[gmx-users] (no subject)

[James Starlight]

Dear Gromacs users!


I want to simulate membrane receptor in the Gromos 56 force field in the
vacuu and I have some methodological questions.


1- I need to edit topology of my structure by adding one DOUBLE covalent
bond between desires atoms ( they have been already placed in the desired
adjacent positions by pymol).

I add string in topology.top [bonds]

 2809  2810 2gb_5

Does it enough? What addition modification of the topology file requires
for the addition covalent bond?

Where I could found names of all bonds parametrs such as gb_5 ?
I've found that number for the C=O pair so as I understood this must
correspond to double planar bond.

2- I've received message that my system consist of 2 negative charges. For
water-souluble proteins I just place 2 counter ions in the SOLVENT to
neitralize this charge. What I should do for the vacuu simulation ?


Thanks!

James
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[gmx-users] Simulation of membrane protein in vacuu

[James Starlight]

Dear Gromacs users!


I want to simulate membrane receptor in the Gromos 56 force field in the
vacuu and I have some methodological questions.


1- I need to edit topology of my structure by adding one DOUBLE covalent
bond between desires atoms ( they have been already placed in the desired
adjacent positions by pymol).

I add string in topology.top [bonds]

 2809  2810 2gb_5

Does it enough? What addition modification of the topology file requires
for the addition covalent bond?

Where I could found names of all bonds parametrs such as gb_5 ?
I've found that number for the C=O pair so as I understood this must
correspond to double planar bond.

2- I've received message that my system consist of 2 negative charges. For
water-souluble proteins I just place 2 counter ions in the SOLVENT to
neitralize this charge. What I should do for the vacuu simulation ?


Thanks!

James
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Re: [gmx-users] Installing & uninstalling of gromacs

[Spring buds]

On Wed, Jan 25, 2012 at 7:42 PM, Mark Abraham wrote:

>  On 25/01/2012 12:54 AM, Spring buds wrote:
>
>
>  Removing files in /usr/local/gromacs has no bearing on the contents of
>> /usr/local/bin.  If you did 'make links' at the end of the installation,
>> you will have dead links in /usr/local/bin that need to be removed, as well.
>>
>> -Justin
>>
>
>
> Dear Justin,
>
> Thanks a lot for your insight.
>
> I did links in the end so there is links in  */usr/local/bin*. After
> uninstall I still have dead links with */usr/local/bin. *could you help
> me how to remove this* *in* **/usr/local/bin*.
>
>
> 1. cd /usr/local/bin
> 2. ls -l
> 3. look for broken links
> 4. sudo rm 
>
> Hint: the majority of them will be named g_xxx so that makes for easy
> wildcarding.
>
> Mark
>
>
> Dear Mark,

Your reply was very helpful. Thanks.



>
>
>
>
>
>
>>
>>
>>>
>>>try make uninstall in the directory where you used make install
>>>before. like Path_to//gromacs-4.5.5
>>>and then make distclean
>>>for a totally clear re-installation, removed the /gromac-4.5.5 and
>>>
>>>re-untar the gromacs-4.5.5.tar.gz
>>>
>>>before that, further check the lib and bin have totally removed or
>>> not.
>>>
>>>
>>> Sure. I will do now
>>>
>>>
>>>Which OS you are working on?
>>>
>>>
>>> Linux (CentOS 5.7)
>>>
>>> Thanks a lot.
>>>
>>>
>>> >
>>> >
>>> > On Tue, Jan 24, 2012 at 2:31 AM, lina >> > wrote:
>>> >>
>>> >> On 24 Jan, 2012, at 1:53, Spring buds >>  > wrote:
>>> >>
>>> >> > Dear Gromacs users,
>>> >> >
>>> >> > Greetings!!!
>>> >> >
>>> >> > I am very new users and I am trying to install grmacs 4.5.5 or
>>>3.3.3 for
>>> >> > past four days. But still I am not able to. So I would like to
>>>ask some
>>> >> > questions which are below.
>>> >> >
>>> >> >
>>> >> > 1.My laptop is a dual core, which means two processors?.So
>>>should I need
>>> >> > to install MPI?
>>> >> >
>>> >> --enable threads
>>> >>
>>> >> > 2.I installed gromacs 4.5.5 with mistakes. To remove
>>>installing, I used
>>> >> > the "which gromacs" and it shows as "/usr/bin/which: no mdrun in
>>> >> >
>>>
>>>  
>>> (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>>> >> > However, I used "rm -rf /usr/local/gromacs" to remove
>>>installing I still can
>>> >> > see tha gromacs files with red background in "/usr/local/bin".
>>>Could you
>>> >> > tell me I removed the gromacs installing?
>>> >>
>>> >> You have not.
>>> >>
>>> >> >
>>> >> > 3.Could you please tell me the very simple steps for
>>>installatios, since
>>> >> > I am a novice.
>>> >>
>>> >> http://www.gromacs.org/Downloads/Installation_Instructions
>>> >>
>>> >> >
>>> >> > Many thanks in advance for your time and help.
>>> >> >
>>> >> > Huang Malai
>>> >> > --
>>> >> > 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
>>> .
>>>
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>>> >> --
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>>> 
>>>
>>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> posting!
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>>> .
>>>
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>>> >
>>> >
>>> >
>>> > --
>>> > gmx-users mailing listgmx-users@gromacs.org
>>> 
>>>
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] umbrella-drug

[parto haghighi]

Dear gmx-users
I am working on lipid membrane+drug system.I should do umbrella
sampling in this procedure:
1.cat drug and lipid
2.energy minimization
3.run npt
4.run md_pull
I want to pull drug into the membrane but gromacs pushes the drug to
the sides of box.and this result is independent of drug location
Also I have used 500 ps for my simulation time but when I use ngmx to
see the process,it runs only 56 ps.why?
What can I do when I want to move drug to the bilayer?
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[gmx-users] the difference between fixing and freezing and position restraint

[Banafsheh Mehrazma]

Hi everyone;

I wonder what's the difference between fixing and freezing and
position restraining?
I know how to position restrain, but I don't have any idea how we can
fix or freeze.
So I would be glad if you tell me exactly, how we can fix the solute
while the solvent is not, and vice versa. :)

Thank you in advance
B.Mehrazma
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Re: [gmx-users] the difference between fixing and freezing and position restraint

[Justin A. Lemkul]

Banafsheh Mehrazma wrote:

Hi everyone;

I wonder what's the difference between fixing and freezing and
position restraining?
I know how to position restrain, but I don't have any idea how we can
fix or freeze.
So I would be glad if you tell me exactly, how we can fix the solute
while the solvent is not, and vice versa. :)



Freezing is done via freezegrps (and related settings) in the .mdp file.  The 
positions of the frozen atoms are invariant.


Restraining simply applies a biasing potential to the atoms such that 
displacement is disfavored.  The strength of the restraint is controlled by the 
force constant in the posre.itp file.


-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] umbrella-drug

[Justin A. Lemkul]

parto haghighi wrote:

Dear gmx-users
I am working on lipid membrane+drug system.I should do umbrella
sampling in this procedure:
1.cat drug and lipid
2.energy minimization
3.run npt
4.run md_pull
I want to pull drug into the membrane but gromacs pushes the drug to
the sides of box.and this result is independent of drug location
Also I have used 500 ps for my simulation time but when I use ngmx to
see the process,it runs only 56 ps.why?


Perhaps the system crashed?


What can I do when I want to move drug to the bilayer?


Set the .mdp options correctly.  You haven't supplied any relevant information 
as to how you are attempting to pull, but clearly something is wrong with your 
settings.


-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] umbrella-drug

[lina]

On Sat, Jan 28, 2012 at 9:17 PM, parto haghighi
 wrote:
> Dear gmx-users
> I am working on lipid membrane+drug system.I should do umbrella
> sampling in this procedure:
> 1.cat drug and lipid
> 2.energy minimization
> 3.run npt
> 4.run md_pull
> I want to pull drug into the membrane but gromacs pushes the drug to
> the sides of box.and this result is independent of drug location
> Also I have used 500 ps for my simulation time but when I use ngmx to
> see the process,it runs only 56 ps.why?
> What can I do when I want to move drug to the bilayer?
You may want to check the
pull_vec1
and
pull_k

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[gmx-users] free energy tutorial 6

[murat özçelik]

hi all! 
ı am doing tutorial 6 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html
 

ı have a problem.. ı am collect all md.xvg files and run g_bar with below 
command..
g_bar -f md.xvg -o -oi -oh..
the program gave me the following error..

Why does not consist of bar.xvg file

please help me!  thanks...

   :-)  g_bar  (-:

Option Filename  Type Description

  -f md.xvg  Input, Opt!, Mult. xvgr/xmgr file

  -g   ener.edr  Input, Opt., Mult. Energy file
  -obar.xvg  Output, Opt! xvgr/xmgr file
 -oi barint.xvg  Output, Opt! xvgr/xmgr file
 -oh  histogram.xvg  Output, Opt! xvgr/xmgr file

Option   Type   Value   Description

--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel

-[no]w   bool   no  View output .xvg, .xpm, .eps and .pdb files
xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-b   real   0   Begin time for BAR
-e   real   -1  End time for BAR

-tempreal   -1  Temperature (K)
-precint2   The number of digits after the decimal point
-nbmin   int5   Minimum number of blocks for error estimation
-nbmax   int5   Maximum number of blocks for error estimation

-nbinint100 Number of bins for histogram output

md.xvg: 0.0 - 5000.0; lambda = 1.000
foreign lambdas: 0.000 (5250021 pts) 0.050 (5250021 pts)


Writing histogram to histogram.xvg


No results to calculate.
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[gmx-users] isodensity surface

[Nidhi Katyal]

Dear all,
Is there a way to create and visualize isodensity surfaces in Gromacs or
any tool which can work on gromacs compatible file?
Any suggestion would be highly welcomed.
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Re: [gmx-users] free energy tutorial 6

[Justin A. Lemkul]

murat özçelik wrote:

hi all!
ı am doing tutorial 6 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html 
 

ı have a problem.. ı am collect all md.xvg files and run g_bar with 
below command..

g_bar -f md.xvg -o -oi -oh..
the program gave me the following error..
Why does not consist of bar.xvg file



You only provided a single input file (md.xvg) - g_bar requires the .xvg files 
of all the lambda intervals.


-Justin


please help me!  thanks...
   :-)  g_bar  (-:

Option Filename  Type Description
--
--
  -f md.xvg  Input, Opt!, Mult. xvgr/xmgr file
  -g   ener.edr  Input, Opt., Mult. Energy file
  -obar.xvg  Output, Opt! xvgr/xmgr file
 -oi barint.xvg  Output, Opt! xvgr/xmgr file
 -oh  histogram.xvg  Output, Opt! xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-[no]w   bool   no  View output .xvg, .xpm, .eps and .pdb files
xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-b   real   0   Begin time for BAR
-e   real   -1  End time for BAR
-tempreal   -1  Temperature (K)
-precint2   The number of digits after the decimal point
-nbmin   int5   Minimum number of blocks for error estimation
-nbmax   int5   Maximum number of blocks for error estimation
-nbinint100 Number of bins for histogram output

md.xvg: 0.0 - 5000.0; lambda = 1.000
foreign lambdas: 0.000 (5250021 pts) 0.050 (5250021 pts)


Writing histogram to histogram.xvg

No results to calculate.



--


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] isodensity surface

[Sanku M]

You can load your gromacs trajectory file in  VMD 1.9 and then use Volume-map 
tool in the "analysis" section  to calculate the isodensity surface. The GUI of 
the Volume-map tool is pretty user-friendly.



 From: Nidhi Katyal 
To: gmx-users@gromacs.org 
Sent: Saturday, January 28, 2012 11:56 AM
Subject: [gmx-users] isodensity surface
 


Dear all,

Is there a way to create and visualize isodensity surfaces in Gromacs or any 
tool which can work on gromacs compatible file?
Any suggestion would be highly welcomed.

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Re: [gmx-users] Gromacs on GPU

[Benjamin Hall]

Justin A. Lemkul wrote:
> 
> We get junk output with 4.5.4 if the box size is set to zero, for some odd 
> reason, though in principle it should be ignored with "pbc = no" in the .mdp 
> file.  Using any non-zero box results in usable results.  Our OpenMM version 
> is 
> the same, but Cuda is in the 3.x series (can't remember off the top of my 
> head, 
> sorry).
> 

I've tried setting the box size in the gro file but that doesn't seem to work 
(100x100x100nm). Which compiler did you use? I realise that this is an unlikely 
source of trouble but it's another variable to eliminate in testing.

I'll update issue 568 on redmine, which has been closed but appears to be this 
problem.

Thanks & best wishes

Ben


--
Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.h...@ucl.ac.uk




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Re: [gmx-users] Gromacs on GPU

[Justin A. Lemkul]

Benjamin Hall wrote:

Justin A. Lemkul wrote:


We get junk output with 4.5.4 if the box size is set to zero, for some 
odd 
reason, though in principle it should be ignored with "pbc = no" in 
the .mdp 
file.  Using any non-zero box results in usable results.  Our OpenMM 
version is 
the same, but Cuda is in the 3.x series (can't remember off the top of 
my head, 
sorry).




I've tried setting the box size in the gro file but that doesn't seem to 
work (100x100x100nm). Which compiler did you use? I realise that this is 
an unlikely source of trouble but it's another variable to eliminate in 
testing.




Ours is gcc-4.4.6 on a local machine using Cuda 3.2.  On our university's GPU 
cluster, the installation was done with gcc-4.3.4 and Cuda 3.1.  I have not 
tested Cuda 4.0, though it has recently become available to us so it might be 
worth a shot to see if this is another issue.


-Justin

I'll update issue 568 on redmine, which has been closed but appears to 
be this problem.


Thanks & best wishes

Ben


--
Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.h...@ucl.ac.uk 






--


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


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[gmx-users] Force Field for Vacuum simulation

[James Starlight]

Dear Gromacs USers!


I'm looking for good force field for the simulation of the
protein-ligand complex in vacuum.

In accordance to the Justin's tutorial I've found that GROMOS96 43b1
force field might be good choice for that task.

But my version of GROMACS lack for that force field .rtps :(

Could you tell me where I could dwnload this force fields parameters?

Thanks,


James
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[gmx-users] root-mean-square distance

[dina dusti]

Dear Specialists,

I have a problem about computing of radius of micelle by 
root-mean-square-distance. Please help me.
I obtained radius of my micelle 2.4 nm by g_gyrate. 

g_gyrate -f md.xtc -s md.tpr -o gyrate.xvg -b 15
I want compare it by rms distance. 

I use from g_rms as following:
g_rms -f md.xtc -s md.tpr -o distrmsd.xvg -n index.ndx -b 15 
It result me 3.992290e+00 nm after averaging by g_analyze -f distrmsd.xvg -av
(the radius of a spherical micelle is defined as the rms distance of the 
headgroup atoms from the micelle center of mass, how should I define com of 
micelle in g_rms?)
I think I am wrong somewhere. 

May I ask you to help me,Please?

Best Regards
Dina
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Re: [gmx-users] Force Field for Vacuum simulation

[David van der Spoel]

On 2012-01-29 07:20, James Starlight wrote:

Dear Gromacs USers!


I'm looking for good force field for the simulation of the
protein-ligand complex in vacuum.

In accordance to the Justin's tutorial I've found that GROMOS96 43b1
force field might be good choice for that task.

But my version of GROMACS lack for that force field .rtps :(


Because that ff is not well-documented, the only difference with the 
normal gromos43 force field is that the side chains are neutral.


Please check this paper for a comparison of FF for vacuum simulations:

Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel 
& Carl Caleman: Structural stability of electrosprayed proteins: 
temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp. 
8069-8078 (2009)


Could you tell me where I could dwnload this force fields parameters?

Thanks,


James



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Dept. of Cell & Molec. Biol., Uppsala University.
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