain the output formats.

The systems that I want to simulate are fullerene and CNT. But before 


Then neither PRODRG nor xLeap will be of use to you; xLeap might work, but it's 
probably about the hardest way to do it :)


that I will simulate a box of water, spce. In this case is it ok to use 
spc216.pdb (??) or I should use the programs you mentioned?


Use spc216.gro - it's a pre-equilibrated box that is suitable for use in further 
simulations.



Sorry for these simple questions..



Another thing: It is not possible for me to open some web-pages
that users are referring to (some of them are crucial to get the
answer)!! Did you face with the same problem or there is new
web-address for them??
 



If you cite some examples, maybe someone can point you in the right
direction. The Gromacs webpage is currently migrating to a new site;
old webpages can be accessed by appending old to the URL, i.e.
http://oldwww.gromacs.org http://oldwww.gromacs.org/ is the old
home page.

 
For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you 
mentioned, but I can not open links on the page. All of them (check 
force field for example) can not open with like this message Site 
settings could not be loaded...


Use Google to search for PRODRG; the link in the wiki article is incorrect.  But 
as I said above, for your purposes, PRODRG is not useful.


Is it the page I should use to get a pdb file for my system?? I really 
appreciate if you let me know the exact web-address to use PRODRG or 
xLeap (?).
 


Use Google to find things.

This page is probably where you will want to start:

http://www.gromacs.org/WIKI-import/Carbon_Nanotube

-Justin


Thanks a lot,
Jamie
 




-Justin

Thanks for your help,
Jamie

On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli
rodrigo_facci...@uol.com.br
mailto:rodrigo_facci...@uol.com.br
mailto:rodrigo_facci...@uol.com.br
mailto:rodrigo_facci...@uol.com.br wrote:

   Hi,

   If I understood your question, do you want to know how can
you start
   a simulation? So, if I'm correct I recommend this link
   http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In
   this link, there is flowsheet file which is the flowchart to
Gromacs
   simulation.

   Answered your question a little more specific, although
basically,after you get the pdb file, you need to run the
pdb2gmx program. The
   link above explains more details about it.

   I hope that this email helped you.

   Cheers,
   --
   Rodrigo Antonio Faccioli
   Ph.D Student in Electrical Engineering
   University of Sao Paulo - USP
   Engineering School of Sao Carlos - EESC
   Department of Electrical Engineering - SEL
   Intelligent System in Structure Bioinformatics
   http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/
http://laips.sel.eesc.usp.br/

   Phone: 55 (16) 3373-9366 Ext 229
   Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


   On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed
jamie.se...@gmail.com mailto:jamie.se...@gmail.com
   mailto:jamie.se...@gmail.com
mailto:jamie.se...@gmail.com wrote:

   Hi,

   I have a basic question (since I am new). For starting any
   simulation as I understand, is to find a .pdb or .gor
file. Pdb
   files for proteins are already there, but for a new
system what
   is the easiest and quick way to find it (which software etc).
   What about .gro files?

   
   I appreciate your help for solve my basic problems.


   Thanks, Jamie


   

[gmx-users] reliability of NOTES

2009-07-21 Thread Payman Pirzadeh
Hello,
I am trying to prepare the input files for an MD run. After running grompp,
I received the following note:

NOTE 1 [file npt.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

How reliable this note is? And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).
Also, when I changed the thermostat to nose-hoover, it said that it can not
be used with Berendsen barostat. Why?

Payman




-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 12:38 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water



Payman Pirzadeh wrote:
 You were right! The dimensions of the box are zero in the .gro file.
Should
 I change them to the values I have?
 

As long as those vectors define the box size and not necessarily the system
size
(i.e., largest coordinate - smallest coordinate).  You can do this with a
.pdb
file, I think on the CRYST line, if you prefer.

-Justin

 Payman
 
 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Justin A. Lemkul
 Sent: July 16, 2009 12:08 PM
 To: Gromacs Users' List
 Subject: Re: [gmx-users] making a box of water
 
 
 
 Payman Pirzadeh wrote:
 But, I am using a .pdb file as the input of the gromacs. Does the
 preparation of pdb file differ from software to software?

 
 It shouldn't, and I'm not 100% sure on how Gromacs handles system size
from
 a 
 .pdb file (I always use .gro).  What you can try to do is transform your
 .pdb 
 into .gro format with editconf, and read the last line of the .gro file.
 That's 
 any easy way to determine the size of the box Gromacs is finding.
 
 -Justin
 
 Payman

 -Original Message-
 From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Justin A. Lemkul
 Sent: July 16, 2009 11:42 AM
 To: Gromacs Users' List
 Subject: Re: [gmx-users] making a box of water



 Payman Pirzadeh wrote:
 Hello,
 Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced
the
 rvdw cutoff to 10A, but problem was still there.
 Now I made my box bigger by using a visualization software. The new
 dimensions are ~54*63*103.38(all in A). Again the same warning is given
 to
 me about increasing the box size or reduce the rvdw.

 Well, Gromacs doesn't do anything in A, it's all nm, so be sure that
 everything 
 you're doing is consistent with Gromacs conventions.  There is no reason
 that 
 either of those boxe should be complaining about a 1.0-nm cutoff, so
there
 has 
 to be something that messed up along the way.

 -Justin

 Payman 

 -Original Message-
 From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Justin A. Lemkul
 Sent: July 15, 2009 7:32 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] making a box of water



 Payman Pirzadeh wrote:
 Hello,
 I have an .pdb file from another simulation. I want to make the
 appropriate
 input files to run a simulations. I have used grompp to produce the
.tpr
 file, but I get the usual ERROR:

  ERROR: The cut-off length is longer than half the shortest box vector
 or
 longer than the smallest box diagonal element. Increase the box size or
 decrease rvdw.

 I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but
 still
 the problem persists! Smaller rvdw is not good for my system. Any
 suggestions?

 Then you'll have to use a bigger box, most likely.  What is your
smallest
 box 
 vector?  That should indicate the limits of your cutoffs.

 -Justin

 Payman 

 -Original Message-
 From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of David van der Spoel
 Sent: July 15, 2009 12:23 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] making a box of water

 Payman Pirzadeh wrote:
 Thanks Justin. 
 Unfortunately, I realized that after I sent the e-mail. Anyways, I
 started
 running to models: SPCE and TIP4P to check the energies of these
 systems
 to
 figure out where the problem with my own system (six-site model) could
 be.
 I
 will keep you posted. But, I have a question about the compressibility
 factor used in .mdp file. Does that(if it is not a correct value)
truly
 affect the simulation when the reference pressure is set?

 No, only the relaxation rate (with Berendsen scaling) resp. the 
 oscillation period with Parrinello Rahman.

 Payman

 -Original Message-
 From: gmx-users-boun...@gromacs.org
 [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Justin A. Lemkul
 Sent: July 15, 2009 11:38 AM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] making a box of water



 Payman Pirzadeh wrote:
 Hi again,
 I have a question about the .itp files. When e.g. TIP4P.itp the
 atomtypes
 in
 the  [atoms 

[gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

2009-07-21 Thread Laercio Pol Fachin
Hi!
 
In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS is 
approximatedely twice slower than in a installation in an entire HD.
 
If you need to install Linux in dual boot, maybe CentOS is a better choice.
 
Best regards,
Laércio Pol-Fachin

--- Em ter, 21/7/09, gmx-users-requ...@gromacs.org 
gmx-users-requ...@gromacs.org escreveu:



   1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal)

Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST)
From: jagannath mondal jmondal2...@yahoo.co.in
Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU
To: gmx-users@gromacs.org
Message-ID: 410193.9922...@web7906.mail.in.yahoo.com
Content-Type: text/plain; charset=iso-8859-1

Hi,   I was planning to install one of the linux distributions : CENTOS or 
UBUNTU in our xeon 8-core processor.  Can any one suggest which one will be 
better for Gromacs as far as installation and performance is 
concerned?ThanksJagannath


  

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Re: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

2009-07-21 Thread Justin A. Lemkul


I don't see how hard disk space of the OS has anything to do with the speed of 
Gromacs.  Are the machines you refer to identical in terms of hardware (CPU, 
RAM, etc) as well as the compilers used to install the software?


I have installed Gromacs under several different OS - Mac, Ubuntu Linux, 
Yellowdog Linux, and Fedora Linux.  The only real speed difference comes from 
the hardware.


-Justin

Laercio Pol Fachin wrote:

Hi!
 
In a UBUNTU installation in dual boot (with Windows, in my 
case), GROMACS is approximatedely twice slower than in a installation in 
an entire HD.
 
If you need to install Linux in dual boot, maybe CentOS is a better choice.
 
Best regards,

Laércio Pol-Fachin

--- Em *ter, 21/7/09, gmx-users-requ...@gromacs.org 
/gmx-users-requ...@gromacs.org/* escreveu:



   1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal)

Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST)
From: jagannath mondal jmondal2...@yahoo.co.in
http://br.mc515.mail.yahoo.com/mc/compose?to=jmondal2...@yahoo.co.in
Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU
To: gmx-users@gromacs.org
http://br.mc515.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org
Message-ID: 410193.9922...@web7906.mail.in.yahoo.com

http://br.mc515.mail.yahoo.com/mc/compose?to=410193.9922...@web7906.mail.in.yahoo.com
Content-Type: text/plain; charset=iso-8859-1

Hi,   I was planning to install one of the linux distributions :
CENTOS or UBUNTU in our xeon 8-core processor.  Can any one suggest
which one will be better for Gromacs as far as installation and
performance is concerned?ThanksJagannath



Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 
http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/ 
- Celebridades 
http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/ 
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--


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


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[gmx-users] Re: reliability of NOTES

2009-07-21 Thread Justin A. Lemkul



Payman Pirzadeh wrote:

Hello,
I am trying to prepare the input files for an MD run. After running grompp,
I received the following note:

NOTE 1 [file npt.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

How reliable this note is? And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).


Very reliable - the statistical ensemble from the Berendsen thermostat does not 
correspond to any known ensemble.  This has been well-documented in the 
literature for years.


T-coupling choices are listed in the manual:

http://manual.gromacs.org/current/online/mdp_opt.html#tc

Note that V-rescale is one of them :)


Also, when I changed the thermostat to nose-hoover, it said that it can not
be used with Berendsen barostat. Why?


I can't recall having read anything about this in particular, but it's probably 
somewhere in the literature as well.  Use the Parrinello-Rahman barostat instead.


-Justin



Payman




-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 12:38 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water



Payman Pirzadeh wrote:

You were right! The dimensions of the box are zero in the .gro file.

Should

I change them to the values I have?



As long as those vectors define the box size and not necessarily the system
size
(i.e., largest coordinate - smallest coordinate).  You can do this with a
.pdb
file, I think on the CRYST line, if you prefer.

-Justin


Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 12:08 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water



Payman Pirzadeh wrote:

But, I am using a .pdb file as the input of the gromacs. Does the
preparation of pdb file differ from software to software?


It shouldn't, and I'm not 100% sure on how Gromacs handles system size

from
a 
.pdb file (I always use .gro).  What you can try to do is transform your
.pdb 
into .gro format with editconf, and read the last line of the .gro file.
That's 
any easy way to determine the size of the box Gromacs is finding.


-Justin


Payman

-Original Message-
From: gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org]

On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 11:42 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water



Payman Pirzadeh wrote:

Hello,
Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced

the

rvdw cutoff to 10A, but problem was still there.
Now I made my box bigger by using a visualization software. The new
dimensions are ~54*63*103.38(all in A). Again the same warning is given

to

me about increasing the box size or reduce the rvdw.


Well, Gromacs doesn't do anything in A, it's all nm, so be sure that
everything 
you're doing is consistent with Gromacs conventions.  There is no reason
that 
either of those boxe should be complaining about a 1.0-nm cutoff, so

there
has 
to be something that messed up along the way.


-Justin

Payman 


-Original Message-
From: gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org]

On Behalf Of Justin A. Lemkul
Sent: July 15, 2009 7:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water



Payman Pirzadeh wrote:

Hello,
I have an .pdb file from another simulation. I want to make the

appropriate

input files to run a simulations. I have used grompp to produce the

.tpr

file, but I get the usual ERROR:

 ERROR: The cut-off length is longer than half the shortest box vector

or

longer than the smallest box diagonal element. Increase the box size or
decrease rvdw.

I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but

still

the problem persists! Smaller rvdw is not good for my system. Any
suggestions?


Then you'll have to use a bigger box, most likely.  What is your

smallest
box 
vector?  That should indicate the limits of your cutoffs.


-Justin

Payman 


-Original Message-
From: gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org]

On Behalf Of David van der Spoel
Sent: July 15, 2009 12:23 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water

Payman Pirzadeh wrote:
Thanks Justin. 
Unfortunately, I realized that after I sent the e-mail. Anyways, I

started

running to models: SPCE and TIP4P to check the energies of these

systems

to

figure out where the problem with my own system (six-site model) could

be.

I

will keep you posted. But, I have a question about the compressibility
factor used in .mdp file. Does that(if it is not a correct value)

truly

affect the simulation when the reference pressure is set?

No, only the relaxation rate 

[gmx-users] Re: reliability of NOTES

2009-07-21 Thread Vitaly V. Chaban


 Hello,
 I am trying to prepare the input files for an MD run. After running grompp,
 I received the following note:

 NOTE 1 [file npt.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

 How reliable this note is?


It's true.


 And how can I implement V-rescale thermostat in y
 input file (I found nothing in the manual).


Substitute berendsen with V-rescale in the mdp file.


 Also, when I changed the thermostat to nose-hoover, it said that it can not
 be used with Berendsen barostat. Why?

 C'est la vie...


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===
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Re: [gmx-users] PDB and GRO files

2009-07-21 Thread Vitaly V. Chaban
Yeah, we are friendly. :)

Don't hesitate to ask if you experience future problems.

~ Vitaly


On Wed, Jul 22, 2009 at 1:55 AM, Jamie Seyed jamie.se...@gmail.com wrote:

 Thank you for your help and comments.
 -Jamie




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[gmx-users] Re: gmx-users Digest, Vol 63, Issue 110

2009-07-21 Thread Vitaly V. Chaban



 In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS
 is approximatedely twice slower than in a installation in an entire HD.

 If you need to install Linux in dual boot, maybe CentOS is a better choice.



If one believes you, it comes out that non-running windows interfere gromacs
run.


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===
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[gmx-users] How to get the rotational correlation time of the non-equilibrium simulation

2009-07-21 Thread Yanmei Song
Dear Users:

I am wondering how I can get rotation correlation time of non-equilibrium
simulation? is there any command letting me do that? Or I have to do it
manually?

My second question is : if Gromacs can calculate the standard error by using
the blocking average method and how?

Thanks for your help in advance!
-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

2009-07-21 Thread Alexandre Suman de Araujo

Obviously the HD space has nothing to do with GMX performance (unless it is
full, of course), but the use of Ubuntu precompiled packages can affect
drastically the GMX performance, especially if you are also using pre-compiled
MPI library package.

An important rule when you are interested in High Performance
Computing: Compile
ALL your softwares (the last REALLY stable version) using GOOD
compilers (GCC is
fine, but if you have access to Intel or Portland ones is better).

This rule is highly recommended ALSO to your linux kernel.

Never leave the important and easy work of compile your important
programs with
unknown people!

Cheers


--
**
Alexandre Suman de Araujo*
Faculdade de Ciências Farmacêuticas de Ribeirão Preto*
Universidade de São Paulo*
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com  *
CEP: 14040-903* Phone: +55 (16) 3602-4172*
Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222*
**



Quoting Justin A. Lemkul jalem...@vt.edu:



I don't see how hard disk space of the OS has anything to do with the
speed of Gromacs.  Are the machines you refer to identical in terms
of hardware (CPU, RAM, etc) as well as the compilers used to install
the software?

I have installed Gromacs under several different OS - Mac, Ubuntu
Linux, Yellowdog Linux, and Fedora Linux.  The only real speed
difference comes from the hardware.

-Justin

Laercio Pol Fachin wrote:

Hi!
 In a UBUNTU installation in dual boot (with Windows, in my case),
GROMACS is approximatedely twice slower than in a installation in an
entire HD.
 If you need to install Linux in dual boot, maybe CentOS is a better choice.
 Best regards,
Laércio Pol-Fachin

--- Em *ter, 21/7/09, gmx-users-requ...@gromacs.org
/gmx-users-requ...@gromacs.org/* escreveu:


   1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal)

Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST)
From: jagannath mondal jmondal2...@yahoo.co.in
http://br.mc515.mail.yahoo.com/mc/compose?to=jmondal2...@yahoo.co.in
Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU
To: gmx-users@gromacs.org
http://br.mc515.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org
Message-ID: 410193.9922...@web7906.mail.in.yahoo.com

http://br.mc515.mail.yahoo.com/mc/compose?to=410193.9922...@web7906.mail.in.yahoo.com
Content-Type: text/plain; charset=iso-8859-1

Hi,   I was planning to install one of the linux distributions :
CENTOS or UBUNTU in our xeon 8-core processor.  Can any one suggest
which one will be better for Gromacs as far as installation and
performance is concerned?ThanksJagannath



Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10
http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/ - Celebridades 
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--


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


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WEBMAIL - IFSC - Instituto de Física de São Carlos

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Re: [gmx-users] PDB and GRO files

2009-07-21 Thread Alexandre Suman de Araujo

Hi Jamie.

Another (free)options to generate the coordinate files (pdb or gro, they are
basically the same and can be converted into another using the trjconv tool)
are Molden and VMD.

With Molden you can build a molecule from scratch easily. I recommend it to
draw
small molecules like drugs.

VMD (version 1.8.7) has two tools that can be what you are looking for. With
Molefacture plugin you can draw small molecules and peptides. With Nanotube
Builder plugin you can easily build the CNTs you are interested. To construct
fullerenes I don't konw any VMD plugin, but probably somebody has already done
some plugin or script to generate this kind of molecules, try to search in
google by fullerenes and VMD

Cheers


--
**
Alexandre Suman de Araujo*
Faculdade de Ciências Farmacêuticas de Ribeirão Preto*
Universidade de São Paulo*
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com  *
CEP: 14040-903* Phone: +55 (16) 3602-4172*
Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222*
**


Quoting Jamie Seyed jamie.se...@gmail.com:


Hi Justin,

On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu wrote:




Jamie Seyed wrote:


Hi,
Thanks for your comments. But I do not know how to get (or make) the pdb
file if it is not made (let say for a new system). Are you using special
software to do that to make a pdb or gro file, before starting the
simulation?



That's going to depend entirely upon what that system is.  Building a
protein or peptide is not so trivial.  Building a small molecule is fairly
straightforward using programs like PRODRG (online) or xLeap (part of
AmberTools).

That said, if your goal is to simulate some arbitrary small molecules, the
previous advice of using pdb2gmx will not apply.  You will have to build the
topologies yourself.



Is the result of using these programs a pdb file or gro.. would you
please explain a little bit?
The systems that I want to simulate are fullerene and CNT. But before that I
will simulate a box of water, spce. In this case is it ok to use
spc216.pdb (??) or I should use the programs you mentioned?
Sorry for these simple questions..




Another thing: It is not possible for me to open some web-pages that users

are referring to (some of them are crucial to get the answer)!! Did
you face
with the same problem or there is new web-address for them??




If you cite some examples, maybe someone can point you in the right
direction. The Gromacs webpage is currently migrating to a new site; old
webpages can be accessed by appending old to the URL, i.e.
http://oldwww.gromacs.org is the old home page.



For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you
mentioned, but I can not open links on the page. All of them (check force
field for example) can not open with like this message Site settings could
not be loaded...
Is it the page I should use to get a pdb file for my system?? I really
appreciate if you let me know the exact web-address to use PRODRG or xLeap
(?).

Thanks a lot,
Jamie





-Justin

 Thanks for your help,

Jamie

On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli 
rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote:

   Hi,

   If I understood your question, do you want to know how can you start
   a simulation? So, if I'm correct I recommend this link
   http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In
   this link, there is flowsheet file which is the flowchart to Gromacs
   simulation.

   Answered your question a little more specific, although basically,
 after you get the pdb file, you need to run the pdb2gmx program. The
   link above explains more details about it.

   I hope that this email helped you.

   Cheers,
   --
   Rodrigo Antonio Faccioli
   Ph.D Student in Electrical Engineering
   University of Sao Paulo - USP
   Engineering School of Sao Carlos - EESC
   Department of Electrical Engineering - SEL
   Intelligent System in Structure Bioinformatics
   http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/
   Phone: 55 (16) 3373-9366 Ext 229
   Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


   On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com
   mailto:jamie.se...@gmail.com wrote:

   Hi,

   I have a basic question (since I am new). For starting any
   simulation as I understand, is to find a .pdb or .gor file. Pdb
   files for proteins are already there, but for a new system what
   is the easiest and quick way to find it (which software etc).
   What about .gro files?


   I appreciate your help for solve my basic problems.

   Thanks, 

[gmx-users] genconf

2009-07-21 Thread Payman Pirzadeh
OK! Thanks for the tips on thermostat.

I multiplied my .gro file by using the command genconf. My original box
has non-zero charge, but the generated bigger box has some charges:

 

NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04

 

Then, during minimization, the system experiences a large positive potential
and infinite force. Is there a technicality in using genconf that I am
missing? Doesn't it read the dimensions of the box from .gro file to make
sure no particles are overlapping with the original box? Or no particle is
coming from the new one in the old one?

 

Payman

 

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Vitaly V. Chaban
Sent: July 21, 2009 4:53 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: reliability of NOTES

 


Hello,
I am trying to prepare the input files for an MD run. After running grompp,
I received the following note:

NOTE 1 [file npt.mdp, line unknown]:
 The Berendsen thermostat does not generate the correct kinetic energy
 distribution. You might want to consider using the V-rescale thermostat.

How reliable this note is? 


It's true.
 

And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).


Substitute berendsen with V-rescale in the mdp file. 


Also, when I changed the thermostat to nose-hoover, it said that it can not
be used with Berendsen barostat. Why?

C'est la vie...


-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698 
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===

___
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] genconf

2009-07-21 Thread Justin A. Lemkul



Payman Pirzadeh wrote:

OK! Thanks for the tips on thermostat.

I multiplied my .gro file by using the command “genconf”. My original 
box has non-zero charge, but the generated bigger box has some charges:


 


Define non-zero.  Is it at least an integer?  Should your system bet net 
neutral at this stage in your system preparation?


-Justin



NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04

 

Then, during minimization, the system experiences a large positive 
potential and infinite force. Is there a technicality in using “genconf” 
that I am missing? Doesn’t it read the dimensions of the box from .gro 
file to make sure no particles are overlapping with the original box? Or 
no particle is coming from the new one in the old one?


 


Payman

 

*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban

*Sent:* July 21, 2009 4:53 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] Re: reliability of NOTES

 



Hello,
I am trying to prepare the input files for an MD run. After running
grompp,
I received the following note:

NOTE 1 [file npt.mdp, line unknown]:
 The Berendsen thermostat does not generate the correct kinetic energy
 distribution. You might want to consider using the V-rescale
thermostat.

How reliable this note is?


It's true.
 


And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).


Substitute berendsen with V-rescale in the mdp file.


Also, when I changed the thermostat to nose-hoover, it said that it
can not
be used with Berendsen barostat. Why?

C'est la vie...


--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua 
mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com 
mailto:vvcha...@gmail.com

skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===




___
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--


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


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RE: [gmx-users] genconf

2009-07-21 Thread Payman Pirzadeh
In my previous e-mail, I posted the amount of charge given by GROMACS:

 NOTE 2 [file sixsitemodel.top, line 8]:
 
   System has non-zero total charge: -1.220703e-04

Also, I run the system without multiplication, and it runs fine without any
notes on the presence of a net charge!!! But, as soon as it is multiplied,
then it gives notes of net charge!

Payman







-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:
 OK! Thanks for the tips on thermostat.
 
 I multiplied my .gro file by using the command genconf. My original 
 box has non-zero charge, but the generated bigger box has some charges:
 
  

Define non-zero.  Is it at least an integer?  Should your system bet net 
neutral at this stage in your system preparation?

-Justin

 
 NOTE 2 [file sixsitemodel.top, line 8]:
 
   System has non-zero total charge: -1.220703e-04
 
  
 
 Then, during minimization, the system experiences a large positive 
 potential and infinite force. Is there a technicality in using genconf 
 that I am missing? Doesn't it read the dimensions of the box from .gro 
 file to make sure no particles are overlapping with the original box? Or 
 no particle is coming from the new one in the old one?
 
  
 
 Payman
 
  
 
 *From:* gmx-users-boun...@gromacs.org 
 [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban
 *Sent:* July 21, 2009 4:53 PM
 *To:* gmx-users@gromacs.org
 *Subject:* [gmx-users] Re: reliability of NOTES
 
  
 
 
 Hello,
 I am trying to prepare the input files for an MD run. After running
 grompp,
 I received the following note:
 
 NOTE 1 [file npt.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale
 thermostat.
 
 How reliable this note is?
 
 
 It's true.
  
 
 And how can I implement V-rescale thermostat in y
 input file (I found nothing in the manual).
 
 
 Substitute berendsen with V-rescale in the mdp file.
 
 
 Also, when I changed the thermostat to nose-hoover, it said that it
 can not
 be used with Berendsen barostat. Why?
 
 C'est la vie...
 
 
 -- 
 Vitaly V. Chaban, Ph.D. (ABD)
 School of Chemistry
 V.N. Karazin Kharkiv National University
 Svoboda sq.,4, Kharkiv 61077, Ukraine
 email: cha...@univer.kharkov.ua 
 mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com 
 mailto:vvcha...@gmail.com
 skype: vvchaban, mob.: +38-097-8259698
 http://www-rmn.univer.kharkov.ua/chaban.html
 ===
 !!! Looking for a postdoctoral position !!!
 ===
 
 
 
 
 ___
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the 
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 


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


___
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Re: [gmx-users] genconf

2009-07-21 Thread Justin A. Lemkul



Payman Pirzadeh wrote:

In my previous e-mail, I posted the amount of charge given by GROMACS:


NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04


Also, I run the system without multiplication, and it runs fine without any
notes on the presence of a net charge!!! But, as soon as it is multiplied,
then it gives notes of net charge!



Then I'm more confused (and hence why I asked the first time).  You said your 
original system had a non-zero charge.  Now you say that there were no notes 
about net charge, so the original system was uncharged.


Depending on the size of your system, small rounding errors can accumulate and 
cause tiny fractional charges.  I don't know if this is problematic or not (in 
terms of the system charge that mdrun finds), but it could be why you are seeing 
this note.


-Justin


Payman







-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:

OK! Thanks for the tips on thermostat.

I multiplied my .gro file by using the command genconf. My original 
box has non-zero charge, but the generated bigger box has some charges:


 


Define non-zero.  Is it at least an integer?  Should your system bet net 
neutral at this stage in your system preparation?


-Justin


NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04

 

Then, during minimization, the system experiences a large positive 
potential and infinite force. Is there a technicality in using genconf 
that I am missing? Doesn't it read the dimensions of the box from .gro 
file to make sure no particles are overlapping with the original box? Or 
no particle is coming from the new one in the old one?


 


Payman

 

*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban

*Sent:* July 21, 2009 4:53 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] Re: reliability of NOTES

 



Hello,
I am trying to prepare the input files for an MD run. After running
grompp,
I received the following note:

NOTE 1 [file npt.mdp, line unknown]:
 The Berendsen thermostat does not generate the correct kinetic energy
 distribution. You might want to consider using the V-rescale
thermostat.

How reliable this note is?


It's true.
 


And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).


Substitute berendsen with V-rescale in the mdp file.


Also, when I changed the thermostat to nose-hoover, it said that it
can not
be used with Berendsen barostat. Why?

C'est la vie...


--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua 
mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com 
mailto:vvcha...@gmail.com

skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===




___
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
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--


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


___
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RE: [gmx-users] genconf

2009-07-21 Thread Payman Pirzadeh
I am so sorry! I had sth in mind and I wrote sth else!!!
My original box has zero charges and GROMACS shows no notes on this.
As soon as the box is multiplies, then the note regarding the net charge
shows up and causes the simulation to crash.

Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:25 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:
 In my previous e-mail, I posted the amount of charge given by GROMACS:
 
 NOTE 2 [file sixsitemodel.top, line 8]:

   System has non-zero total charge: -1.220703e-04
 
 Also, I run the system without multiplication, and it runs fine without
any
 notes on the presence of a net charge!!! But, as soon as it is multiplied,
 then it gives notes of net charge!
 

Then I'm more confused (and hence why I asked the first time).  You said
your 
original system had a non-zero charge.  Now you say that there were no notes

about net charge, so the original system was uncharged.

Depending on the size of your system, small rounding errors can accumulate
and 
cause tiny fractional charges.  I don't know if this is problematic or not
(in 
terms of the system charge that mdrun finds), but it could be why you are
seeing 
this note.

-Justin

 Payman
 
 
 
 
 
 
 
 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Justin A. Lemkul
 Sent: July 21, 2009 6:13 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] genconf
 
 
 
 Payman Pirzadeh wrote:
 OK! Thanks for the tips on thermostat.

 I multiplied my .gro file by using the command genconf. My original 
 box has non-zero charge, but the generated bigger box has some charges:

  
 
 Define non-zero.  Is it at least an integer?  Should your system bet net

 neutral at this stage in your system preparation?
 
 -Justin
 
 NOTE 2 [file sixsitemodel.top, line 8]:

   System has non-zero total charge: -1.220703e-04

  

 Then, during minimization, the system experiences a large positive 
 potential and infinite force. Is there a technicality in using genconf 
 that I am missing? Doesn't it read the dimensions of the box from .gro 
 file to make sure no particles are overlapping with the original box? Or 
 no particle is coming from the new one in the old one?

  

 Payman

  

 *From:* gmx-users-boun...@gromacs.org 
 [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban
 *Sent:* July 21, 2009 4:53 PM
 *To:* gmx-users@gromacs.org
 *Subject:* [gmx-users] Re: reliability of NOTES

  


 Hello,
 I am trying to prepare the input files for an MD run. After running
 grompp,
 I received the following note:

 NOTE 1 [file npt.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic
energy
  distribution. You might want to consider using the V-rescale
 thermostat.

 How reliable this note is?


 It's true.
  

 And how can I implement V-rescale thermostat in y
 input file (I found nothing in the manual).


 Substitute berendsen with V-rescale in the mdp file.


 Also, when I changed the thermostat to nose-hoover, it said that it
 can not
 be used with Berendsen barostat. Why?

 C'est la vie...


 -- 
 Vitaly V. Chaban, Ph.D. (ABD)
 School of Chemistry
 V.N. Karazin Kharkiv National University
 Svoboda sq.,4, Kharkiv 61077, Ukraine
 email: cha...@univer.kharkov.ua 
 mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com 
 mailto:vvcha...@gmail.com
 skype: vvchaban, mob.: +38-097-8259698
 http://www-rmn.univer.kharkov.ua/chaban.html
 ===
 !!! Looking for a postdoctoral position !!!
 ===


 

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

-- 


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


___
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Re: [gmx-users] genconf

2009-07-21 Thread Justin A. Lemkul



Payman Pirzadeh wrote:

I am so sorry! I had sth in mind and I wrote sth else!!!
My original box has zero charges and GROMACS shows no notes on this.
As soon as the box is multiplies, then the note regarding the net charge
shows up and causes the simulation to crash.



Well, then, like I said, this is probably an accumulation of rounding errors. 
It can probably be ignored.  The reason for the crash is more likely some kind 
of atomic overlap generated by the use of genconf.


-Justin


Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:25 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:

In my previous e-mail, I posted the amount of charge given by GROMACS:


NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04

Also, I run the system without multiplication, and it runs fine without

any

notes on the presence of a net charge!!! But, as soon as it is multiplied,
then it gives notes of net charge!



Then I'm more confused (and hence why I asked the first time).  You said
your 
original system had a non-zero charge.  Now you say that there were no notes


about net charge, so the original system was uncharged.

Depending on the size of your system, small rounding errors can accumulate
and 
cause tiny fractional charges.  I don't know if this is problematic or not
(in 
terms of the system charge that mdrun finds), but it could be why you are
seeing 
this note.


-Justin


Payman







-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:

OK! Thanks for the tips on thermostat.

I multiplied my .gro file by using the command genconf. My original 
box has non-zero charge, but the generated bigger box has some charges:


 

Define non-zero.  Is it at least an integer?  Should your system bet net



neutral at this stage in your system preparation?

-Justin


NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04

 

Then, during minimization, the system experiences a large positive 
potential and infinite force. Is there a technicality in using genconf 
that I am missing? Doesn't it read the dimensions of the box from .gro 
file to make sure no particles are overlapping with the original box? Or 
no particle is coming from the new one in the old one?


 


Payman

 

*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban

*Sent:* July 21, 2009 4:53 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] Re: reliability of NOTES

 



Hello,
I am trying to prepare the input files for an MD run. After running
grompp,
I received the following note:

NOTE 1 [file npt.mdp, line unknown]:
 The Berendsen thermostat does not generate the correct kinetic

energy

 distribution. You might want to consider using the V-rescale
thermostat.

How reliable this note is?


It's true.
 


And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).


Substitute berendsen with V-rescale in the mdp file.


Also, when I changed the thermostat to nose-hoover, it said that it
can not
be used with Berendsen barostat. Why?

C'est la vie...


--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua 
mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com 
mailto:vvcha...@gmail.com

skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===




___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before

posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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




--


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


___
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please 

RE: [gmx-users] genconf

2009-07-21 Thread Payman Pirzadeh
Yes and no!
Sometimes there is an overlap, but sometimes I could find nothing! In the
simplest case, how can we avoid overlaps in a way that the crystal structure
is maintained under pbc?
Can the option -dist help here?

Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:
 I am so sorry! I had sth in mind and I wrote sth else!!!
 My original box has zero charges and GROMACS shows no notes on this.
 As soon as the box is multiplies, then the note regarding the net charge
 shows up and causes the simulation to crash.
 

Well, then, like I said, this is probably an accumulation of rounding
errors. 
It can probably be ignored.  The reason for the crash is more likely some
kind 
of atomic overlap generated by the use of genconf.

-Justin

 Payman
 
 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Justin A. Lemkul
 Sent: July 21, 2009 6:25 PM
 To: Gromacs Users' List
 Subject: Re: [gmx-users] genconf
 
 
 
 Payman Pirzadeh wrote:
 In my previous e-mail, I posted the amount of charge given by GROMACS:

 NOTE 2 [file sixsitemodel.top, line 8]:

   System has non-zero total charge: -1.220703e-04
 Also, I run the system without multiplication, and it runs fine without
 any
 notes on the presence of a net charge!!! But, as soon as it is
multiplied,
 then it gives notes of net charge!

 
 Then I'm more confused (and hence why I asked the first time).  You said
 your 
 original system had a non-zero charge.  Now you say that there were no
notes
 
 about net charge, so the original system was uncharged.
 
 Depending on the size of your system, small rounding errors can accumulate
 and 
 cause tiny fractional charges.  I don't know if this is problematic or not
 (in 
 terms of the system charge that mdrun finds), but it could be why you are
 seeing 
 this note.
 
 -Justin
 
 Payman







 -Original Message-
 From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Justin A. Lemkul
 Sent: July 21, 2009 6:13 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] genconf



 Payman Pirzadeh wrote:
 OK! Thanks for the tips on thermostat.

 I multiplied my .gro file by using the command genconf. My original 
 box has non-zero charge, but the generated bigger box has some charges:

  
 Define non-zero.  Is it at least an integer?  Should your system bet
net
 
 neutral at this stage in your system preparation?

 -Justin

 NOTE 2 [file sixsitemodel.top, line 8]:

   System has non-zero total charge: -1.220703e-04

  

 Then, during minimization, the system experiences a large positive 
 potential and infinite force. Is there a technicality in using genconf

 that I am missing? Doesn't it read the dimensions of the box from .gro 
 file to make sure no particles are overlapping with the original box? Or

 no particle is coming from the new one in the old one?

  

 Payman

  

 *From:* gmx-users-boun...@gromacs.org 
 [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban
 *Sent:* July 21, 2009 4:53 PM
 *To:* gmx-users@gromacs.org
 *Subject:* [gmx-users] Re: reliability of NOTES

  


 Hello,
 I am trying to prepare the input files for an MD run. After running
 grompp,
 I received the following note:

 NOTE 1 [file npt.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic
 energy
  distribution. You might want to consider using the V-rescale
 thermostat.

 How reliable this note is?


 It's true.
  

 And how can I implement V-rescale thermostat in y
 input file (I found nothing in the manual).


 Substitute berendsen with V-rescale in the mdp file.


 Also, when I changed the thermostat to nose-hoover, it said that it
 can not
 be used with Berendsen barostat. Why?

 C'est la vie...


 -- 
 Vitaly V. Chaban, Ph.D. (ABD)
 School of Chemistry
 V.N. Karazin Kharkiv National University
 Svoboda sq.,4, Kharkiv 61077, Ukraine
 email: cha...@univer.kharkov.ua 
 mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com 
 mailto:vvcha...@gmail.com
 skype: vvchaban, mob.: +38-097-8259698
 http://www-rmn.univer.kharkov.ua/chaban.html
 ===
 !!! Looking for a postdoctoral position !!!
 ===


 

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Re: [gmx-users] genconf

2009-07-21 Thread Justin A. Lemkul



Payman Pirzadeh wrote:

Yes and no!
Sometimes there is an overlap, but sometimes I could find nothing! In the
simplest case, how can we avoid overlaps in a way that the crystal structure
is maintained under pbc?
Can the option -dist help here?



Maybe.  I've never had to use it.  I've replicated a few systems using genconf 
-nbox (water and lipids), but I've never encountered any problems.  In theory, 
PBC should be maintained since all genconf is doing is translating your system 
by a certain factor according to box dimensions.


-Justin


Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:

I am so sorry! I had sth in mind and I wrote sth else!!!
My original box has zero charges and GROMACS shows no notes on this.
As soon as the box is multiplies, then the note regarding the net charge
shows up and causes the simulation to crash.



Well, then, like I said, this is probably an accumulation of rounding
errors. 
It can probably be ignored.  The reason for the crash is more likely some
kind 
of atomic overlap generated by the use of genconf.


-Justin


Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:25 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:

In my previous e-mail, I posted the amount of charge given by GROMACS:


NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04

Also, I run the system without multiplication, and it runs fine without

any

notes on the presence of a net charge!!! But, as soon as it is

multiplied,

then it gives notes of net charge!


Then I'm more confused (and hence why I asked the first time).  You said
your 
original system had a non-zero charge.  Now you say that there were no

notes

about net charge, so the original system was uncharged.

Depending on the size of your system, small rounding errors can accumulate
and 
cause tiny fractional charges.  I don't know if this is problematic or not
(in 
terms of the system charge that mdrun finds), but it could be why you are
seeing 
this note.


-Justin


Payman







-Original Message-
From: gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org]

On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf



Payman Pirzadeh wrote:

OK! Thanks for the tips on thermostat.

I multiplied my .gro file by using the command genconf. My original 
box has non-zero charge, but the generated bigger box has some charges:


 

Define non-zero.  Is it at least an integer?  Should your system bet

net

neutral at this stage in your system preparation?

-Justin


NOTE 2 [file sixsitemodel.top, line 8]:

  System has non-zero total charge: -1.220703e-04

 

Then, during minimization, the system experiences a large positive 
potential and infinite force. Is there a technicality in using genconf


that I am missing? Doesn't it read the dimensions of the box from .gro 
file to make sure no particles are overlapping with the original box? Or



no particle is coming from the new one in the old one?

 


Payman

 

*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban

*Sent:* July 21, 2009 4:53 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] Re: reliability of NOTES

 



Hello,
I am trying to prepare the input files for an MD run. After running
grompp,
I received the following note:

NOTE 1 [file npt.mdp, line unknown]:
 The Berendsen thermostat does not generate the correct kinetic

energy

 distribution. You might want to consider using the V-rescale
thermostat.

How reliable this note is?


It's true.
 


And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).


Substitute berendsen with V-rescale in the mdp file.


Also, when I changed the thermostat to nose-hoover, it said that it
can not
be used with Berendsen barostat. Why?

C'est la vie...


--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua 
mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com 
mailto:vvcha...@gmail.com

skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!!! Looking for a postdoctoral position !!!
===




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Please 

Re: [gmx-users] genconf

2009-07-21 Thread Mark Abraham

Payman Pirzadeh wrote:

Yes and no!
Sometimes there is an overlap, but sometimes I could find nothing! In the
simplest case, how can we avoid overlaps in a way that the crystal structure
is maintained under pbc?
Can the option -dist help here?


Replicating a box that was not designed for periodicity will always have 
this problem. Whether the box is too small or two large, there will 
either be steric clashes, or vacuums that will need filling. The general 
solution is to equilibrate your box under PBC prior to replication. Now 
the box size and the atomic spacings will be plausible, and the 
replication will not of necessity introduce artifacts.


Mark
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