date:20111130

Hey :)

I think I recall there was a way to suppress writing step*.pdb files,
but I couldn't find it. Anyone know from the top of his/her head?
Otherwise I'll go and check the source...
Oh, trust me... I know what I'm doing ;) Even though it's insane... :D

Groetjes,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] modify the gromacs4.5.5 code: using cout

2011-11-30 Thread 杜波

dear teacher,

i want to modify the gromacs4.5.5 code ,can i use function "cout" which is
introuduce in c++.

i add the code
#include 
#include 
at the head of the md.c

but when i make , there is a error "
md.c:103:20: error: iostream: No such file or directory"

thanks
regards,
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303 ; +8613820062885
E-mail: 2008d...@gmail.com ; dubo2...@tju.edu.cn
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] modify the gromacs4.5.5 code: using cout

2011-11-30 Thread Carsten Kutzner

Use fprintf(stdout, "…");

Carsten


On Nov 30, 2011, at 12:27 PM, 杜波 wrote:

> dear teacher,
> 
> i want to modify the gromacs4.5.5 code ,can i use function "cout" which is 
> introuduce in c++.
> 
> i add the code 
>   #include 
>   #include 
> at the head of the md.c 
> 
> but when i make , there is a error "
> md.c:103:20: error: iostream: No such file or directory"
> 
> thanks 
> regards,
> Bo Du
> Department of Polymer Science and Engineering,
> School of Chemical Engineering and technology,
> Tianjin University, Weijin Road 92, Nankai District 300072,
> Tianjin City P. R. China
> Tel/Fax: +86-22-27404303 ; +8613820062885
> E-mail: 2008d...@gmail.com ; dubo2...@tju.edu.cn
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

Re: [gmx-users] Suppress writing step*.pdb files

2011-11-30 Thread Mark Abraham


On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote:

Hey :)

I think I recall there was a way to suppress writing step*.pdb files,
but I couldn't find it. Anyone know from the top of his/her head?
Otherwise I'll go and check the source...
Oh, trust me... I know what I'm doing ;) Even though it's insane... :D



From src/mdlib/constr.c:

constr->maxwarn = 999;
env = getenv("GMX_MAXCONSTRWARN");
if (env)
{
constr->maxwarn = 0;
sscanf(env,"%d",&constr->maxwarn);
if (fplog)
{
fprintf(fplog,
"Setting the maximum number of constraint warnings 
to %d\n",

constr->maxwarn);
}
if (MASTER(cr))
{
fprintf(stderr,
"Setting the maximum number of constraint warnings 
to %d\n",

constr->maxwarn);
}
}
if (constr->maxwarn < 0 && fplog)
{
fprintf(fplog,"maxwarn < 0, will not stop on constraint errors\n");
}

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Suppress writing step*.pdb files




Mark Abraham wrote:

On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote:

Hey :)

I think I recall there was a way to suppress writing step*.pdb files,
but I couldn't find it. Anyone know from the top of his/her head?
Otherwise I'll go and check the source...
Oh, trust me... I know what I'm doing ;) Even though it's insane... :D



 From src/mdlib/constr.c:

constr->maxwarn = 999;
env = getenv("GMX_MAXCONSTRWARN");
if (env)
{
constr->maxwarn = 0;
sscanf(env,"%d",&constr->maxwarn);
if (fplog)
{
fprintf(fplog,
"Setting the maximum number of constraint warnings 
to %d\n",

constr->maxwarn);
}
if (MASTER(cr))
{
fprintf(stderr,
"Setting the maximum number of constraint warnings 
to %d\n",

constr->maxwarn);
}
}
if (constr->maxwarn < 0 && fplog)
{
fprintf(fplog,"maxwarn < 0, will not stop on constraint errors\n");
}



According to manual Appendix A.4, the GMX_SUPPRESS_DUMP variable should also 
work here.


-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Suppress writing step*.pdb files

Thanks guys! I see I'm using an outdated manual...

Tsjerk

On Wed, Nov 30, 2011 at 1:28 PM, Justin A. Lemkul  wrote:
>
>
> Mark Abraham wrote:
>>
>> On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote:
>>>
>>> Hey :)
>>>
>>> I think I recall there was a way to suppress writing step*.pdb files,
>>> but I couldn't find it. Anyone know from the top of his/her head?
>>> Otherwise I'll go and check the source...
>>> Oh, trust me... I know what I'm doing ;) Even though it's insane... :D
>>>
>>
>>  From src/mdlib/constr.c:
>>
>>    constr->maxwarn = 999;
>>    env = getenv("GMX_MAXCONSTRWARN");
>>    if (env)
>>    {
>>        constr->maxwarn = 0;
>>        sscanf(env,"%d",&constr->maxwarn);
>>        if (fplog)
>>        {
>>            fprintf(fplog,
>>                    "Setting the maximum number of constraint warnings to
>> %d\n",
>>                    constr->maxwarn);
>>        }
>>        if (MASTER(cr))
>>        {
>>            fprintf(stderr,
>>                    "Setting the maximum number of constraint warnings to
>> %d\n",
>>                    constr->maxwarn);
>>        }
>>    }
>>    if (constr->maxwarn < 0 && fplog)
>>    {
>>        fprintf(fplog,"maxwarn < 0, will not stop on constraint errors\n");
>>    }
>>
>
> According to manual Appendix A.4, the GMX_SUPPRESS_DUMP variable should also
> work here.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Unit of r in radial distribution function

2011-11-30 Thread bipin singh

Hello,

Please let me know what is the unit of r (nm or A) in the radial
distribution function
output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units.

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

Re: [gmx-users] Unit of r in radial distribution function




bipin singh wrote:

Hello,

Please let me know what is the unit of r (nm or A) in the radial
distribution function
output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units.



Units used by all programs are discussed in Chapter 2 of the manual.

-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Unit of r in radial distribution function

Hi Bipin,

Gromacs uses nm.

Cheers,

Tsjerk

On Wed, Nov 30, 2011 at 3:32 PM, bipin singh  wrote:
> Hello,
>
> Please let me know what is the unit of r (nm or A) in the radial
> distribution function
> output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units.
>
> --
> ---
> Regards,
> Bipin Singh
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_select

2011-11-30 Thread mohammad agha

Dear Prof.

I have a system consists of 10 micelle after production simulation. How can I 
select a micelle with 92 monomer?
I know that I should use from g_select, but I don't know which argument is 
proper for me. I also checked -select help in g_select program.
Please help me.

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

Re: [gmx-users] g_select




mohammad agha wrote:

Dear Prof.

I have a system consists of 10 micelle after production simulation. How 
can I select a micelle with 92 monomer?
I know that I should use from g_select, but I don't know which argument 
is proper for me. I also checked -select help in g_select program.

Please help me.



If you just need an index group with a single micelle, use make_ndx and choose 
the residue numbers that comprise the micelle.  g_select can do the same, but 
this tool is better suited for more complex operations and creation of dynamic 
indices.


-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Unit of r in radial distribution function

2011-11-30 Thread bipin singh

Thanks.
On Wed, Nov 30, 2011 at 20:06, Tsjerk Wassenaar  wrote:
> Hi Bipin,
>
> Gromacs uses nm.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Nov 30, 2011 at 3:32 PM, bipin singh  wrote:
>> Hello,
>>
>> Please let me know what is the unit of r (nm or A) in the radial
>> distribution function
>> output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no 
>> units.
>>
>> --
>> ---
>> Regards,
>> Bipin Singh
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



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

[gmx-users] how to understand this sentence

The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)

I don't understand the fatal error message it has been given during a
simple run,

I tested with large box already, during editconf I used -d 30 already,

it's a very small peptide, the box dimension is   63.95000  60.76600  62.99900

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

[gmx-users] Re: how to understand this sentence

https://docs.google.com/open?id=0B93SVRfpVVg3NTVjMmY0NzEtM2UzOC00MDEwLWI2OWMtZjEyZDQ5NzM1YWVh

I uploaded the files here.

is it the box still small?

Thanks,

On Thu, Dec 1, 2011 at 12:25 AM, lina  wrote:
> The Y-size of the box (1.999239) times the triclinic skew factor
> (1.00) is smaller than the number of DD cells (2) times the
> smallest allowed cell size (1.00)
>
> I don't understand the fatal error message it has been given during a
> simple run,
>
> I tested with large box already, during editconf I used -d 30 already,
>
> it's a very small peptide, the box dimension is   63.95000  60.76600  62.99900
>
> Thanks
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Hydrophobic cores

2011-11-30 Thread 김현식


Dear Experts,
 
Hi, 
 
Is there any tools in gromacs to get "Hydrophobic cores" of protein ?
 
 
Best,
Hyun  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Spherical Position Restrain from the center of the Box

2011-11-30 Thread Ricardo O. S. Soares

Hello dear GMX Users,

Through scripting, I have an itp-like file to restrain all atoms that are NOT 
within a 30 angstroms radius from the center (a trimmer + water + ions).
This selection includes both protein and solvent atoms, which may be a problem 
when assigning this selection to the TOP file.
Is there a way to include this whole selection into the top file directly? 
Where/how could that be? 

I've searched for solutions for a while, with no avail.


Thanks,


 


---
 Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São 
Paulo.  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Spherical Position Restrain from the center of the Box

Hi Ricardo,

Unfortunately that is not possible. What you can do is rearrange the water
in the structure and use two water moleculetypes, one with and one without
position restraints. It might be nice to have something like
global_position_restraints, added under [ system ], but that needs to be
implemented first.

Cheers,

Tsjerk

On Nov 30, 2011 6:03 PM, "Ricardo O. S. Soares" 
wrote:

Hello dear GMX Users,

Through scripting, I have an itp-like file to restrain all atoms that are
NOT within a 30 angstroms radius from the center (a trimmer + water + ions).
This selection includes both protein and solvent atoms, which may be a
problem when assigning this selection to the TOP file.
Is there a way to include this whole selection into the top file directly?
Where/how could that be?
I've searched for solutions for a while, with no avail.

Thanks,





---

Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São
Paulo.

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

Re: [gmx-users] Hydrophobic cores




김현식 wrote:

Dear Experts,
 
Hi,
 
Is there any tools in gromacs to get "Hydrophobic cores" of protein ?
 
 


I suppose that depends on what your definition is, but in all likelihood no, not 
directly.  A program like g_sas can give you nonpolar and polar surface areas as 
well as volumes and surface atoms, which, through crafty use of index groups, 
may provide you with something useful.


-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] MM/PBSA Gromacs

2011-11-30 Thread R.S.K.Vijayan

Dear Gromacs users

Is there any script  that does a PB or GB calculation to perform a
MM/PB(GB)SA free energy  calculation in Gromacs. Similar to the MMPBSA.py
script available in Amber.  I find a similar question raised by a user a
couple of years back.  Any successful implementation


Vijayan.R



On Wed, Nov 30, 2011 at 1:26 PM, Justin A. Lemkul  wrote:

>
>
> 김현식 wrote:
>
>> Dear Experts,
>>  Hi,
>>  Is there any tools in gromacs to get "Hydrophobic cores" of protein ?
>>
>>
>
> I suppose that depends on what your definition is, but in all likelihood
> no, not directly.  A program like g_sas can give you nonpolar and polar
> surface areas as well as volumes and surface atoms, which, through crafty
> use of index groups, may provide you with something useful.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] MM/PBSA Gromacs

2011-11-30 Thread Per Larsson

Hi!

There is support in gromacs for gb calculations. However, I'm currently 
investigating some recent reports about  unstable simulations (unfolding 
proteins), so my advice is to use the code with caution.

Thanks
/Per


30 nov 2011 kl. 20:04 skrev "R.S.K.Vijayan" :

> Dear Gromacs users
> 
> Is there any script  that does a PB or GB calculation to perform a 
> MM/PB(GB)SA free energy  calculation in Gromacs. Similar to the MMPBSA.py 
> script available in Amber.  I find a similar question raised by a user a 
> couple of years back.  Any successful implementation
> 
> 
> Vijayan.R  
> 
> 
> 
> On Wed, Nov 30, 2011 at 1:26 PM, Justin A. Lemkul  wrote:
> 
> 
> 김현식 wrote:
> Dear Experts,
>  Hi,
>  Is there any tools in gromacs to get "Hydrophobic cores" of protein ?
>  
> 
> I suppose that depends on what your definition is, but in all likelihood no, 
> not directly.  A program like g_sas can give you nonpolar and polar surface 
> areas as well as volumes and surface atoms, which, through crafty use of 
> index groups, may provide you with something useful.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] gas-phase protein simulation

2011-11-30 Thread Shi, Huilin

Hi,

I would like to run a gas-phase protein simulation (with charge state of  +8).
I have read this paper : Biochemistry, 2007, 47, 933-945.

In the method section of vaccum simulation, it is said
 "For the remaining parameters, the same settings were used as in the water 
simulations,
except that the periodic boundary conditions were turned off and no cutoffs 
whatsoever were used."

I am confused about "no cutoffs whatsoever were used".
Does that mean setting all the cutoffs to be zero?
In the md.mdp file, can I use the following

"; NEIGHBORSEARCHING PARAMETERS
nstlist  = 0
ns-type  = simple
pbc  = no
rlist= 0

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = cut-off
rcoulomb = 0
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw = 0"

Do I need to set rcoulomb/rvdw to zero or some other number?

Thank you.


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

Re: [gmx-users] g_select

mohammad agha wrote:
Thanks for your reply, but how can I define residue numbers of one 
micelle from between 10 micelle that all of them are same and only were 
differ at the number of monomer in micelle.

May I know how, please?

Well, now the problem is potentially more complicated.  Two approaches:

1. Using make_ndx, you can create an index file of any micelle if you know all 
of the residue numbers.  Please type "help" at the make_ndx prompt for example 
usage.  It is easy to do.

2. If you do not know which residues comprise the micelle(s) and you don't want 
to figure it out manually (I wouldn't), then you need g_select with some 
geometric criteria.  Again, there is help available (see g_select -h for how to 
invoke help) and search the archives for related posts.

It would be far more efficient for you and for those who might help you if you 
post what you've tried and failed at, rather than leaving us to guess what might 
work.

-Justin

*From:* Justin A. Lemkul 
*To:* mohammad agha ; Discussion list for GROMACS 
users 

*Sent:* Wednesday, November 30, 2011 7:03 PM
*Subject:* Re: [gmx-users] g_select

mohammad agha wrote:
 > Dear Prof.
 >
 > I have a system consists of 10 micelle after production simulation. 
How can I select a micelle with 92 monomer?
 > I know that I should use from g_select, but I don't know which 
argument is proper for me. I also checked -select help in g_select program.

 > Please help me.
 >

If you just need an index group with a single micelle, use make_ndx and 
choose the residue numbers that comprise the micelle.  g_select can do 
the same, but this tool is better suited for more complex operations and 
creation of dynamic indices.

-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

--

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

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] gas-phase protein simulation

2011-11-30 Thread David van der Spoel

yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well.

Toodle pip!

On Nov 30, 2011, at 8:39 PM, "Shi, Huilin"  wrote:

> Hi,
> 
> I would like to run a gas-phase protein simulation (with charge state of  
> +8). 
> I have read this paper : Biochemistry, 2007, 47, 933-945.
> 
> In the method section of vaccum simulation, it is said
>  "For the remaining parameters, the same settings were used as in the water 
> simulations, 
> except that the periodic boundary conditions were turned off and no cutoffs 
> whatsoever were used."
> 
> I am confused about "no cutoffs whatsoever were used".
> Does that mean setting all the cutoffs to be zero?
> In the md.mdp file, can I use the following
> 
> "; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 0
> ns-type  = simple
> pbc  = no
> rlist= 0
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = cut-off
> rcoulomb = 0
> epsilon_rf   = 78
> epsilon_r= 1
> vdw-type = Cut-off
> rvdw = 0"
> 
> Do I need to set rcoulomb/rvdw to zero or some other number?
> 
> Thank you.
> 
> 
> Huilin
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] gas-phase protein simulation




Shi, Huilin wrote:

Hi,

I would like to run a gas-phase protein simulation (with charge state 
of  +8).

I have read this paper : Biochemistry, 2007, 47, 933-945.

In the method section of vaccum simulation, it is said
 "For the remaining parameters, the same settings were used as in the 
water simulations,
except that the periodic boundary conditions were turned off and no 
cutoffs whatsoever were used."


I am confused about "no cutoffs whatsoever were used".
Does that mean setting all the cutoffs to be zero?
In the md.mdp file, can I use the following

"; NEIGHBORSEARCHING PARAMETERS
nstlist  = 0
ns-type  = simple
pbc  = no
rlist= 0

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = cut-off
rcoulomb = 0
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw = 0"

Do I need to set rcoulomb/rvdw to zero or some other number?



Your settings are correct, although epsilon_r and epsilon_rf are unnecessary.

-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_select

2011-11-30 Thread mohammad agha

Thanks for your reply.
Best Regards

 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Wednesday, November 30, 2011 11:27 PM
Subject: Re: [gmx-users] g_select

mohammad agha wrote:
> Thanks for your reply, but how can I define residue numbers of one micelle 
> from between 10 micelle that all of them are same and only were differ at the 
> number of monomer in micelle.
> May I know how, please?

Well, now the problem is potentially more complicated.  Two approaches:

1. Using make_ndx, you can create an index file of any micelle if you know all 
of the residue numbers.  Please type "help" at the make_ndx prompt for example 
usage.  It is easy to do.

2. If you do not know which residues comprise the micelle(s) and you don't want 
to figure it out manually (I wouldn't), then you need g_select with some 
geometric criteria.  Again, there is help available (see g_select -h for how to 
invoke help) and search the archives for related posts.

It would be far more efficient for you and for those who might help you if you 
post what you've tried and failed at, rather than leaving us to guess what 
might work.

-Justin

> 
> 
> *From:* Justin A. Lemkul 
> *To:* mohammad agha ; Discussion list for GROMACS users 
> 
> *Sent:* Wednesday, November 30, 2011 7:03 PM
> *Subject:* Re: [gmx-users] g_select
> 
> 
> 
> mohammad agha wrote:
>  > Dear Prof.
>  >
>  > I have a system consists of 10 micelle after production simulation. How 
>can I select a micelle with 92 monomer?
>  > I know that I should use from g_select, but I don't know which argument is 
>proper for me. I also checked -select help in g_select program.
>  > Please help me.
>  >
> 
> If you just need an index group with a single micelle, use make_ndx and 
> choose the residue numbers that comprise the micelle.  g_select can do the 
> same, but this tool is better suited for more complex operations and creation 
> of dynamic indices.
> 
> -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
> 
> 
> 
> 

-- 

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    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
> 

-- 

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

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

[gmx-users] compiling with the PGI compiler

2011-11-30 Thread Chris Neale

I am using a new cluster of Xeons and, to get the most efficient 
compilation, I have compiled gromacs-4.5.4 separately with the intel, 
pathscale, and pgi compilers.


With the pgi compiler, I am most concerned about this floating point 
overflow warning:


...
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
[ 19%] Building C object 
src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o

[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
PGC-W-0129-Floating point overflow. Check constants and constant 
expressions 
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/gmxlib/trajana/nbsearch.c: 
166)

PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 19%] Building C object 
src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o

[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
...


There are also a lot of warnings about a type cast, which seems less 
like a real problem:


...
[ 85%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_xml.c.o
[ 85%] Building C object src/mdlib/CMakeFiles/md.dir/nsgrid.c.o
[ 85%] Building C object src/mdlib/CMakeFiles/md.dir/stat.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin_bar.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_double.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/pull.c.o
PGC-W-0095-Type cast required for this conversion 
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/pull.c: 1213)
PGC-W-0095-Type cast required for this conversion 
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/pull.c: 1213)

PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/force.c.o
PGC-W-0095-Type cast required for this conversion 
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/force.c: 519)

PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/fft5d.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_parallel_3dfft.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/qmmm.c.o
[ 88%] Building C object src/mdlib/CMakeFiles/md.dir/vcm.c.o
PGC-W-0095-Type cast required for this conversion 
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/vcm.c: 83)

PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 88%] Building C object src/mdlib/CMakeFiles/md.dir/sim_util.c.o
...


###

I compiled like this:

module purge
module load pgi64/11.8 openmpi_pgi64/1.4.3_ofed
module load cmake/2.8.5
export CCDIR=/opt/pgi/linux86-64/11.8/bin

## set the location of the single precision FFTW isntallation
export FFTW_LOCATION=/home/nealechr/exe/pgi/fftw-3.1.2/exec

# Nothing below this line usually needs to be changed

export CXX=pgCC
export CC=pgcc

cmake ../source/ \
  -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
  -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
  -DCMAKE_INSTALL_PREFIX=$(pwd) \
  -DGMX_X11=OFF \
  -DCMAKE_CXX_COMPILER=${CCDIR}/pgCC \
  -DCMAKE_C_COMPILER=${CCDIR}/pgcc \
  -DGMX_PREFER_STATIC_LIBS=ON \
  -DGMX_MPI=OFF


make

make install


##

I don't get any similar errors with the intel or pathscale compilers 
(although intel gives me "icc: command line warning #10159: invalid 
argument for option '-m'" a lot) and the pathscale compilation appears 
to be hung on "[ 84%] Building C object 
src/tools/CMakeFiles/gmxana.dir/gmx_rms.c.o", but I'll post a separate 
ticket for that if it remains hung for a long time.


If anybody has run into this warning, or knows enough to be sure that I 
don't need to worry about it during mdrun (it seems to be in an analysis 
file, but I'm not entirely sure), then I would be happy to hear about 
it. A gmx-users search for PGI returned zero results. I saw something 
here, but it was not very specific about the problem with pgi ( 
http://www.levlafayette.com/node/175 ).


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o

2011-11-30 Thread Chris Neale


Dear users:

My compilation with the pathscale compiler hangs for over an hour on the 
gmx_rms.c.o file (or perhaps the one that comes next).


[ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o
[ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o
[ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_potential.c.o
[ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rama.c.o
[ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rdf.c.o
[ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rms.c.o
[hangs here]

I compiled like this:

module purge
module load pathscale/4.0.11
module load openmpi_pathscale64/1.4.3_ofed
module load cmake/2.8.5
export CCDIR=/opt/ekopath/4.0.11/bin

## set the location of the single precision FFTW isntallation
export FFTW_LOCATION=/home/nealechr/exe/pathscale/fftw-3.1.2/exec

# Nothing below this line usually needs to be changed

export CXX=pathCC
export CC=pathcc

cmake ../source/ \
  -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
  -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
  -DCMAKE_INSTALL_PREFIX=$(pwd) \
  -DGMX_X11=OFF \
  -DCMAKE_CXX_COMPILER=${CCDIR}/pathCC \
  -DCMAKE_C_COMPILER=${CCDIR}/pathcc \
  -DGMX_PREFER_STATIC_LIBS=ON \
  -DGMX_MPI=OFF


make

make install

#

If anybody has successfully compiled with the pathscale compiler, I 
would love to hear any suggestions that you can offer.


I have tried 3 fresh installations, and I have also tried cntrl^C and 
then run make again without a clean. It's always the same.


Thank you,
Chris.

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] what's the parameters for angle restraints in mdp file

2011-11-30 Thread Chunxia Gao

Dear gmx users:

Do anybody know what is the parameters for angle restraints in mdp file, like 
distance restraint it will have like disre = simple and dihedral restraints 
will have dihre = yes, and what about for angle restraints? nothing? just 
defined the force constant and that atom index in topology file will be ok?

Thanks for answering back in advance.

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

RE: [gmx-users] gas-phase protein simulation

2011-11-30 Thread Shi, Huilin

Hi,

Thank you for your reply.

My concern is that if  rcoulomb and rvdw are set to be zero, does it mean that
there are no coulombic and van der waals forces involved in the simulation?

I guess there are still coulombic and van der waals forces between atoms of a 
single protein molecule.

Or does setting the cutoff to be zero just mean there is no forces between 
neighbored molecules?

Thanks.


Huilin

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of David van der Spoel [sp...@xray.bmc.uu.se]
Sent: Wednesday, November 30, 2011 3:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gas-phase protein simulation

yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well.

Toodle pip!

On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" 
mailto:huil...@imail.iu.edu>> wrote:

Hi,

I would like to run a gas-phase protein simulation (with charge state of  +8).
I have read this paper : Biochemistry, 2007, 47, 933-945.

In the method section of vaccum simulation, it is said
 "For the remaining parameters, the same settings were used as in the water 
simulations,
except that the periodic boundary conditions were turned off and no cutoffs 
whatsoever were used."

I am confused about "no cutoffs whatsoever were used".
Does that mean setting all the cutoffs to be zero?
In the md.mdp file, can I use the following

"; NEIGHBORSEARCHING PARAMETERS
nstlist  = 0
ns-type  = simple
pbc  = no
rlist= 0

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = cut-off
rcoulomb = 0
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw = 0"

Do I need to set rcoulomb/rvdw to zero or some other number?

Thank you.


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

Re: [gmx-users] gas-phase protein simulation




Shi, Huilin wrote:

Hi,

Thank you for your reply.

My concern is that if  rcoulomb and rvdw are set to be zero, does it 
mean that

there are no coulombic and van der waals forces involved in the simulation?

I guess there are still coulombic and van der waals forces between atoms 
of a single protein molecule.


Or does setting the cutoff to be zero just mean there is no forces 
between neighbored molecules?




Setting cutoffs to zero means infinite cutoffs - all interactions are 
calculated.

-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_select dynamic indices

2011-11-30 Thread Yao Yao

Hi Gmxers,

I used g_dist to find all water molecules within 5 Angstrom of a protein in a 
trajectory with a little surprise that gromacs directly prints out those water 
on my screen rather than in an output file.
Since in each frame, those water molecules are not the same, I realize I need 
to make a dynamic index or indices for them.
However I do not see any flag I could possibly introduce those water in 
g_select and then use -on flag to produce a dynamic index.
Anyone has met this before?

Thanks,

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

RE: [gmx-users] how to understand this sentence

2011-11-30 Thread Dallas Warren

Have you run g_energy on the .edr file and extracted the box dimensions during 
the run to see what has been happening to them?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of lina
> Sent: Thursday, 1 December 2011 3:26 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] how to understand this sentence
> 
> The Y-size of the box (1.999239) times the triclinic skew factor
> (1.00) is smaller than the number of DD cells (2) times the
> smallest allowed cell size (1.00)
> 
> I don't understand the fatal error message it has been given during a
> simple run,
> 
> I tested with large box already, during editconf I used -d 30 already,
> 
> it's a very small peptide, the box dimension is   63.95000  60.76600
> 62.99900
> 
> Thanks
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 "

2011-11-30 Thread Chunxia Gao

Dear gmx users:


I am using the free energy to calculate the ligand binding affinity to protein, 
during the decouple process, I need to put some restraint between the protein 
and the ligand, e.g. distance restraint.

But distance restraint is only for intramolecular, so I need to make a hybrid 
[moleculetype] section that includes the protein and the ligand, which means 
the ligand sort of  becoming a residue of the protein. In this case, I do not 
know how to put my ligand in the couple-moltype? or I need to manually put all 
these state B for the ligand? 

Anyway, so I manually put all these B-state parameters for the ligand, as I 
turned the B state charge to zero, when I did the grompp, it showed up a note:  
State B has non-zero total charge: 5.80e+01. so what does it mean? What can 
I do for this?

Will be really appreciated for answering back.

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

Re: [gmx-users] g_select dynamic indices




Yao Yao wrote:

Hi Gmxers,

I used g_dist to find all water molecules within 5 Angstrom of a protein 
in a trajectory with a little surprise that gromacs directly prints out 
those water on my screen rather than in an output file.


According to g_dist -h, that's what you should expect :)

Since in each frame, those water molecules are not the same, I realize I 
need to make a dynamic index or indices for them.
However I do not see any flag I could possibly introduce those water in 
g_select and then use -on flag to produce a dynamic index.


The index groups are output by g_select.  Try g_select -select "help all" for 
examples of how to create groups.


-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 "

Chunxia Gao wrote:

Dear gmx users:

I am using the free energy to calculate the ligand binding affinity to protein,
during the decouple process, I need to put some restraint between the protein
and the ligand, e.g. distance restraint.

But distance restraint is only for intramolecular, so I need to make a hybrid [moleculetype] section that includes the protein and the ligand, which means the ligand sort of becoming a residue of the protein. In this case, I do not know how to put my ligand in the couple-moltype? or I need to manually put all these state B for the ligand?

Anyway, so I manually put all these B-state parameters for the ligand, as I
turned the B state charge to zero, when I did the grompp, it showed up a note:
State B has non-zero total charge: 5.80e+01. so what does it mean? What can
I do for this?

Will be really appreciated for answering back.

I would think you could avoid all these problems by using the pull code for a
restraint, rather than an intramolecular distance restraint. The error with a
net charge of +58 seems to indicate that whatever you're doing to the topology
is turning on (likely) every charge in the system, rather than just those of
some small part of it.

-Justin

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

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] control Distance between the solute and the box for 3 directions seperately

2011-11-30 Thread mu xiaojia

Dear gmx-users,

I want to make a long nano-fiber composed of many non-covalently bonded
proteins, it elongates along the Z axial direction.

in editconf, we can define the "Distance between the solute and the box",
but it works for x,y and z directions at the same time.

e.g. my command
editconf -f protein.gro -o protein_box.gro -c -d 1.0 -bt cubic,then the
out come would be a box with  of at least 1.0 nm "between any two periodic
images of a protein".

What should I do if I want to set the distance for z axis smaller than x
and y? which means, let the molecules along Z "see" each other within 2nm?


Thanks!

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

Re: [gmx-users] control Distance between the solute and the box for 3 directions seperately

2011-11-30 Thread Mark Abraham


On 1/12/2011 10:24 AM, mu xiaojia wrote:

Dear gmx-users,

I want to make a long nano-fiber composed of many 
non-covalently bonded proteins, it elongates along the Z axial direction.


in editconf, we can define the "Distance between the solute and the 
box", but it works for x,y and z directions at the same time.


e.g. my command
editconf -f protein.gro -o protein_box.gro -c -d 1.0 -bt cubic,   
 then the out come would be a box with  of at least 1.0 nm "between 
any two periodic images of a protein".


What should I do if I want to set the distance for z axis smaller than 
x and y? which means, let the molecules along Z "see" each other 
within 2nm?




Observe the box created by -d 1.0 and then start again with editconf 
-box and choose dimensions you want.


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

Re: [gmx-users] how to understand this sentence

2011-11-30 Thread Mark Abraham


On 1/12/2011 3:25 AM, lina wrote:

The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)

I don't understand the fatal error message it has been given during a
simple run,

I tested with large box already, during editconf I used -d 30 already,

it's a very small peptide, the box dimension is   63.95000  60.76600  62.9990


Your system may be too small to parallelize over the number of 
processors you are using (and as usual, it would have been a good idea 
to supply your mdrun command line unless you enjoy wasting time when 
people make wrong guesses).


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] control Distance between the solute and the box for 3 directions seperately




mu xiaojia wrote:

Dear gmx-users,

I want to make a long nano-fiber composed of many non-covalently bonded 
proteins, it elongates along the Z axial direction.


in editconf, we can define the "Distance between the solute and the 
box", but it works for x,y and z directions at the same time.


e.g. my command 
editconf -f protein.gro -o protein_box.gro -c -d 1.0 -bt cubic,then 
the out come would be a box with  of at least 1.0 nm "between any two 
periodic images of a protein".


What should I do if I want to set the distance for z axis smaller than x 
and y? which means, let the molecules along Z "see" each other within 2nm? 



Set the box size manually with editconf -box.  Beware that if you make a 
rectangular box around your nanofiber, if it rotates, you may violate the 
minimum image convention.


-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_select dynamic indices

2011-11-30 Thread Yao Yao

Hi Justin,

Thanks for your hints. I feel the string in g_select is pretty much like tck/tl 
in VMD. 

However I have not figured out the way to select a customized group defined in 
.ndx file.

And one more question I have, maybe more general, if I have, say, 100 frames, 
g_select will give me 100 dynamic indices in the .ndx file,
I am wondering if there is a way (might be some script) that can help me choose 
automatically for further processing, like g_hbond, and then I can program to 
collect all frames and average them.
In other words, there many commands in gromacs that require users to "Select a 
group", I am wondering if I can make this "choice" in a script rather than when 
I see the prompt.

thanks,

Yao

 From: Justin A. Lemkul 
To: Yao Yao ; Discussion list for GROMACS users 

Sent: Wednesday, November 30, 2011 1:57 PM
Subject: Re: [gmx-users] g_select dynamic indices

Yao Yao wrote:
> Hi Gmxers,
> 
> I used g_dist to find all water molecules within 5 Angstrom of a protein in a 
> trajectory with a little surprise that gromacs directly prints out those 
> water on my screen rather than in an output file.

According to g_dist -h, that's what you should expect :)

> Since in each frame, those water molecules are not the same, I realize I need 
> to make a dynamic index or indices for them.
> However I do not see any flag I could possibly introduce those water in 
> g_select and then use -on flag to produce a dynamic index.

The index groups are output by g_select.  Try g_select -select "help all" for 
examples of how to create groups.

-Justin

-- 

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

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

Re: [gmx-users] g_select dynamic indices




Yao Yao wrote:


Hi Justin,

Thanks for your hints. I feel the string in g_select is pretty much like 
tck/tl in VMD.
However I have not figured out the way to select a customized group 
defined in .ndx file.




There's one example in the help text that is almost exactly what you want, is it 
not?


All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
  "Close to protein" resname LIG and within 0.5 of group "Protein"

And one more question I have, maybe more general, if I have, say, 100 
frames, g_select will give me 100 dynamic indices in the .ndx file,
I am wondering if there is a way (might be some script) that can help me 
choose automatically for further processing, like g_hbond, and then I 
can program to collect all frames and average them.
In other words, there many commands in gromacs that require users to 
"Select a group", I am wondering if I can make this "choice" in a script 
rather than when I see the prompt.




http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

You'll have to analyze each frame individually, and then post-process your 
output to get the averages.


-Justin

--


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


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] how to understand this sentence

On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham  wrote:
> On 1/12/2011 3:25 AM, lina wrote:
>>
>> The Y-size of the box (1.999239) times the triclinic skew factor
>> (1.00) is smaller than the number of DD cells (2) times the
>> smallest allowed cell size (1.00)
>>
>> I don't understand the fatal error message it has been given during a
>> simple run,
>>
>> I tested with large box already, during editconf I used -d 30 already,
>>
>> it's a very small peptide, the box dimension is   63.95000  60.76600
>>  62.9990
>
> Your system may be too small to parallelize over the number of processors
> you are using (and as usual, it would have been a good idea to supply your
> mdrun command line unless you enjoy wasting time when people make wrong
> guesses).

As you can see it's a very small job, so I just run on laptop,

now I changed the mdrun -nt 4
it showed:
Fatal error:
The X-size of the box (3.994507) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (4) times the
smallest allowed cell size (1.00)


The Fatal error about the Y-size when I used mdrun -nt 8

can you guess which is wrong here. on the last email the URL contains
the md.mdp, topol.top and .gro files to run a mdrun.

Thanks,

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

Re: [gmx-users] how to understand this sentence

Now I used mdrun -nt 2

it showed:

Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.

and mdrun -nt 1 it showed:

Program mdrun, VERSION 4.5.4-dev-20110711-dadcb
Source code file:
/var/local/cache/git-build/gromacs/src/gromacs/mdlib/ns.c, line: 2544

Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.


On Thu, Dec 1, 2011 at 11:38 AM, lina  wrote:
> On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham  wrote:
>> On 1/12/2011 3:25 AM, lina wrote:
>>>
>>> The Y-size of the box (1.999239) times the triclinic skew factor
>>> (1.00) is smaller than the number of DD cells (2) times the
>>> smallest allowed cell size (1.00)
>>>
>>> I don't understand the fatal error message it has been given during a
>>> simple run,
>>>
>>> I tested with large box already, during editconf I used -d 30 already,
>>>
>>> it's a very small peptide, the box dimension is   63.95000  60.76600
>>>  62.9990
>>
>> Your system may be too small to parallelize over the number of processors
>> you are using (and as usual, it would have been a good idea to supply your
>> mdrun command line unless you enjoy wasting time when people make wrong
>> guesses).
>
> As you can see it's a very small job, so I just run on laptop,
>
> now I changed the mdrun -nt 4
> it showed:
> Fatal error:
> The X-size of the box (3.994507) times the triclinic skew factor
> (1.00) is smaller than the number of DD cells (4) times the
> smallest allowed cell size (1.00)
>
>
> The Fatal error about the Y-size when I used mdrun -nt 8
>
> can you guess which is wrong here. on the last email the URL contains
> the md.mdp, topol.top and .gro files to run a mdrun.
>
> Thanks,
>
>>
>> Mark
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Analysis of Protein Complex

2011-11-30 Thread Saba Ferdous

Dear Sir,

I am studying a protein complex. I have perforemed 10ns simulations. I
saved snapshots every10ps. sp all snap shopts I got were 1000.

Now I want to analyse them with respect to interactions. I want to check
the binding surfaces and binding points which come closer and incontact
during simulations. Can you devise me a way to perform such kind of
analysis. Further more I am interested to know the binding energies as
well. What sort of other analysis can be done on this complex.

-- 
Saba Ferdous
Research Scholar (M. Phil)
National Center for Bioinformatics
Quaid-e-Azam University, Islamabad
Pakistan
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Analysis of Protein Complex