[gmx-users] Re: Hi, May I ask you a question about the free energy calculation tutorial?

2011-12-31 Thread Justin A. Lemkul 



yywang wrote:





At 2011-12-31 04:42:12,"Justin A. Lemkul" mailto:jalem...@vt.edu>> wrote:



yywang wrote:

 Dear Justin Lemkul,
 I find a tutorial about the free energy calculation by g_bar in 
Gromacs.  (  
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html)
 I have a question when I use this tutorail. That is I cannot 
use muti-cores in cluster. When I try to use mpirun -np 2 or more, an 
error occured (There is no domain decomposition for 2 nodes that is 
compatible with the given box and a minimum cell size of 6.46036 nm 228 
Change the number of nodes or mdrun option -rdd)
 But when i turn the mpirun off ,eg mpirun -np 1 mdrun -nt 2 ,  
everything is OK.


I do not know the basis for why MPI vs. threading would lead to different 
behavior.  I use threading by default on a dual-core machine since the tutorial 
system is small.


 Since my model is a little big, the speed of use 1 core and 2 
threads is too slow, is there any method to change this situation, or do 
you know any paramater that control this?



Are we still talking about the tutorial system?  It is quite small.  The DD cell 
size you've posted above seems to be from a different system.  I cannot offer 
personalized advice for individual systems that I've not worked with.  The best 
information is online:


 
>http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm


-Justin


Sorry I haven`t express my idea well. I use your tutorial to calculation the 
free energy of a big system of my own,which is a big system of 24, atoms, 
so this speed is too slow for me and I am trying to run it on big clusters.
Thanks any way.


The simple decoupling procedure in the tutorial is likely not suitable for very 
large systems; by changing many degrees of freedom simultaneously in this way, 
convergence is exceptionally hard to achieve.  I suspect the very large size of 
the DD cells is related to the couple-intramol parameter, which for large 
systems results in explicit pair interactions, which occur within the same DD 
cell.  Refer to the manual for a more suitable setting and the reasons why you 
might want to adjust certain parameters.  Good luck.


-Justin

--


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


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Re: [gmx-users] Re: hi Gromacs error

2011-07-28 Thread Justin A. Lemkul 


Sorry all, disregard this.  It was intended to be sent to someone else.  Stupid 
email autocompletion...


-Justin

Justin A. Lemkul wrote:



Please add the attached file to the gromos43a1p.ff directory.

-Justin

kalai arasan wrote:

justin,
I am sorry to disturb you again, i just like to convey the 
information i got another error while using version 4.5.3


--- 


Program pdb2gmx, VERSION 4.5.3 Source code file: resall.c, line: 581

Fatal error:
Residue 'HISE' not found in residue topology database
--- 



I searched in many links but i am not able to solve it.

On Fri, Jul 29, 2011 at 12:34 AM, Justin A. Lemkul > wrote:



I believe this was a bug in Gromacs that was fixed many years ago.
 Version 3.3 is antiquated and severely outdated.  I would advise
you to upgrade to version 4.5.4 and try again with the attached
files, which have been reformatted to be compatible with the newer
version.  Beyond this, I cannot suggest any other remedy.

-Justin

kalai arasan wrote:

Justin,

  Thank you for the files, but still i am facing
problem. Now it showing

--__--__- 


Program pdb2gmx, VERSION 3.3
Source code file: resall.c, line: 331

Fatal error:
in .rtp file at line:


--__--__--__- 


Please help me out to solve the problem.
with regards
kalai

On Wed, Jul 27, 2011 at 4:49 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   The files are attached.  Please read the README carefully.

   -Justin


   kalai arasan wrote:

   Justin,
   I am kalai from India, working in gromacs.
  
http://oldwww.gromacs.org/pipermail/gmx-users/2008-January/031964.html 


 

  
>

   I am facing the error while running pdb2gmx command, i
saw from
   above link that you can solve this problem, please help
me out.
   Below i mention the error.

  
--__--__-- 


   Program pdb2gmx, VERSION 3.3
   Source code file: h_db.c, line: 85

   Fatal error:
   wrong format in input file ffG43a1p.hdb on line
   2 7  OW
  
--__--__--____-- 



   -- P.Kalaiarasan
   National Centre of Applied Human Genetics
   School of Life Sciences
   JNU
   New Delhi
   India


   -- ====

   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

   >

   ====




-- P.Kalaiarasan
National Centre of Applied Human Genetics
School of Life Sciences
JNU
New Delhi
India


-- ==__==

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


==__==




--
P.Kalaiarasan
National Centre of Applied Human Genetics
School of Life Sciences
JNU
New Delhi
India





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalem

[gmx-users] Re: hi Gromacs error

2011-07-28 Thread Justin A. Lemkul 



Please add the attached file to the gromos43a1p.ff directory.

-Justin

kalai arasan wrote:

justin,
I am sorry to disturb you again, i just like to convey the 
information i got another error while using version 4.5.3 



---
Program pdb2gmx, VERSION 4.5.3 
Source code file: resall.c, line: 581


Fatal error:
Residue 'HISE' not found in residue topology database
---

I searched in many links but i am not able to solve it.

On Fri, Jul 29, 2011 at 12:34 AM, Justin A. Lemkul > wrote:



I believe this was a bug in Gromacs that was fixed many years ago.
 Version 3.3 is antiquated and severely outdated.  I would advise
you to upgrade to version 4.5.4 and try again with the attached
files, which have been reformatted to be compatible with the newer
version.  Beyond this, I cannot suggest any other remedy.

-Justin

kalai arasan wrote:

Justin,

  Thank you for the files, but still i am facing
problem. Now it showing

--__--__-
Program pdb2gmx, VERSION 3.3
Source code file: resall.c, line: 331

Fatal error:
in .rtp file at line:


--__--__--__-
Please help me out to solve the problem.
with regards
kalai

On Wed, Jul 27, 2011 at 4:49 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   The files are attached.  Please read the README carefully.

   -Justin


   kalai arasan wrote:

   Justin,
   I am kalai from India, working in gromacs.
 
 http://oldwww.gromacs.org/pipermail/gmx-users/2008-January/031964.html



 
 >
   I am facing the error while running pdb2gmx command, i
saw from
   above link that you can solve this problem, please help
me out.
   Below i mention the error.

 
 --__--__--

   Program pdb2gmx, VERSION 3.3
   Source code file: h_db.c, line: 85

   Fatal error:
   wrong format in input file ffG43a1p.hdb on line
   2 7  OW
 
 --__--__--____--


   -- P.Kalaiarasan
   National Centre of Applied Human Genetics
   School of Life Sciences
   JNU
   New Delhi
   India


   -- ====

   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

   >

   ====




-- 
P.Kalaiarasan

National Centre of Applied Human Genetics
School of Life Sciences
JNU
New Delhi
India


-- 
==__==


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


==__==




--
P.Kalaiarasan
National Centre of Applied Human Genetics
School of Life Sciences
JNU
New Delhi
India



--


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 list

Re: [gmx-users] Re: hi questions about installing GROMACS

2009-09-04 Thread Amit Choubey 
hi,
thank you for extending the help but luckily i have figured out what was
going wrong. I have been able to install the package.

Thank you,
Amit

On Fri, Sep 4, 2009 at 1:30 PM, Vitaly V. Chaban  wrote:

> I am trying to install GROMACS (version 4.0) on my local machine. I tried
>> to
>> follow the supplied simple instruction in the INSTALL file. The
>> ./configure
>> step works but the "make" command doesnt work. My bash prints out  "make:
>> *** No targets specified and no makefile found.  Stop."
>>
>> What should i do for this? Should i save the GROMACS Directory somewhere
>> else?
>>
>>
> Hi,
>
> What does your configure script finish with?
>
>
> --
> 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, cell.: +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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[gmx-users] Re: hi questions about installing GROMACS

2009-09-04 Thread Vitaly V. Chaban 
>
> I am trying to install GROMACS (version 4.0) on my local machine. I tried
> to
> follow the supplied simple instruction in the INSTALL file. The ./configure
> step works but the "make" command doesnt work. My bash prints out  "make:
> *** No targets specified and no makefile found.  Stop."
>
> What should i do for this? Should i save the GROMACS Directory somewhere
> else?
>
>
Hi,

What does your configure script finish with?


-- 
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, cell.: +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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[gmx-users] Re: Hi

2008-03-25 Thread Justin A. Lemkul 

Please keep correspondence on the gmx-users listserv, so that an archived copy
will be preserved for others to benefit from later.  See my replies below.

Quoting sudheer babu <[EMAIL PROTECTED]>:

> Hi Mr. Justin,
> Sorry for the posting my question to your personal mail,
> You made me clear so many doubts in gromacs , Thanks for that. But I have
> one doubt since one week trying get answer by different ways, but I didn't
> find, that is FF for protein in POPC. you replied me that read literature I
> read it. I found that using united atom FF( Berger) for lipid and all atom
> FF(OPLS) for protein, in case of membrane protein simulation,i tried to use
> in this way but it showing error, when I do minimisation
> I mentioned  FF in .top in this way,

Well, what is the error?  It is of no use to say that something didn't work. 
What were you doing?  What was the *exact* command you issued?  What was the
*exact* error message?

>
> Include forcefield parameters
> #include "ffoplsaa.itp"   - for protein
> #include "ffgmx.itp-  for lipid
> #include "lipid.itp"
> #include "popc.itp"

Right; this is a problem.  Inclusion of both ffoplsaa.itp and ffgmx.itp will
probably cause the two to fight.  If you look through the list archives
thoroughly, you will find an excellent procedure written by Chris Neale related
to exactly how to do this.  You may also want to refer to Chapter 5 of the
manual for general information on topologies.

> Pls give me detail explanation  and suggest, normally which FFs use when
> protein inserted into POPC

Refer to the literature.  I have seen papers that have used Gromos96 and OPLS-AA
for membrane protein simulations.  The choice is up to you, based on what you
find and what you believe to be most applicable to your system.

-Justin

> Thanks in advance.
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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