from:"rama david"

[gmx-users] Comparing the simulation

2013-07-20 Thread rama david

Dear Friends,
 I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )

In First Experiment, I put the two XX peptide far from each other 2.0 nm,
 and run the simulation.
In the second experiment I put the two YY peptide seperated by 2.0 nm.
and run the simulation.
  In nvt I used the sane parameter, but In NPT, MD simulation I run
the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P 1
for
YY peptide.
  I found that peptide YY interaction start at 80ns and XX interaction
start at 10 ns.


   I have following Question.
 1.Is it possible to compare  two MD simulation which used the
same barostat   but having the different tau_P ( Relaxation time).

2. Could I make the interpretation that  XX peptide start interact
more early   than YY ??

3. Would we compare  the result between the simulation that uses the
different barostat ant thermostat but still using the same Force field.


I am looking forward for reply.


With Best Wishes,
Rama David
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Re: [gmx-users] Comparing the simulation

2013-07-20 Thread rama david

Dear Justin,
Thank you for your Prompt Reply.

I run a at least 4-5 run of each peptide.
The result are like the xx peptide form beta structure early than yy
peptide in each run.
I just used the different tau_P ( relaxation time ) for NPT and MD
production run.
XX tau_p = 2 YY tau_p= 1

NVT parameter are same.

On these basis can I make the interpretation that XX form beta sheet
structure early than YY
though they uses the same barostat but different tau_P ??

With Best Wishes and Regards,
Rama David

On Sat, Jul 20, 2013 at 4:49 PM, Justin Lemkul jalem...@vt.edu wrote:

On 7/20/13 5:27 AM, rama david wrote:

Dear Friends,
I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )

In First Experiment, I put the two XX peptide far from each other 2.0 nm,
and run the simulation.
In the second experiment I put the two YY peptide seperated by 2.0 nm.
and run the simulation.
In nvt I used the sane parameter, but In NPT, MD simulation I run
the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P
1
for
YY peptide.
I found that peptide YY interaction start at 80ns and XX interaction
start at 10 ns.

I have following Question.
1.Is it possible to compare two MD simulation which used the
same barostat but having the different tau_P ( Relaxation time).

You'll have to examine pressure distributions very carefully, but I am
inherently suspicious of trying to salvage results that were based on a
mistake.

2. Could I make the interpretation that XX peptide start
interact
more early than YY ??

Based on one simulation of each? No.

3. Would we compare the result between the simulation that uses the
different barostat ant thermostat but still using the same Force field.

If you are altering both thermostat and barostat, I would be extremely
skeptical of the results. Apply consistent methods.

-Justin

--
==**

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Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu |
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[gmx-users] Problem in g_enemat in Gromacs 4.5.5

2013-07-06 Thread rama david

Hi Friends,
 I am working on peptide self assembly.
 I simulated two peptide which are random coil and apart from each other.
As the time process they start to interact and form antiparallel beta sheet
structure.
   My plan is to find the energy difference in random coil to beta
shhet structure.
 I added protein1 protein2 group in mdp file I run g_energy coomand


 Output:

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
  1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
 13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
 17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
 21  Volume  22  Density 23  pV  24
Enthalpy
 25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
 29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
 33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
 37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
 41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
 45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
 49  Mu-Z50
Coul-SR:protein1-protein1
 51  LJ-SR:protein1-protein1 52
LJ-LR:protein1-protein1
 53  Coul-14:protein1-protein1   54
LJ-14:protein1-protein1
 55  Coul-SR:protein1-protein2   56
LJ-SR:protein1-protein2
 57  LJ-LR:protein1-protein2 58
Coul-14:protein1-protein2
 59  LJ-14:protein1-protein2 60
Coul-SR:protein1-rest
 61  LJ-SR:protein1-rest 62
LJ-LR:protein1-rest
 63  Coul-14:protein1-rest   64
LJ-14:protein1-rest
 65  Coul-SR:protein2-protein2   66
LJ-SR:protein2-protein2
 67  LJ-LR:protein2-protein2 68
Coul-14:protein2-protein2
 69  LJ-14:protein2-protein2 70
Coul-SR:protein2-rest
 71  LJ-SR:protein2-rest 72
LJ-LR:protein2-rest
 73  Coul-14:protein2-rest   74
LJ-14:protein2-rest
 75  Coul-SR:rest-rest   76
LJ-SR:rest-rest
 77  LJ-LR:rest-rest 78
Coul-14:rest-rest
 79  LJ-14:rest-rest 80
T-Protein
 81  T-non-Protein   82
Lamb-Protein
 83  Lamb-non-Protein


.But when I gave the command :


g_enemat_mpi -f ../energy.edr -groups groups.dat   -etot ener.xvg

   I ended with following Missery :


Opened ../energy.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):protein1-protein1 (0,0)in
energy file
WARNING! could not find group (null):protein1-protein2 (0,1)in energy file
group 1WARNING! could not find group (null):protein2-protein2 (1,1)in
energy file

Will select half-matrix of energies with 6 elements
Last energy frame read 20 time 20.000
Will build energy half-matrix of 2 groups, 6 elements, over 21 frames
Segmentation fault (core dumped)




I will be thankful for any suggestion.

Thank you in Advance.
With best Wishes.
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[gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david

Dear Friends,
  I simulated the 4 peptide in water box .
As they come close to each other they start to from anti-parallel
beta sheet structure.



Now I want to draw the Free energy surface for the
same ..How is  there pot energy ???

Would you please tell me how to do it ..

( I read about g_sham -h, I tried it, but not understand properly)

I will be very grateful for your suggestion and help..




With Best Wishes,
Rama David
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Re: [gmx-users] REMD temperature spacing formula

2013-04-04 Thread rama david

Dear

http://folding.bmc.uu.se/remd/ this may help you.


With best regards


On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:

 Dear all,

 We are stuck at the last stage of running a successful REMD.
 We have obtained average potential energy by fitting the energy values from
 initial MD.
 We want to get the temperature spacing for 72 replicas, starting from 280K.
 We have gone through numerous papers, but none of them explain clearly how
 they got the spacing values.
 Is there any equation/formula/web utility which gives the spacing?

 Any help will be highly appreciated.

 Thank you.
 Nikunj  Suhani
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Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david

Thank you justin,

I read the articles, archive and also g_sham -h,

As I mentioned in previous mail, I simulated four random coil peptide ,
they started to form
Beta sheet structure after 20 ns ..( simulation time 100ns )

My interest is how to draw the Free energy diagram for Potential energy and
Structures...(eg. RMSD, Gyrate, different cluster ,
with different structure at particular time ) .

Would you please tell me how to do it in gromacs with command line and
needed input.

I tried it a lot but not able to find the way ..

I will be a very grateful to you for ur help ..

With best Regards
Rama david.

On Thu, Apr 4, 2013 at 1:56 PM, Justin Lemkul jalem...@vt.edu wrote:

On 4/4/13 2:14 AM, rama david wrote:

Dear Friends,
I simulated the 4 peptide in water box .
As they come close to each other they start to from anti-parallel
beta sheet structure.

Now I want to draw the Free energy surface for the
same ..How is there pot energy ???

Would you please tell me how to do it ..

( I read about g_sham -h, I tried it, but not understand properly)

I will be very grateful for your suggestion and help..

The logic behind g_sham was just posted to this list no more than a few
days ago.

http://lists.gromacs.org/**pipermail/gmx-users/2013-**March/079810.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2013-March/079810.html

It calculates a free energy surface as a function of two variables of your
choosing. As David noted (http://lists.gromacs.org/**
pipermail/gmx-users/2013-**March/079813.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2013-March/079813.html),
the result may not correspond to a true quantitative representation of free
energy differences, though.

-Justin

--
==**==

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

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Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david

Thank you a lot justin for offering me help.

I am interested to use g_sham ..( And if the other command give me my
output, I am also interested to know the other way )

I was confuse with the input that I have to give with g_sham.

I proceed the following command

g_energy is used to get potential ( pot.xvg )
g_rmsdist is used to get rmsdist.xvg
What sis next

My confusion start with the input to give the g_sas ...

As you mention
The input file is simple. It can be one of two forms:

time x y

or simply:

x y

But what is flag for command input and out put.

I also read g_sham -h and manual.
Please accept my apology.

I will be grateful to you for help ...

With best regards,
Rama david.

On Thu, Apr 4, 2013 at 6:24 PM, Justin Lemkul jalem...@vt.edu wrote:

On 4/4/13 5:50 AM, rama david wrote:

Thank you justin,

I read the articles, archive and also g_sham -h,

As I mentioned in previous mail, I simulated four random coil peptide ,
they started to form
Beta sheet structure after 20 ns ..( simulation time 100ns )

My interest is how to draw the Free energy diagram for Potential energy
and
Structures...(eg. RMSD, Gyrate, different cluster ,
with different structure at particular time ) .

Would you please tell me how to do it in gromacs with command line and
needed input.

The command issued depends on what you're doing. If you want help in that
respect, post the command that you're using and seek specific assistance.
There are too many permutations of possibly correct ways of doing
something for me to offer you a guess.

The input file is simple. It can be one of two forms:

time x y

or simply:

x y

In the latter case, use the -notime option of g_sham.

Choose your favorite parsing language to extract values from the output of
g_energy, g_rms, etc to create the combined file.

-Justin

--
==**==

Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david

Dear Justin,

Thank you a lot for help and kind passion to listen me.

I finally come with the my desired out put.
I

I am grateful to you for help.

With Best Wishes,
Rama david

On Thu, Apr 4, 2013 at 7:09 PM, Justin Lemkul jalem...@vt.edu wrote:

On 4/4/13 9:37 AM, rama david wrote:

Thank you a lot justin for offering me help.

I am interested to use g_sham ..( And if the other command give me my
output, I am also interested to know the other way )

I was confuse with the input that I have to give with g_sham.

I proceed the following command

g_energy is used to get potential ( pot.xvg )
g_rmsdist is used to get rmsdist.xvg
What sis next

My confusion start with the input to give the g_sas ...

As you mention
The input file is simple. It can be one of two forms:

time x y

or simply:

x y

But what is flag for command input and out put.

You need to create your own input, parsing the values from pot.xvg and
rmsdist.xvg. The combined file (.xvg) is then passed to g_sham -f.

-Justin

--
==**==

[gmx-users] REMD general protocol ...

2013-04-02 Thread rama david

Dear friends,
  I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I  thoroughly search the Mailing-list Archive for the REMD problem.
It was a really helpful to start.

 My system consist of peptide + water.

I used the following work-flow, Would you please help me to find out
my mistakes...

1. energy minimesation for peptide  + solvent
2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
3. Make tpr file for each nvt run
4. Then separate  equilibration for each temp ( 4 equilibration steps  )
5. Then made NPT.mdp file for each temp ( 4 temp )
6. Then again equilibration for NPT at 4 temp.( 4 equilibration  steps )
7.   Then run md production  with -replex 1000  -multi 4  command ..

To determine the temp I used web-server  http://folding.bmc.uu.se/remd/

Please suggest me any improvements that are  possible to implement in
my work flow.

I will be very grateful to you for your help and suggestion.

With Best Regards,
Rama David
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Re: [gmx-users] REMD general protocol ...

2013-04-02 Thread rama david

Thank you Massimo sandal, Justin and mark ,

I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in REMD .
So I want to conform protocol from the Expert and experience person )

I will be grateful to you  for your suggestion.





On Tue, Apr 2, 2013 at 6:45 PM, massimo sandal deviceran...@gmail.comwrote:

 I would look on some paper which temperature ranges and conditions
 (NPT/NVT) were used for systems of a similar size and with a similar aim.


 2013/4/2 rama david ramadavidgr...@gmail.com

  Dear friends ,
  Thank you justin and Mark for your suggestion
 
  I increases my temp range from 310-360 K
  Now I get 20 replicas .
 
  Is in such large temp range wlll it be good to use NPT.
 
  Would you tell me the temp differences in which box instability generally
  arises ..
 
 
 
  Is my working-flow right or need to change much
 
 
  Thank you
  With Best Regards..
 
 
 
 
  On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund er...@xray.bmc.uu.se
  wrote:
 
  
   On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote:
  
   
   
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
  I am naive to the Replica exchange Molecular dynamics (
  REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I  thoroughly search the Mailing-list Archive for the REMD problem.
It was a really helpful to start.
   
 My system consist of peptide + water.
   
I used the following work-flow, Would you please help me to find out
my mistakes...
   
1. energy minimesation for peptide  + solvent
2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
3. Make tpr file for each nvt run
4. Then separate  equilibration for each temp ( 4 equilibration
 steps
   )
5. Then made NPT.mdp file for each temp ( 4 temp )
6. Then again equilibration for NPT at 4 temp.( 4 equilibration
   steps )
7.   Then run md production  with -replex 1000  -multi 4  command ..
   
To determine the temp I used web-server
  http://folding.bmc.uu.se/remd/
   
Please suggest me any improvements that are  possible to implement
 in
my work flow.
   
   
Such a narrow range of temperatures defeats the purpose of using
 REMD.
   Normally, a much larger range is used over many more simulations.  For
   near-ambient temperatures, NPT can be used, but if you include much
  higher
   temperatures, you should use NVT due to box instability upon exchanges.
   
-Justin
  
   Sure, the enhanced sampling is basically gone, but you can deduce
   temperature dependences from such simulations and to some extent
 benefit
   from the mixing, can't you?
  
   Erik
  
   
--

   
Justin A. Lemkul, Ph.D.
Research Scientist
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] REMD general protocol ...

2013-04-02 Thread rama david

Thank you justin.
I will do the same.

On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:

On 4/2/13 9:24 AM, rama david wrote:

Thank you Massimo sandal, Justin and mark ,

I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in REMD .
So I want to conform protocol from the Expert and experience person )

I will be grateful to you for your suggestion.

The best training experience would be to take a simple example from the
literature and reproduce it. It is very hard to try to teach someone
completely via email, especially since we do not know the scope and goals
of what you are doing.

With respect to the question about pressure coupling stability over 310 -
360 K, I don't know offhand what to expect, but in general, I think this is
a standard limitation within REMD and you'll probably encounter it. Again,
find a protocol for a similar system and try to get things working. It
will be easier to help you if you have a known objective that has been
demonstrated to work.

-Justin

--
==**==

Re: [gmx-users] enough time for simulation

2013-01-08 Thread rama david

Dear Mohammad,

 I am not a specialist in gromacs.
To observe these phenomenon the time scale is much up to 1microsecond .
So which forcefield you decided to use ???

People generally use Martini Coarse Grain FF for these type of work.

You have to run the system up to you reach your desire result.

With Best Wishes and Regards,
Rama David.



On Tue, Jan 8, 2013 at 12:55 PM, mohammad agha mra...@yahoo.com wrote:
 Dear GROMACS Specialists,

 I have one system consists of many surfactant molecules that they create 
 several micelles. How should I know that time of simulation is enough or not? 
 that means where is the enough time for equilibrium of system?
 To creation of micelles, the small oligomers are merged together and make 
 bigger micelles. When the system reach to equilibrium, the grow of micelles 
 is finished and the size of them are constant and they aren't merged together 
 to make bigger micelles. How I should understand that where is the time for 
 equilibrium of system and the time of finish of micelles growing. I work with 
 NPT ensemble.

 May I ask you to answer me, Please?

 Thanks in advance.
 Best Regards
 Sara

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[gmx-users] About g_enemat problem

2012-12-27 Thread rama david

-- Forwarded message --
From: rama david ramadavidgr...@gmail.com
Date: Wed, Dec 26, 2012 at 9:55 PM
Subject: About g_enemat problem
To: gmx-users-ow...@gromacs.org


Hi Gromacs friend.

I simulated a system containing random peptide
I found that as they start to interact they change there secondary conformation.

I want to determine the interaction potential energy of two peptide only.
I make new mdp file containing  the energygrps protein1 and protein2
I rerun the mdrun
Now When I gave the command g_enemat it replied like

Opened md-rerun.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):protein1-protein1 (0,0)in
energy file
WARNING! could not find group (null):protein1-protein2 (0,1)in energy file
group 1WARNING! could not find group (null):protein2-protein2 (1,1)in
energy file

Will select half-matrix of energies with 6 elements
Last energy frame read 10 time 10.000
Will build energy half-matrix of 2 groups, 6 elements, over 11 frames
Segmentation fault (core dumped)


I face the same problem in another system also...




but when I wrote the command g_energy I received


Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
  1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4  LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8  Disper.-corr.
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12  Kinetic-En.
 13  Total-Energy14  Temperature 15  Pres.-DC16  Pressure
 17  Constr.-rmsd18  Box-X   19  Box-Y   20  Box-Z
 21  Volume  22  Density 23  pV  24  Enthalpy
 25  Vir-XX  26  Vir-XY  27  Vir-XZ  28  Vir-YX
 29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32  Vir-ZY
 33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36  Pres-XZ
 37  Pres-YX 38  Pres-YY 39  Pres-YZ 40  Pres-ZX
 41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44  Box-Vel-XX
 45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48  Mu-Y
 49  Mu-Z50  Coul-SR:protein1-protein1
 51  LJ-SR:protein1-protein1 52  LJ-LR:protein1-protein1
 53  Coul-14:protein1-protein1   54  LJ-14:protein1-protein1
 55  Coul-SR:protein1-protein2   56  LJ-SR:protein1-protein2
 57  LJ-LR:protein1-protein2 58  Coul-14:protein1-protein2
 59  LJ-14:protein1-protein2 60  Coul-SR:protein1-SOL
 61  LJ-SR:protein1-SOL  62  LJ-LR:protein1-SOL
 63  Coul-14:protein1-SOL64  LJ-14:protein1-SOL
 65  Coul-SR:protein2-protein2   66  LJ-SR:protein2-protein2
 67  LJ-LR:protein2-protein2 68  Coul-14:protein2-protein2
 69  LJ-14:protein2-protein2 70  Coul-SR:protein2-SOL
 71  LJ-SR:protein2-SOL  72  LJ-LR:protein2-SOL
 73  Coul-14:protein2-SOL74  LJ-14:protein2-SOL
 75  Coul-SR:SOL-SOL 76  LJ-SR:SOL-SOL
 77  LJ-LR:SOL-SOL   78  Coul-14:SOL-SOL
 79  LJ-14:SOL-SOL   80  T-Protein   81  T-non-Protein   82  Lamb-Protein
 83  Lamb-non-Protein





Where am I wrong ???

Is there any other way to do these ???





I also want to check the change in entropy of sol and protein ..How to
check it ???

Please give me the suggestion.I will be a very thankfull to you.

With Best Wishes and regards,
Rama david
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Re: [gmx-users] About the biotin parameter.....

2012-11-28 Thread rama david

Hi justin thank you for suggestion.

I think to Calculate the free energy of solvation of biotin, I hve to use
the method
as per your tuotorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html

Is these right or I have to do anything else???

With Best Wishes and regards,
Rama david

On Wed, Nov 28, 2012 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/28/12 12:20 AM, rama david wrote:

Hi justin,

Thank you for your suggestion.

I read the ATB paper but the paper does not mention any thing related to
the biotin.

Probably not, it's too complex to be considered a model compound.

When I mail them, they replied ..

To clarify the validation:
There are different levels of validation criteria used in the ATB.
The one which is available on the ATB web-site for a given molecule is the
validation of the topology against the compatibility with the GROMOS force
field. The output contains energies for bonded parameters.
The validation described in the paper is the validation against the
experimental hydration free energy of small organic molecules. Biotin was
not a part of the validation dataset.

What should I have to do..???

Validation of a method (i.e., the ATB algorithm) and validation of the
resulting parameters are different concepts. It is still incumbent upon
you to demonstrate that the parameters you got from somewhere else (i.e.,
ATB) are suitable for what you intend. If you were to manually derive the
parameters, you'd have to do the same thing. There is no guarantee that
any service (PRODRG, ATB, etc) are inherently correct. ATB is generally
quite good, but any reviewer worth his salt is going to ask whether or not
you have evidence that the biotin parameters you chose are actually going
to represent reality before you go spending a lot of time running
simulations, collecting data, and making conclusions.

The underlying validation of Gromos96 parameters involves calculating free
energies of solvation for model compounds, which are then mapped back to
the desired molecule (usually some biomolecule like an amino acid). So, in
theory, you could:

1. Calculate the free energy of solvation of biotin, if it is known
2. Run test simulations of biotin in your protein and verify that it
engages in known interactions

Those are just what come to mind immediately, but you should consult the
literature for other cofactors and see how they were parameterized.
Gromos96 includes parameters for ATP, FAD, FMN, and others, so clearly
there is methodology somewhere to which you can refer.

-Justin

--
==**==

Re: [gmx-users] About the biotin parameter.....

2012-11-28 Thread rama david

Hi justin,
Thank you for help

With Best wishes and Regards,
Rama david

On Wed, Nov 28, 2012 at 7:09 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/28/12 8:08 AM, rama david wrote:

Hi justin thank you for suggestion.

I think to Calculate the free energy of solvation of biotin, I hve to use
the method
as per your tuotorial

http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/free_energy/**index.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html

Is these right or I have to do anything else???

That is the general workflow, though the .mdp settings will need to be
modified and you will need to do both van der Waals and Coulombic
transformations. I would also assume that you will need longer simulations
and more lambda points to define the transformation, since biotin is
considerably more complex than methane.

-Justin

--
==**==

[gmx-users] Fwd: Validation of topology ....

2012-11-27 Thread rama david

Dear Gromacs friends,
 I want to simulate a system containing the biotin.
I get the topology from ATB.
   I want to validate these toplogy for my use .
So please could some one told me the way how I can do it ??
I never had any such experience.
Is these is any tutorial regarding to these.
These is most difficult but needed things in MD.

With best wishes and regards,
Rama David.
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Re: [gmx-users] About the biotin parameter.....

2012-11-27 Thread rama david

Hi justin,

Thank you for your suggestion.

I read the ATB paper but the paper does not mention any thing related to
the biotin.

When I mail them, they replied ..

To clarify the validation:
There are different levels of validation criteria used in the ATB.
The one which is available on the ATB web-site for a given molecule is the
validation of the topology against the compatibility with the GROMOS force
field. The output contains energies for bonded parameters.
The validation described in the paper is the validation against the
experimental hydration free energy of small organic molecules. Biotin was
not a part of the validation dataset.


What should I have to do..???
Please give me the suggestion.

With best wishes and regards,
Rama david
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[gmx-users] Validation of topology ....

2012-11-26 Thread rama david

Dear Gromacs friends,
 I want to simulate a system containing the biotin.
I get the topology from ATB.
   I want to validate these toplogy for my use .
So please could some one told me the way how I can do it ??
I never had any such experience.
Is these is any tutorial regarding to these.
These is most difficult but needed things in MD.

With best wishes and regards,
Rama David.
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Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

2012-11-22 Thread rama david

Hi justin,
Thank you for reply.
As per your suggestion,
The whole protein should always be the group for the
surface calculation. Whatever subset of those atoms (i.e. residues of
interest) can be the output group.

So as per your suggestion I have to select the protein as my option 1 and
for output I have to select the hydrophilic residues or hydrophobic
residues as per my choice Is these is right ??? or Am I wrong???
( That means I have to make to index file that contain two groups
hydrophilic and hydrophobic residues.)

Would you please tell me why not select the protein as output, as I am
calculating the change in the hydrophilic and hydrophobic surface area of
protein...???

As per the manual,

The program will ask for a group for the surface calculation and a
group for the output. The
calculation group should always consists of all the non-solvent atoms in the
system. The output group can be the whole or part of the calculation group.

As two protein comes closer in simulation they formed the antiparrallel
beta strand, I want to find the change in hydrophilic and hydrophobic
surface area of protein...

With Best Wishes and Regards,
Rama david

On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/22/12 2:36 AM, rama david wrote:

Dear user ,
I simulate the two protein in random coil position, when they come close
they form antiparallel beta sheet structure.
I want to calculate the change in hydrophilic and hydrophobic surface
area over my simulation time.
For usig g_sas Should I have to make the different index group for
hydrophilic and hydrophobic residues
Or should only have to select the option protein both the time.

The whole protein should always be the group for the surface calculation.
Whatever subset of those atoms (i.e. residues of interest) can be the
output group.

-Justin

--
==**==

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

2012-11-22 Thread rama david

Thank you justin

With best wishes and regards,
Rama David

On Fri, Nov 23, 2012 at 12:45 AM, Justin Lemkul jalem...@vt.edu wrote:

On 11/22/12 1:54 PM, rama david wrote:

Would you please tell me why not select the protein as output, as I am
calculating the change in the hydrophilic and hydrophobic surface area of
protein...???

You can certainly do that. Perhaps I misunderstood the original post. I
thought you were curious about the solvent exposure of certain residues.
If you only care about the evolution of total polar and nonpolar surface
areas, then choose Protein for both groups.

-Justin

As per the manual,

The program will ask for a group for the surface calculation and a
group for the output. The
calculation group should always consists of all the non-solvent atoms in
the
system. The output group can be the whole or part of the calculation
group.

As two protein comes closer in simulation they formed the antiparrallel
beta strand, I want to find the change in hydrophilic and hydrophobic
surface area of protein...

With Best Wishes and Regards,
Rama david

On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/22/12 2:36 AM, rama david wrote:

Dear user ,
I simulate the two protein in random coil position, when they come
close
they form antiparallel beta sheet structure.
I want to calculate the change in hydrophilic and hydrophobic
surface
area over my simulation time.
For usig g_sas Should I have to make the different index group for
hydrophilic and hydrophobic residues
Or should only have to select the option protein both the time.

The whole protein should always be the group for the surface
calculation.
Whatever subset of those atoms (i.e. residues of interest) can be the
output group.

-Justin

--
====

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

====

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Re: [gmx-users] Vizualization with VMD: no image appears

2012-11-21 Thread rama david

Dear,
   -o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file.
And then load it in vmd or pymol u can see it

On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix frau...@ipb-halle.dewrote:

 Hi.

 Try to load in a .gro file of your system first. After that, use the load
 data into molecule option to load in the .xtc.

 -Ursprüngliche Nachricht-
 Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
 Im Auftrag von shch406
 Gesendet: Mittwoch, 21. November 2012 17:47
 An: gmx-users@gromacs.org
 Betreff: [gmx-users] Vizualization with VMD: no image appears

 Dear Gromacs users

 To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
 file to eliminate water molecules and velocities remaining protein
 coordinates only.
 However, when I load this reduced file to VMD no image on screen appears,
 nevertheless VMD have identified the file as a Gromacs compress trajectory
 file.
 What may be the cause of this?

 The corresponding command is as follows:

 trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel

 where MT.xtc contains ~10 frames, defau.ndx is default groups index file.
 Group 2 (Protein-H) was chosen handling dialog.

 Merci pour votre collaboration,
 Igor Shchechkin




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Re: [gmx-users] About the biotin parameter.....

2012-11-15 Thread rama david

Hi Justin thank you,

The ATB server link for Biotin are as follow..
http://compbio.biosci.uq.edu.au/atb/download.py?molid=5783
compbio.biosci.uq.edu.au/atb/download.py?molid=2212

Now should I need to do QM calculations, free energy simulations, and
empirical refinement.
What is your opinion on these topics.

Is there any free available software for these work???( I never did any QM
calclation, Sorry for these basic Question).

With Best Wishes and Regards,
Rama David.

On Thu, Nov 15, 2012 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/15/12 9:47 AM, rama david wrote:

Hi Gromacs Friends,

I want to do the simulation of system containing the
biotin.
I know that the charge calculated by prodrg is not good.
I want to use the GROMOS96 53a6 force field or OPLS force field.
( 1st choice is GROMOS second choice is OPLS)

Please would you tell me how to get topologies for biotin with correct
charge.

Most molecules in the Gromos force fields can be reasonably built from the
charge group building blocks. For biotin, the only trick is the thioether
functional group, but perhaps there are parameters for that. I know there
has been a lot of recent work expanding the Gromos force fields, so someone
may have done that already.

If suitable parameters aren't available, you need to read the primary
literature for the parameter set you're using and derive parameters in a
suitable way, which for Gromos would typically involve some preliminary QM
calculations, free energy simulations, and empirical refinement. The ATB
server is also a possibility; it performs much better than PRODRG, but
anything you get from an automated server should be validated first before
being used in any simulation you care about.

-Justin
--
==**==

Re: [gmx-users] About the biotin parameter.....

2012-11-15 Thread rama david

Should I need to corret charge ...???

On Thu, Nov 15, 2012 at 11:51 PM, rama david ramadavidgr...@gmail.comwrote:

Hi Justin thank you,

The ATB server link for Biotin are as follow..
http://compbio.biosci.uq.edu.au/atb/download.py?molid=5783
compbio.biosci.uq.edu.au/atb/download.py?molid=2212

Now should I need to do QM calculations, free energy simulations, and
empirical refinement.
What is your opinion on these topics.

Is there any free available software for these work???( I never did any QM
calclation, Sorry for these basic Question).

With Best Wishes and Regards,
Rama David.

On Thu, Nov 15, 2012 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/15/12 9:47 AM, rama david wrote:

Hi Gromacs Friends,

Please would you tell me how to get topologies for biotin with correct
charge.

Most molecules in the Gromos force fields can be reasonably built from
the charge group building blocks. For biotin, the only trick is the
thioether functional group, but perhaps there are parameters for that. I
know there has been a lot of recent work expanding the Gromos force fields,
so someone may have done that already.

-Justin
--
==**==

Re: [gmx-users] About periodic image of system.......

2012-11-12 Thread rama david

Thank you for your reply.


On Sun, Nov 11, 2012 at 8:30 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/11/12 4:51 AM, rama david wrote:

 Hi justin ,

 Thank you a lot for your explaination.

 My opinion  on the working of g_mindist -pi is that when it shows the
 distance between two atom
 of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it
 periodic image, and it is the violation of pbc.
 Is these is right??? ( That is the shortest Periodic distance should be
 larger than vdw cut off 1.4 )


 This is correct, when considering a single molecule, i.e. it can't see
 itself. If you have two proteins, and you choose the blanket Protein
 group, you haven't determined anything, because now the calculation
 involves multiple molecules.


  If it is right, g_mindist say that  The shortest periodic distance is
 0.154938 (nm) at time 16162 (ps),
 between atoms 223 and 3270
 This is less than 1.4 then Why it is not problem..???


 Because they're in separate molecules.  Did you ever do as I suggested and
 visualize this frame?  It will be immediately apparent that there is no
 problem.  Please refer to textbooks or even simple Google searching for
 explanations of the minimum image convention.  As I said, it is described
 in almost every reference text.


 -Justin

 --
 ==**==

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

 ==**==
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Re: [gmx-users] About periodic image of system.......

2012-11-11 Thread rama david

Hi justin ,

Thank you a lot for your explaination.

My opinion on the working of g_mindist -pi is that when it shows the
distance between two atom
of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it
periodic image, and it is the violation of pbc.
Is these is right??? ( That is the shortest Periodic distance should be
larger than vdw cut off 1.4 )

If it is right, g_mindist say that The shortest periodic distance is
0.154938 (nm) at time 16162 (ps),
between atoms 223 and 3270
This is less than 1.4 then Why it is not problem..???

As per your previous reply,

The confusion likely arises from the fact that you're selecting Protein,
which actually contains multiple molecules, rather than a single protein
molecule. Atoms can come pretty close during a simulation, especially if
they are involved in, for instance, hydrogen bonds.

These means whenever I have to check the protein pbc , I have to make the
index file for each chain, and have to select the pbc for that???

Please accept my apology if I repiting the same questions. but it is
really confusing to me..

With best Wishes and Regards..
Rama david

On Sun, Nov 11, 2012 at 12:47 AM, Justin Lemkul jalem...@vt.edu wrote:

On 11/10/12 10:22 AM, rama david wrote:

Thank you justin,

I actually check these file in vmd by seeing its periodic image , but
I not seen any problem in PBC.

As per you, If protein contain multiple chain, I have to make the index
group for each one.
Then I have to check each one by g_mindist -pi Is these right???

I suspect that would be more appropriate.

But what wiil be the problem if I used the whole group
Still I not get the your explanation..Pardon me, but please explain it
again??

I don't know how to say it differently. The minimum image convention,
periodicity, and neighbor searching are all covered in almost every
simulation textbook, and some elements are described on gromacs.org and
in the manual.

-Justin

--
==**==

[gmx-users] About periodic image of system.......

2012-11-10 Thread rama david

Dear expert,

I am simulating the protein-ligand system.

Mdp file parameter are

 Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
vdw-type= Cut-off
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation



 the command line and out-put is shown for box preparation are as follow

editconf_mpi -f process.pdb -o princ.pdb -box 11.4  10.7  10.7 -princ -c

new system size :  8.576  4.832  4.220
shift   :  5.003  5.426  6.257 (nm)
new center  :  5.700  5.350  5.350 (nm)
new box vectors : 11.400 10.700 10.700 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :1305.19   (nm^3)

I put the 40 ns production run.


When I checked the pbc by command


 g_mindist_mpi -od pbc-1.xvg -w -pi  -s md.tpr -f md.xtc -b 12000

I got the following result..
The shortest periodic distance is 0.154938 (nm) at time 16162 (ps),
between atoms 223 and 3270

 Atom 223 is protein chain A atom and 3270 is chain B ( ligand atom) .

 I process on xtc file by -pbc nojump and got the nojump.xtc file

I  run the above g_mindist_mpi command on these XTC file . I get

The shortest periodic distance is 3.39417 (nm) at time 12350 (ps),
between atoms 2706 and 3241





So is my system is seeing its periodic image..and I have to rerun..???

(The box  i  used in simulation is  larger than -d 1.0 )

Am I making mistake in comand line???

All suggestion are welcome .


With best wishes and regards,

Rama david.
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Re: [gmx-users] ff parameters

2012-11-10 Thread rama david

Dear ali,

the tutorial link you given used the G43a1 ,
The opls-AA and G43a1 paramete4r are different.

To choose the right parameter for system is a very important step in
simulation.

With best wishes and regards,
Rama david


On Sat, Nov 10, 2012 at 12:10 PM, Ali Alizadeh 
ali.alizadehmoja...@gmail.com wrote:

 Dear Justin

 I confused, in your tutorial, parameters of ff for example:  OPLS-AA

 rlist=rvdw=rcoulomb=1

 but in another tutorial i saw :

 rlist=rcoulomb=0.9

 rvdw= 1.4 or .8

 www-personal.umich.edu/~amadi/fwspidr_tutor.pdf


 --
 Sincerely

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Re: [gmx-users] About periodic image of system.......

2012-11-10 Thread rama david

Hi justin ,
Thank you for reply.
Mdp parameters are as follow ,

; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 0.9; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9; short-range electrostatic cutoff (in nm)
vdw-type= Cut-off
rvdw= 1.4; short-range van der Waals cutoff (in nm)

I choose the protein for g_mindist option..

Please could you explain me what am getting and why it is not violation of
pbc

Sorry for these basic question, but I am confuse with these result


With best wishes and regards,
Rama david.

On Sat, Nov 10, 2012 at 6:55 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/10/12 5:42 AM, rama david wrote:

 Dear expert,

 I am simulating the protein-ligand system.

 Mdp file parameter are

   Neighborsearching
 ns_type = grid  ; search neighboring grid cells
 nstlist = 5 ; 10 fs
 rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
 rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
 vdw-type= Cut-off
 rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
 ; Electrostatics
 coulombtype = PME   ; Particle Mesh Ewald for long-range
 electrostatics
 pme_order   = 4 ; cubic interpolation



   the command line and out-put is shown for box preparation are as follow

 editconf_mpi -f process.pdb -o princ.pdb -box 11.4  10.7  10.7 -princ -c

 new system size :  8.576  4.832  4.220
  shift   :  5.003  5.426  6.257 (nm)
 new center  :  5.700  5.350  5.350 (nm)
 new box vectors : 11.400 10.700 10.700 (nm)
 new box angles  :  90.00  90.00  90.00 (degrees)
 new box volume  :1305.19   (nm^3)

 I put the 40 ns production run.


 When I checked the pbc by command


   g_mindist_mpi -od pbc-1.xvg -w -pi  -s md.tpr -f md.xtc -b 12000


 You shouldn't use -b here.  You should be checking the entire trajectory
 for problems.


  I got the following result..
 The shortest periodic distance is 0.154938 (nm) at time 16162 (ps),
 between atoms 223 and 3270

   Atom 223 is protein chain A atom and 3270 is chain B ( ligand atom) .


 What group did you choose for analysis, System?  This is not a problem.
  PBC artifacts only arise when a molecule sees itself.


I process on xtc file by -pbc nojump and got the nojump.xtc file

 I  run the above g_mindist_mpi command on these XTC file . I get

 The shortest periodic distance is 3.39417 (nm) at time 12350 (ps),
 between atoms 2706 and 3241


 This also looks fine, given the cutoffs described above, even without
 knowing what these atoms are.






 So is my system is seeing its periodic image..and I have to rerun..???


 I see no evidence of a problem.


  (The box  i  used in simulation is  larger than -d 1.0 )

 Am I making mistake in comand line???


 Aside from what's noted above, no.

 -Justin

 --
 ==**==

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 Research Scientist
 Department of Biochemistry
 Virginia Tech
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 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] ff parameters,

2012-11-10 Thread rama david

Hi justin,
If you dont mind please give the link for gromacs 4 paper , it will surely
help
me to decide ff and parameter...

Thank you in advance,

With best wishes and regards,
Rama david

On Sat, Nov 10, 2012 at 6:58 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/10/12 7:09 AM, Ali Alizadeh wrote:

Dear Rama

Thank you for your reply dear Rama,

I'm really sorry,

My link was wrong,

This link is correct:

cinjweb.umdnj.edu/~kerrigje/**pdf_files/fwspidr_tutor.pdfhttp://cinjweb.umdnj.edu/~kerrigje/pdf_files/fwspidr_tutor.pdf

Of course this tutorial do not use opls-aa but it says some of
parameters about opls ff .(page-4)

I have no idea where these parameters come from (even the ones in Berk's
notes). I have never seen people use such settings with Gromos96, and
those listed in the table conflict with the protocols in the Gromos96
literature. Settings for OPLS-AA are less clear. It is very common to use
1.0-nm cutoffs (and in fact was the case in the Gromacs 4 paper), though
the original OPLS literature used different cutoffs depending upon what
types of molecules were present, which is not possible in Gromacs. You
should read lots of papers by people who use OPLS-AA for similar types of
systems and evaluate their success or inaccuracies.

-Justin

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Re: [gmx-users] About periodic image of system.......

2012-11-10 Thread rama david

Dear justin,

Thank you for your reply and explanation,

My ligand is protein( 4 amino acid peptide).
The group in index file PROTEIN contain both ligand
and protein.

The box size is 11.4942 10.7884 10.7884 at the time 16162 (ps).

The box size I given in editconf is 11.4 10.7 10.7

So please would you told me the reason for my g_mindist value less than vdw
cut off 1.4 ?

With best wishes and regards,
Rama david

On Sat, Nov 10, 2012 at 7:26 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/10/12 8:44 AM, rama david wrote:

Hi justin ,
Thank you for reply.
Mdp parameters are as follow ,

; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 0.9; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9; short-range electrostatic cutoff (in nm)
vdw-type= Cut-off
rvdw= 1.4; short-range van der Waals cutoff (in nm)

I choose the protein for g_mindist option..

Please could you explain me what am getting and why it is not violation of
pbc

Before you said you had a protein and ligand. Is the ligand itself
actually a protein?

PBC artifacts arise when you violate the minimum image convention, that
is, the same interaction is calculated multiple times, thus leading to
erroneous contributions to the forces and flawed dynamics. If you avoid
double-counting of interactions by setting an appropriately sized box,
these don't occur.

The only way I would see any spurious interactions occurring in your case
is if the box massively shrank (which probably would have caused the system
to crash anyway) or if any protein molecules unfolded. Stable, well-folded
proteins placed in suitably sized boxes generally do not experience PBC
artifacts, and the evidence you have presented thus far is not indicative
of any problem.

-Justin

--
==**==

Re: [gmx-users] About periodic image of system.......

2012-11-10 Thread rama david

Thank you justin,

I actually check these file in vmd by seeing its periodic image , but
I not seen any problem in PBC.

As per you, If protein contain multiple chain, I have to make the index
group for each one.
Then I have to check each one by g_mindist -pi Is these right???

But what wiil be the problem if I used the whole group
Still I not get the your explanation..Pardon me, but please explain it
again??

On Sat, Nov 10, 2012 at 8:34 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/10/12 10:02 AM, rama david wrote:

Dear justin,

Thank you for your reply and explanation,

My ligand is protein( 4 amino acid peptide).
The group in index file PROTEIN contain both ligand
and protein.

The box size is 11.4942 10.7884 10.7884 at the time 16162 (ps).

The box size I given in editconf is 11.4 10.7 10.7

So please would you told me the reason for my g_mindist value less than
vdw
cut off 1.4 ?

Look at what those atoms are at that particular time point. The confusion
likely arises from the fact that you're selecting Protein, which actually
contains multiple molecules, rather than a single protein molecule. Atoms
can come pretty close during a simulation, especially if they are involved
in, for instance, hydrogen bonds.

-Justin

--
==**==

Re: [gmx-users] Multiple protein simulations in a box

2012-11-02 Thread rama david

Dear Rajeswari,
 May I ask you why you want to do the multiple protein simulation.??
Please mention the purpose clearly, otherwise it is hard to understand
what you are doing  and what you need???,

With best wishes and Regards,
Rama David


On Fri, Nov 2, 2012 at 3:22 PM, Rajeswari A. rajeswari.biot...@gmail.comwrote:

 Dear Gromacs Users,
 I want to simulate multiple number of proteins in a box. I am very confused
 in choosing what MD method will be useful to solve my problem. Can i do it
 with regular molecular dynamics simulations? I am not sure whether
 diffusion of solutes are taken care in standard MD. or should i opt
 brownian dynamics for this purpose? Is there any special method where i can
 do simulate multiple proteins in a box?

 Thank you.
 Rajeswari.
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Re: [gmx-users] about tc_grps in mdp file...

2012-11-02 Thread rama david

thank you..


On Fri, Nov 2, 2012 at 3:56 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/2/12 1:13 AM, rama david wrote:

 Dear all,
   I am running a system with sol 40646 atom and ion, NA 629 CL 634.
 At the time of nvt and npt should i have to make different *tc_grps* for

 ion and sol or should be make one group
 Nonprotein ( these include sol + ion)..these is default.


 http://www.gromacs.org/**Documentation/Terminology/**Thermostatshttp://www.gromacs.org/Documentation/Terminology/Thermostats

 -Justin

 --
 ==**==

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 Research Scientist
 Department of Biochemistry
 Virginia Tech
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 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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[gmx-users] about tc_grps in mdp file...

2012-11-01 Thread rama david

Dear all,
 I am running a system with sol 40646 atom and ion, NA 629 CL 634.
At the time of nvt and npt should i have to make different *tc_grps* for
ion and sol or should be make one group
Nonprotein ( these include sol + ion)..these is default.

With Best wishes and regards,
Rama david
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[gmx-users] REMD queries

2012-10-13 Thread rama david

Hi friends ,
I am new to the REMD simulation.
I read some thread from archive but they not clarify by queries that why I
am asking you  on forum

 I have following Queries:

1.  I want to simulate protein by remd at physiological temp ( 310).

 So my initial temp of replica should be 310 or less than that???
2.  I read some thread for archive but not get the exact protocol :

   As per the   http://www.gromacs.org/Documentation/How-tos/REMD
link I have to do the seperate NVT for each replica...

But Should for NPT and Production run  I have to do the same thing ???

Or please help me to set the proper protocol..


When I used the T-remd  http://folding.bmc.uu.se/remd/

for NVT

*ERROR*: Can not do constant volume yet!

So how to determine temp for the nvt ???




Is it possible to run replica directly in the production run ???



These may be simple  question but as  new to REMD these question putting me
in a great trouble

For NPT with constrained I got following result

Summary of input and derived variables. VariableValue Pdes0.1 Temperature
range310 - 350 Number of water molecules3000 Number of protein
atoms284 Including
all H~ 431 Number of hydrogens in protein~ 62 Number of constraints~ 284 Number
of vsites~ 0 Number of degrees of freedom~ 27568Energy loss due to
constraints1.18 (kJ/mol K)


Should I have to use these same value for NVT and production MD ???

or for production MD I have to use NPT Constraints in the protein: fully
flexible

I just confused with these options.

So please give me proper protocol.

Thank you in advance.

With best wishes and regards
Rama david,
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Re: [gmx-users] Martini FF for Sec structure changes...

2012-10-10 Thread rama david

Thank you for your reply,

Are these Cg can be used in Gromacs.

Thank you in advance.

With best wishes and regards,

Rama david

On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote:

Martini FF cannot model changes in secondary structure ... other CG FF
can. You'll find them easily in the literature. Notably the ones from
Deserno or Derreumaux.

On Oct 10, 2012, at 2:03 PM, rama david wrote:

Hi friends,

I planed to use the martini force-field for my simulation study of
peptide.

The peptides are initially alpha-helix in nature. As they come together
they formed amyloid fibre( Antiparallel Beta structure).

Is it is possible to study the secondary structure backbone study by
martini force field.

I read in there tutorial that the Secondary structure is predefined
therefore they are statics through out the simulation.
Conformational changes that produces changes in Sec structure are out of
scope in martini. only tertiary structure are free defined to change..

So what to do ???
How to use Martini FF to study secondary structure ???

Is there any way to use coarse grained FF to use for study in Sec.
structure???

With Best wishes and regards,
Rama David
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Re: [gmx-users] Martini FF for Sec structure changes...

2012-10-10 Thread rama david

Hi thank you

Please told me the name of Freely available software on which these FF can
be used ..


Thank you in advance

With best wishes and regards,
Rama david


On Wed, Oct 10, 2012 at 6:26 PM, XAvier Periole x.peri...@rug.nl wrote:


 Nope, but on other softwares.


 On Oct 10, 2012, at 2:50 PM, rama david wrote:

  Thank you for your reply,

 Are these Cg can be used in Gromacs.

 Thank you in advance.

 With best wishes and regards,

 Rama david

 On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote:


 Martini FF cannot model changes in secondary structure ... other CG FF
 can. You'll find them easily in the literature. Notably the ones from
 Deserno or Derreumaux.


 On Oct 10, 2012, at 2:03 PM, rama david wrote:

 Hi friends,


 I planed to use the martini force-field for my simulation study of
 peptide.

 The peptides are initially alpha-helix in nature. As they come together
 they formed amyloid fibre( Antiparallel Beta structure).

 Is it is possible to study the secondary structure backbone study by
 martini force field.

 I read in there tutorial that the Secondary structure is predefined
 therefore they are statics through out the simulation.
 Conformational changes that  produces  changes in Sec structure are out
 of
 scope in martini. only  tertiary structure are free defined to change..


 So what to do ???
 How to use Martini FF to study secondary structure ???

 Is there any way to use coarse grained FF to use for study in Sec.
 structure???


 With Best wishes and regards,
 Rama David
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Re: [gmx-users] Interaction study for peptide-receptor..

2012-10-09 Thread rama david

Hi,

Yes it is possible to screen peptides as ligand.

But for these following information is needed

1. Binding site of peptide and ligand
2. Which residues in peptide are important for binding.

After you simply do the mutation on the desired peptide.Performed the MD
upto 50 ns

Find the interaction energy.

As the MD need a lot of time , you can´t use it for the large library.
I plan to do only 5 simulation.

With best wishes and regards.
Rama david

On Wed, Oct 10, 2012 at 6:54 AM, Justin Lemkul jalem...@vt.edu wrote:

On 10/9/12 9:17 PM, Liu Shiyong wrote:

Justin,

Single mutation for four residue. The number of mutants is 4x19=76
Of course , that is a tiny peptide library.

Of course one can design many different mutants with a 4-residue peptide
(far more than 76 in fact, considering all possible combinations of all 20
amino acids), but I do not believe that is the intent of the OP here.
Referring to the original post:

http://lists.gromacs.org/**pipermail/gmx-users/2012-**October/075182.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2012-October/075182.html

It seems that 4 total simulations are intended (perhaps 4 simulations with
replicates).

-Justin

On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul jalem...@vt.edu wrote:

On 10/9/12 8:43 PM, Liu Shiyong wrote:

Hi,

Your expectation from MD is too much than reality.

Peptide design is an open problem. Lots of elegant protocols are
available. However, to my understanding, the core problem is still
about protein-peptide docking and scoring. MD simulation only helps on
some special cases. It is impossible that MD simulation is used to for
screening peptide library.

I would hardly call 4 different mutants a library. Plenty of methods
exist
to enhance the sampling of such systems and have been used to great
effect.
Computationally expensive to pull off properly? Yes. Impossible? In
this
case, I would say no.

-Justin

On Thu, Oct 4, 2012 at 9:16 PM, rama david ramadavidgr...@gmail.com
wrote:

Thank you for reply,
I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the receptor binding site and used the the solid support
to the binding site and did simulation.
So if I freeze the group is it will ok ??
Is it possible in gromacs to fix the residue on solid immobilized
surface.
If it is how to do it??

my question is How to decide which group are remove and which group
should
keep in simulation.

thank you in advance
Thank you for giving your valuable time and advice to me.

With best wishes and regards,
Rama david

On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis
teva...@gmail.comwrote:

I don't think AutoDock and Vina are suitable for peptide docking. I
would
first try the FlexPepDocking module of Rosetta which does ab initio
folding
of the peptide on the receptor, while moving the side-chains of the
protein
but leaves its backbone intact. Rosetta implements a knowledge-based
scoring, which has been specifically designed for this task and is as
fast
as Vina or AutoDock.

I would first do that and if I wouldn't get any reasonable results
then
I
would move to MD starting from the top scored protein-peptide
complexes
created by Rosetta.

Thomas

On 4 October 2012 15:08, rama david ramadavidgr...@gmail.com wrote:

Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto
the
mark.

Is the freezing of group can affect my system?? How much efficiency I
get
by these work??
As these group are going to freeze in four simulation so if it affect
one
ligand it affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??

If you have any other way please suggest it..

With best wishes and regards
Rama david

On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
francesco.ot...@gmail.com**wrote:

Hi,
as far as I know, freezing just set velocities to 0 so you gain
nothing
freezing atoms.

By the way, have you tried docking? It takes into account multiple
conformation and
orientation of the peptide and, depending upon the implemented

algorithm,

also
protein sidechain orientation.

Francesco

2012/10/4 rama david ramadavidgr...@gmail.com

thank you Justin for reply.

I dont know about long range interactions.
But as I freeze the group I think it will improve my computational

speed.

So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most
probably

Re: [gmx-users] Interaction energy..

2012-10-08 Thread rama david

Hi justin,
As per your advice,

 g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 0 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
Segmentation fault (core dumped)

What is the reason  ???

thank you in advance.


With best wishes and regards
Rama david.






On Sat, Oct 6, 2012 at 6:47 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/6/12 6:26 AM, rama david wrote:

 Hi justin,

 I tried as per your suggestion.

 command line

 g_enemat -f ener.edr -groups groups.dat -temp 310  -nolj -free

 the out put is like ,



 Opened ener.edr as single precision energy file
 Will read groupnames from inputfile
 Read 2 groups
 group 0WARNING! could not find group (null):energy-energy (0,0)in energy
 file
 WARNING! could not find group (null):energy-extra34 (0,1)in energy file
 group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
 file

 Will select half-matrix of energies with 3 elements
 Last energy frame read 5 time 1.000
 Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
 Segmentation fault (core dumped)

 why program not work ?? Is it  bug??? or Am I doing any stupid mistake???


 It might be a bug, but I'm not sure yet.  Please run the command without
 the -free option (and thus without -temp) to further reduce complexity.
  Then manually add the -coul flag.  It should be set by default, but at
 this point the screen output seems to indicate that no energy terms are
 being detected.


 -Justin

 --
 ==**==

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

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Re: [gmx-users] how to center the protein?

2012-10-08 Thread rama david

you can put the protein in center by adding flag -center to trjconv ( see
trjconv -h)

use the proper index file ( if you made ) -n ..

You can also use the -pbc cluster and extract the specific time frame by
flag -dump

see trjconv very carefully ,It has the way to do it.

With best wishes and regards
Rama david

On Mon, Oct 8, 2012 at 3:06 PM, Albert mailmd2...@gmail.com wrote:

Dear:

I am using the command:

trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol

trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans

to extract a frame of my md simulation and I found my protein is not in
the centre of simulation box. here is a figure for it:

https://dl.dropbox.com/u/**56271062/position.jpghttps://dl.dropbox.com/u/56271062/position.jpg

as we cab see the protein is just in the corner of box and the water
molecules (lefft sphere) in the protein was separate from protein and on
the otherside of box.

THX
Albert
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Re: [gmx-users] Interaction energy..

2012-10-08 Thread rama david

Hi justin,
I correct command as follow and
 g_enemat -f ener.edr -groups groups.dat -coul -lj

out-put is like


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 9 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames
Segmentation fault (core dumped)


On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/8/12 5:40 AM, rama david wrote:

 Hi justin,

 As per your advice,

   g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


 Opened ener.edr as single precision energy file
 Will read groupnames from inputfile
 Read 2 groups
 group 0WARNING! could not find group (null):energy-energy (0,0)in energy
 file
 WARNING! could not find group (null):energy-extra34 (0,1)in energy file
 group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
 file

 Will select half-matrix of energies with 0 elements
 Last energy frame read 5 time 1.000
 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
 Segmentation fault (core dumped)

 What is the reason  ???


 I told you to add the -coul flag, not -nocoul.  With the above command,
 you're explicitly telling g_enemat to not do anything useful.


 -Justin

 --
 ==**==

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

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Re: [gmx-users] Interaction energy..

2012-10-08 Thread rama david

Hi justin,


g_enemat -f ener.edr -groups groups.dat -coul -nolj


Out-put is like

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)


Thank you in advance
Rama david.



 Let me be a bit more specific again.  I previously suggested there was a
 problem with the -lj flag activating more than one option in the code, so
 that is a potential problem.  I suggested adding -nolj -coul to test this
 theory.  Please use those options (not -coul -lj) and see what happens.

 -Justin


 On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/8/12 5:40 AM, rama david wrote:

  Hi justin,

 As per your advice,

g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


 Opened ener.edr as single precision energy file
 Will read groupnames from inputfile
 Read 2 groups
 group 0WARNING! could not find group (null):energy-energy (0,0)in energy
 file
 WARNING! could not find group (null):energy-extra34 (0,1)in energy file
 group 1WARNING! could not find group (null):extra34-extra34 (1,1)in
 energy
 file

 Will select half-matrix of energies with 0 elements
 Last energy frame read 5 time 1.000
 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
 Segmentation fault (core dumped)

 What is the reason  ???


  I told you to add the -coul flag, not -nocoul.  With the above command,
 you're explicitly telling g_enemat to not do anything useful.


 -Justin

 --
 ====


 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
 h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 

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 --
 ==**==

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 Virginia Tech
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 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] Interaction energy..

2012-10-06 Thread rama david

Hi justin,

the out put of g_energy are like

-
  1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
 13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
 17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
 21  Volume  22  Density 23  pV  24
Enthalpy
 25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
 29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
 33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
 37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
 41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
 45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
 49  Mu-Z50
Coul-SR:energy-energy
 51  LJ-SR:energy-energy 52
LJ-LR:energy-energy
 53  Coul-14:energy-energy   54
LJ-14:energy-energy
 55  Coul-SR:energy-extra34  56
LJ-SR:energy-extra34
 57  LJ-LR:energy-extra3458
Coul-14:energy-extra34
 59  LJ-14:energy-extra3460
Coul-SR:energy-rest
 61  LJ-SR:energy-rest   62
LJ-LR:energy-rest
 63  Coul-14:energy-rest 64
LJ-14:energy-rest
 65  Coul-SR:extra34-extra34 66
LJ-SR:extra34-extra34
 67  LJ-LR:extra34-extra34   68
Coul-14:extra34-extra34
 69  LJ-14:extra34-extra34   70
Coul-SR:extra34-rest
 71  LJ-SR:extra34-rest  72
LJ-LR:extra34-rest
 73  Coul-14:extra34-rest74
LJ-14:extra34-rest
 75  Coul-SR:rest-rest   76
LJ-SR:rest-rest
 77  LJ-LR:rest-rest 78
Coul-14:rest-rest
 79  LJ-14:rest-rest 80
T-Protein
 81  T-non-Protein   82
Lamb-Protein
 83  Lamb-non-Protein




When I used g_enemat with the groups.dat file like these

2
extra34
energy

I got the output


roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)


Now When I changed the groups.dat like

2
energy
extra34

( change in the order of the index groups )

I got the following output,

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 6 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames
Segmentation fault (core dumped)




So What is wrong ??
Is I am doing any wrong ??



 2. I am using the temp 310 so the reference temp by default is 300 Should
I have to change it to 310

(-tempreal   300 reference temperature for free energy
calculation )

Any suggestion on these topic, is helpful to me.


Thank you in advance,



With best wishes and regards,
Rama david.
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Re: [gmx-users] Interaction energy..

2012-10-06 Thread rama david

Hi justin,

I tried as per your suggestion.

command line

g_enemat -f ener.edr -groups groups.dat -temp 310  -nolj -free

the out put is like ,



Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)

why program not work ?? Is it  bug??? or Am I doing any stupid mistake???

Thank you in advance ..



With best wishes and regards,
Rama david

On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/6/12 2:28 AM, rama david wrote:

 Hi justin,

 the out put of g_energy are like

 --**--**-
1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
 LJ-14
5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
 Disper.-corr.
9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
 Kinetic-En.
   13  Total-Energy14  Temperature 15  Pres.-DC16
 Pressure
   17  Constr.-rmsd18  Box-X   19  Box-Y   20
 Box-Z
   21  Volume  22  Density 23  pV  24
 Enthalpy
   25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
 Vir-YX
   29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
 Vir-ZY
   33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
 Pres-XZ
   37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
 Pres-ZX
   41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
 Box-Vel-XX
   45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
 Mu-Y
   49  Mu-Z50
 Coul-SR:energy-energy
   51  LJ-SR:energy-energy 52
 LJ-LR:energy-energy
   53  Coul-14:energy-energy   54
 LJ-14:energy-energy
   55  Coul-SR:energy-extra34  56
 LJ-SR:energy-extra34
   57  LJ-LR:energy-extra3458
 Coul-14:energy-extra34
   59  LJ-14:energy-extra3460
 Coul-SR:energy-rest
   61  LJ-SR:energy-rest   62
 LJ-LR:energy-rest
   63  Coul-14:energy-rest 64
 LJ-14:energy-rest
   65  Coul-SR:extra34-extra34 66
 LJ-SR:extra34-extra34
   67  LJ-LR:extra34-extra34   68
 Coul-14:extra34-extra34
   69  LJ-14:extra34-extra34   70
 Coul-SR:extra34-rest
   71  LJ-SR:extra34-rest  72
 LJ-LR:extra34-rest
   73  Coul-14:extra34-rest74
 LJ-14:extra34-rest
   75  Coul-SR:rest-rest   76
 LJ-SR:rest-rest
   77  LJ-LR:rest-rest 78
 Coul-14:rest-rest
   79  LJ-14:rest-rest 80
 T-Protein
   81  T-non-Protein   82
 Lamb-Protein
   83  Lamb-non-Protein




 When I used g_enemat with the groups.dat file like these

 2
 extra34
 energy

 I got the output


 roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
 file
 WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
 WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
 WARNING! could not find group (null):extra34-energy (0,1)in energy file
 group 1WARNING! could not find group (null):energy-energy (1,1)in energy
 file

 Will select half-matrix of energies with 4 elements
 Last energy frame read 5 time 1.000
 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
 Segmentation fault (core dumped)


 Now When I changed the groups.dat like

 2
 energy
 extra34

 ( change in the order of the index groups )

 I got the following output,

 Opened ener.edr as single precision energy file
 Will read groupnames from inputfile
 Read 2 groups
 group 0WARNING! could not find group (null):energy-energy (0,0)in energy
 file
 WARNING! could not find group (null):energy-extra34 (0,1)in energy file
 group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
 file

 Will select half-matrix of energies with 6 elements
 Last energy frame read 5 time 1.000
 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames
 Segmentation fault (core dumped)



 Based on the energy names, this is the appropriate setup, but
 unfortunately I have no idea why it does not work.  I have noticed that
 there is a problem with g_enemat - the -lj flag specifies both LJ-SR and
 LJ-LR terms to be written - which may be complicating matters.  Please try
 your command with -nolj to test.




 So What is wrong ??
 Is I am doing any wrong ??



   2. I am using the temp 310 so the reference temp by default is 300
 Should
 I have to change it to 310

 (-tempreal   300

Re: [gmx-users] Interaction energy calculation..

2012-10-05 Thread rama david

Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it

Would you explain me in detail??

With best wishes and regards,
Rama david.


On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 5:49 AM, rama david wrote:

 Hi Friends,

 I want to study the interaction energy between the selected residues of
 protein and ligand.

 ( Non-bonded energy should include : vanderwall and electrostatics)

 How to do it???


 This is what the energygrps keyword in the .mdp file is for.  Beware the
 interpretation and utility of these quantities.

 -Justin

 --
 ==**==

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

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Re: [gmx-users] Interaction energy calculation..

2012-10-05 Thread rama david

Hi justin,
thank you for reply.

With best wishes and regards
Rama david.



On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 6:15 AM, rama david wrote:

 Hi justin,
 I completed the simulation ,
 Now I want to use the selected residues of protein and ligand.
 How to do it

 Would you explain me in detail??


 Create a new .tpr file from an .mdp file with suitable energygrps.  Use
 mdrun -rerun to recalculate energies.


 -Justin

 --
 ==**==

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

 ==**==
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Re: [gmx-users] Interaction energy..

2012-10-05 Thread rama david

Thank you for your Help.

I did the following tc-groups

tcoupl= V-rescale; modified Berendsen thermostat
tc-grps=  extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time constant, in ps
ref_t=  310310 310 ; reference temperature, one for each
group, in K
;

Energy contain the residues that i needed
extra34 contain all the remaining ligand and receptor atom
non-protein contain sol and ion.

I got the energy file after mdrun -rerun

I used the g_energy term

It give me the following output
End your selection with an empty line or a zero.
---
  1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
 13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
 17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
 21  Volume  22  Density 23  pV  24
Enthalpy
 25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
 29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
 33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
 37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
 41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
 45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
 49  Mu-Z50  T-extra34   51  T-non-Protein   52
T-energy
 53  Lamb-extra3454
Lamb-non-Protein
 55  Lamb-energy


So I confused. though it shows the energy group, which option should i have
to choose ??

What is Lamb-energy???

Is I did any mistake??? or I have to use any else command ??

Thank you in advance

With best wishes and regards.
Rama david.






On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 10:16 AM, rama david wrote:

 Hi gromacs friends,

 I completed the simulation of receptor and ligand,
 I visualized the trajectory in the vmd I found  most of the time C
 terminal
 (ARG) interact with receptor ( 320 ASP) .
 I want to find out these interaction energy between these two residues in
 the simulation.



 How to find  these interaction energy

 ( include the LJ and electrostatic interaction)..


 I explained how to do this already.  You need properly set energygrps in
 the .mdp file and an index file that specifies those groups.  The
 quantities you want will then be in the .edr file like all other energy
 terms.

 -Justin

 --
 ==**==

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

 ==**==
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Re: [gmx-users] Interaction energy..

2012-10-05 Thread rama david

Hi justin,
Ok now I get
I have to modify mdp parameter ..

Thank you,
With best wishes and regards,
Rama david

On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 11:46 AM, rama david wrote:

 Thank you for your Help.

 I did the following tc-groups

 tcoupl= V-rescale; modified Berendsen thermostat
 tc-grps=  extra34 Non-Protein energy; two coupling groups -
 more accurate
 tau_t= 0.10.1 0.1; time constant, in ps
 ref_t=  310310 310 ; reference temperature, one for each
 group, in K
 ;

 Energy contain the residues that i needed
 extra34 contain all the remaining ligand and receptor atom
 non-protein contain sol and ion.

 I got the energy file after mdrun -rerun

 I used the g_energy term

 It give me the following output
 End your selection with an empty line or a zero.
 --**--**---
1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
 LJ-14
5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
 Disper.-corr.
9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
 Kinetic-En.
   13  Total-Energy14  Temperature 15  Pres.-DC16
 Pressure
   17  Constr.-rmsd18  Box-X   19  Box-Y   20
 Box-Z
   21  Volume  22  Density 23  pV  24
 Enthalpy
   25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
 Vir-YX
   29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
 Vir-ZY
   33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
 Pres-XZ
   37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
 Pres-ZX
   41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
 Box-Vel-XX
   45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
 Mu-Y
   49  Mu-Z50  T-extra34   51  T-non-Protein   52
 T-energy
   53  Lamb-extra3454
 Lamb-non-Protein
   55  Lamb-energy


 So I confused. though it shows the energy group, which option should i
 have
 to choose ??

 What is Lamb-energy???


 It is related to temperature coupling.


  Is I did any mistake??? or I have to use any else command ??


 I have told you to use energygrps (which is described in the manual) and
 you're specifying tc-grps.  Temperature coupling and energy calculation
 groups are very different concepts.


 -Justin

 --
 ==**==

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

 ==**==
 --
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 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Interaction energy..

2012-10-05 Thread rama david

Hi,
 I got the result by g_energy.
Thank you for these .

but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put

roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)

i used the following groups.dat file

2
extra34
energy


What is reason for the error ?? Is I did any mistake again??

Thank you in advance.


With best wishes and regards,

Rama david


On Fri, Oct 5, 2012 at 10:32 PM, rama david ramadavidgr...@gmail.comwrote:

 Hi justin,
 Ok now I get
 I have to modify mdp parameter ..

 Thank you,
 With best wishes and regards,
 Rama david

 On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 11:46 AM, rama david wrote:

 Thank you for your Help.

 I did the following tc-groups

 tcoupl= V-rescale; modified Berendsen thermostat
 tc-grps=  extra34 Non-Protein energy; two coupling groups -
 more accurate
 tau_t= 0.10.1 0.1; time constant, in ps
 ref_t=  310310 310 ; reference temperature, one for each
 group, in K
 ;

 Energy contain the residues that i needed
 extra34 contain all the remaining ligand and receptor atom
 non-protein contain sol and ion.

 I got the energy file after mdrun -rerun

 I used the g_energy term

 It give me the following output
 End your selection with an empty line or a zero.
 --**--**---
1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
 LJ-14
5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
 Disper.-corr.
9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
 Kinetic-En.
   13  Total-Energy14  Temperature 15  Pres.-DC16
 Pressure
   17  Constr.-rmsd18  Box-X   19  Box-Y   20
 Box-Z
   21  Volume  22  Density 23  pV  24
 Enthalpy
   25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
 Vir-YX
   29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
 Vir-ZY
   33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
 Pres-XZ
   37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
 Pres-ZX
   41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
 Box-Vel-XX
   45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
 Mu-Y
   49  Mu-Z50  T-extra34   51  T-non-Protein   52
 T-energy
   53  Lamb-extra3454
 Lamb-non-Protein
   55  Lamb-energy


 So I confused. though it shows the energy group, which option should i
 have
 to choose ??

 What is Lamb-energy???


 It is related to temperature coupling.


  Is I did any mistake??? or I have to use any else command ??


 I have told you to use energygrps (which is described in the manual)
 and you're specifying tc-grps.  Temperature coupling and energy
 calculation groups are very different concepts.


 -Justin

 --
 ==**==

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

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] Interaction study for peptide-receptor..

2012-10-04 Thread rama david

thank you Justin for reply.

I dont know about long range interactions.
But as I freeze the group I think it will improve my computational speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??

Should I do Essential Dynamics ??? or Principle component analysis ???

Would you suggest me any general protocol for such work??

Thank you in Advance

With Best Wishes and regards.
Rama David

On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:

On 10/4/12 2:01 AM, rama david wrote:

Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up of 4 amino acids. I know the interaction pattern of
peptide and receptor.
I plan to mutate single residue each at a time and run 4 simulation .
So I will have the 4 different simulation that contain the mutated
residues
and the wild one.

Then afterward from the interaction energy I want to select the peptide
which is showing
stronger interaction than others.

As mention I know the binding site, If I freeze the remaining portion in
receptor
that not involved in binding , Is it going to affect my screening process
???

Potentially. Do you know that the binding interactions and the mutations
will only perturb local residues? Do you know that there are no long-range
motions to be considered?

I think you gain very little by freezing portions of the system, and risk
more than you gain.

-Justin

--
==**==

Re: [gmx-users] Interaction study for peptide-receptor..

2012-10-04 Thread rama david

Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.

Is the freezing of group can affect my system?? How much efficiency I get
by these work??
As these group are going to freeze in four simulation so if it affect one
ligand it  affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and  used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??

If you have any other way please suggest it..

With best wishes and regards
Rama david


On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 Hi,
 as far as I know, freezing just set velocities to 0 so you gain nothing
 freezing atoms.

 By the way, have you tried docking? It takes into account multiple
 conformation and
 orientation of the peptide and, depending upon the implemented algorithm,
 also
 protein sidechain orientation.

 Francesco


 2012/10/4 rama david ramadavidgr...@gmail.com

  thank you Justin for reply.
 
  I dont know about long range interactions.
  But as I freeze the group I think it will improve my computational speed.
  So is there any way to find out or decide which group should be
  freeze, and which group should affect my interaction most probably??
 
  Should I do Essential Dynamics ??? or Principle component analysis ???
 
  Would you suggest me any general protocol for such work??
 
  Thank you in Advance
 
 
  With Best Wishes and regards.
  Rama David
 
  On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:
 
  
  
   On 10/4/12 2:01 AM, rama david wrote:
  
   Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
   study.Receptor consist a single chain.
   Peptide is made up  of  4 amino acids. I know the interaction pattern
 of
   peptide and receptor.
   I plan to mutate single residue each at a time and  run 4 simulation .
   So I will have the 4 different simulation that contain the mutated
   residues
   and the wild one.
  
  
   Then afterward from the interaction energy I want to select the
 peptide
   which is showing
   stronger interaction than others.
  
   As  mention I know the binding site, If I freeze the remaining portion
  in
   receptor
   that not involved in binding , Is it going to affect my screening
  process
   ???
  
  
   Potentially.  Do you know that the binding interactions and the
 mutations
   will only perturb local residues?  Do you know that there are no
  long-range
   motions to be considered?
  
   I think you gain very little by freezing portions of the system, and
 risk
   more than you gain.
  
   -Justin
  
   --
   ==**==
  
   Justin A. Lemkul, Ph.D.
   Research Scientist
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu | (540) 231-9080
   http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  
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Re: [gmx-users] Interaction study for peptide-receptor..

2012-10-04 Thread rama david

Thank you justin and franscisco,
I have practical data that claim that only a particular residue that is c
terminal residue  is
involve in binding.
  but when I generate the docking data other residues most of the time
comes to play.
I know the binding of natural ligand ( peptide ) and the position.
so I think if I mutate only these residue and simulate the system I will
get the
structure that is more active. In natural ligand the C terminal is playing
important role.


With simulation i will find interaction energy.
  That will tell me about binding affinity  ( Hope so )
These is my basic idea.

Is any other way to do the same thing..

With best wishes and regards
Rama David


On Thu, Oct 4, 2012 at 5:47 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 2012/10/4 rama david ramadavidgr...@gmail.com

  Hi francesco,
 
  Thank you For reply.
  I did docking but the result are not so impressive.
 

 What does it mean not so impressive? I mean, do you have experimental
 data
 and the comparison with docking doesn't agree with experiments? Have you
 generated
 a sufficient number of complexes (say 100 or more)?

 I used vina and autodock.
  I also did virtual screening in autodock but the result are not upto the
  mark.
 
  Is the freezing of group can affect my system?? How much efficiency I get
  by these work??
 

 It will change a lot the dynamics of your system and I don't think
 calculations
 will be more efficient!


  As these group are going to freeze in four simulation so if it affect one
  ligand it  affect other
  ligand also.
 
  I read article that did the work like me ,
  they sliced the binding residues and  used the inert solid sphere to
  support binding residues
  instead of the freezing group other group.
 
  I think both way should have same effect..Am I right or wrong??
 
  If you have any other way please suggest it..
 

 If you already have docking complexes, you can pick up one complex for each
 peptide, to run an MD, or Free Energy  calculations.
 It strongly depends by the experimentale data you have and what is the
 target
 of your work.


 
  With best wishes and regards
  Rama david
 
 
  On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
  francesco.ot...@gmail.comwrote:
 
   Hi,
   as far as I know, freezing just set velocities to 0 so you gain nothing
   freezing atoms.
  
   By the way, have you tried docking? It takes into account multiple
   conformation and
   orientation of the peptide and, depending upon the implemented
 algorithm,
   also
   protein sidechain orientation.
  
   Francesco
  
  
   2012/10/4 rama david ramadavidgr...@gmail.com
  
thank you Justin for reply.
   
I dont know about long range interactions.
But as I freeze the group I think it will improve my computational
  speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??
   
Should I do Essential Dynamics ??? or Principle component analysis
 ???
   
Would you suggest me any general protocol for such work??
   
Thank you in Advance
   
   
With Best Wishes and regards.
Rama David
   
On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu
 wrote:
   


 On 10/4/12 2:01 AM, rama david wrote:

 Hi gromacs Friends,
  I want to do peptide-receptor ( Protein) interaction
 study.Receptor consist a single chain.
 Peptide is made up  of  4 amino acids. I know the interaction
  pattern
   of
 peptide and receptor.
 I plan to mutate single residue each at a time and  run 4
  simulation .
 So I will have the 4 different simulation that contain the mutated
 residues
 and the wild one.


 Then afterward from the interaction energy I want to select the
   peptide
 which is showing
 stronger interaction than others.

 As  mention I know the binding site, If I freeze the remaining
  portion
in
 receptor
 that not involved in binding , Is it going to affect my screening
process
 ???


 Potentially.  Do you know that the binding interactions and the
   mutations
 will only perturb local residues?  Do you know that there are no
long-range
 motions to be considered?

 I think you gain very little by freezing portions of the system,
 and
   risk
 more than you gain.

 -Justin

 --
 ==**==

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

 ==**==
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Re: [gmx-users] Interaction study for peptide-receptor..

2012-10-04 Thread rama david

Thank you  for reply,
 I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the  receptor binding site and used the the solid support
to the binding site and did simulation.
   So if I freeze  the group is it will ok ??
Is it possible in gromacs to fix the residue on solid immobilized surface.
If it is how to do it??

my question is How to decide which group are remove and which group should
keep in simulation.

thank you in advance
Thank you for giving your valuable time and advice to me.

With best wishes and regards,
Rama david






On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis teva...@gmail.comwrote:

 I don't think AutoDock and Vina are suitable for peptide docking. I would
 first try the FlexPepDocking module of Rosetta which does ab initio folding
 of the peptide on the receptor, while moving the side-chains of the protein
 but leaves its backbone intact. Rosetta implements a knowledge-based
 scoring, which has been specifically designed for this task and is as fast
 as Vina or AutoDock.

 I would first do that and if I wouldn't get any reasonable results then I
 would move to MD starting from the top scored protein-peptide complexes
 created by Rosetta.

 Thomas


 On 4 October 2012 15:08, rama david ramadavidgr...@gmail.com wrote:

  Hi francesco,
 
  Thank you For reply.
  I did docking but the result are not so impressive.
  I used vina and autodock.
  I also did virtual screening in autodock but the result are not upto the
  mark.
 
  Is the freezing of group can affect my system?? How much efficiency I get
  by these work??
  As these group are going to freeze in four simulation so if it affect one
  ligand it  affect other
  ligand also.
 
  I read article that did the work like me ,
  they sliced the binding residues and  used the inert solid sphere to
  support binding residues
  instead of the freezing group other group.
 
  I think both way should have same effect..Am I right or wrong??
 
  If you have any other way please suggest it..
 
  With best wishes and regards
  Rama david
 
 
  On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
  francesco.ot...@gmail.comwrote:
 
   Hi,
   as far as I know, freezing just set velocities to 0 so you gain nothing
   freezing atoms.
  
   By the way, have you tried docking? It takes into account multiple
   conformation and
   orientation of the peptide and, depending upon the implemented
 algorithm,
   also
   protein sidechain orientation.
  
   Francesco
  
  
   2012/10/4 rama david ramadavidgr...@gmail.com
  
thank you Justin for reply.
   
I dont know about long range interactions.
But as I freeze the group I think it will improve my computational
  speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??
   
Should I do Essential Dynamics ??? or Principle component analysis
 ???
   
Would you suggest me any general protocol for such work??
   
Thank you in Advance
   
   
With Best Wishes and regards.
Rama David
   
On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu
 wrote:
   


 On 10/4/12 2:01 AM, rama david wrote:

 Hi gromacs Friends,
  I want to do peptide-receptor ( Protein) interaction
 study.Receptor consist a single chain.
 Peptide is made up  of  4 amino acids. I know the interaction
  pattern
   of
 peptide and receptor.
 I plan to mutate single residue each at a time and  run 4
  simulation .
 So I will have the 4 different simulation that contain the mutated
 residues
 and the wild one.


 Then afterward from the interaction energy I want to select the
   peptide
 which is showing
 stronger interaction than others.

 As  mention I know the binding site, If I freeze the remaining
  portion
in
 receptor
 that not involved in binding , Is it going to affect my screening
process
 ???


 Potentially.  Do you know that the binding interactions and the
   mutations
 will only perturb local residues?  Do you know that there are no
long-range
 motions to be considered?

 I think you gain very little by freezing portions of the system,
 and
   risk
 more than you gain.

 -Justin

 --
 ==**==

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

 ==**==
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Re: [gmx-users] Problem with the installation of Gromacs 4-5.5

2012-10-03 Thread rama david

Hi Deepak,

Is the gromacs is in your path??

Please mention your operating system..

With best wishes and Regards,
rama david

On Thu, Oct 4, 2012 at 11:07 AM, Deepak Ojha alwaysinthem...@gmail.comwrote:

 Dear All
 I want to use Amber force field in Gromacs therefore I installed the
 latest version of Gromacs and
 installed accordingly as per as the instructions given in INSTALL.automake
 file.
 ./configure
 make
 make install

 It works fine and shows the message that installation is complete but
 none of the commands like
 pdb2gmx,mdrun works.Even the luck does not works which is meant to
 test the installation of gromacs.
 What is the issue with the installation.Please help me resolve it.

 Regards
 DeepaK Ojha
 School Of Chemistry

 Selfishness is not living as one wishes to live, it is asking others
 to live as one wishes to live
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Re: [gmx-users] Density measurment

2012-10-02 Thread rama david

Thank you Justin for your reply ,

I tried g_density again after your reply. But I found that
it give density with respect to box dimension and not to time.

g_densmap have xpm output and no the xvg ( I need density or no of water
molecule present in between two peptides with respect to the time )..

Please, would you tell me another way to solve these problem..??

Thank you in advance

Have a nice day.
Rama David

On Tue, Oct 2, 2012 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:

On 10/2/12 7:07 AM, rama david wrote:

Hi Gromacs Users,

I did simulation of two random coil peptides for 100ns.
after 70 ns these peptide get converted to anti parallel beta sheet
structure.
I am interested to see the water density in between these peptideswith
respect to time change
and also the no of water molecule between the peptide with respect to
time.
And at the same time the distance between the peptide..
I need these information in xvg graph.

I found out the distance between peptide by g_mindist
but I not found the appropriate way to calculate density of water with
respect to time
between two peptides..

I used g_density but it not gave me the information as per my need.

There are a variety of options in g_density that might work, like changing
the direction along which the box is sliced, the interval of time examined,
etc. I can envision this working quite well. g_densmap can do similar
functions, and g_rdf can probably provide you with some useful information
as well.

-Justin

--
==**==

Re: [gmx-users] A snapshot at a particular time frame

2012-10-01 Thread rama david

Dear Ravi
   Use trjconv  -dump ... ( time in ps)

With Best wishes and regards
Rama david.

On Mon, Oct 1, 2012 at 11:15 AM, Ravi Kumar Venkatraman 
ravikumarvenkatra...@gmail.com wrote:

 Dear All,
  How to get a snapshot at a particular time frame from the MDS
 run.
 Thank you

 *With Regards,
 Ravi Kumar Venkatraman,
 IPC Dept., IISc,
 Bangalore, INDIA.

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Re: [gmx-users] on tpbconv

2012-09-30 Thread rama david

Yes it will work ..
Just at the time of mdrun add -cpi cpt ( prvious cpt file )

With best wishes and regards..!!

On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote:

 Dear All,

 for my original MD, based on mdp file the total time is 500 ps. After it
 finished,  I have decided to extend the MD run to 2.5 ns.

 I think the following command should be used:

 tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr


 But as for in the original mdp file the total time is 500 ps,is the
 -extend 2000 workable in the tpbconv -s original500ps.tpr -extend 2000
 -o md-0.5ns-to-2.5ns.tpr? Do I need to change the total time in the
 original mdp file from 500 ps to 2000 ps or a time period longer than 2000
 ps, after the original 500 pd finished, in order to make tpbconv -s
 original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr workable?

 I am looking forward to getting your reply.

 Cheers,

 Acoot
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Re: [gmx-users] Calculate Density with respect to time...

2012-09-30 Thread rama david

Thank you for your immediate reply..

I need the xvg graph that will tell me the density of water in between the
protein with respect to time .
g_densmap not give such out put..

Sol please would you tell me  how to do it ???

How to select the Sol that  are only in between the protein ??


Thank you in advance..


With best wishes and regards

Rama David
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Re: [gmx-users] my VMD

2012-08-16 Thread rama david

Hi
do the following ..

open the trajectory in tthe molecule not as seperate molecule..

As example you havre md.gro and md.xtc files..

file == new molecule

load files for md.pdb   open it in vmd ..
then be sure that load files for : sould have the file name for which
you want to see treajectory...here md.gro
through browse open the md.xtc then load it..

With best wishes aned regards..

Rama david


On Wed, Aug 15, 2012 at 3:27 PM, Acoot Brett acootbr...@yahoo.com wrote:
 Dear All,

 I just installed a VMD. And then I load a gro file and a xtc file from a 
 simulation. The bar in the VMD Main window continuously moves, however the 
 protein molecule in the OpenGL Display window does not move.

 Will you please tell me what is the problem, or how can see the whole 
 simulation?

 Cheers,

 Acoot
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Re: [gmx-users] my VMD

2012-08-16 Thread rama david

Sorry md.pdb/md.gro

On Thu, Aug 16, 2012 at 11:34 AM, rama david ramadavidgr...@gmail.com wrote:
 Hi
 do the following ..

 open the trajectory in tthe molecule not as seperate molecule..

 As example you havre md.gro and md.xtc files..

 file == new molecule

 load files for md.pdb   open it in vmd ..
 then be sure that load files for : sould have the file name for which
 you want to see treajectory...here md.gro
 through browse open the md.xtc then load it..

 With best wishes aned regards..

 Rama david


 On Wed, Aug 15, 2012 at 3:27 PM, Acoot Brett acootbr...@yahoo.com wrote:
 Dear All,

 I just installed a VMD. And then I load a gro file and a xtc file from a 
 simulation. The bar in the VMD Main window continuously moves, however the 
 protein molecule in the OpenGL Display window does not move.

 Will you please tell me what is the problem, or how can see the whole 
 simulation?

 Cheers,

 Acoot
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Re: [gmx-users] grommp warning

2012-08-15 Thread rama david

Thank you Mark for reply.

as you said ...
Depends whether rigidity or scaling make more sense in your model of
real physics, which depends what's in your system.

My system is generally consist of proteins or peptides ( single ,
double or many)..

I am using option com Is it right

As per your answer in these archieve...
http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html


Under NPT the box size changes each step. You are using position
restraints to a pre-defined set of reference coordinates. This option
allows you to choose how those *reference coordinates* should change
when the box size changes (respectively do not scale them at all, scale
them all, or scale their COM but leave their internal geometry fixed).
Position restraints are then applied using the updated reference
coordinates.


In some archives I found if any one used freeze group
suggested to use refcoord_scaling = no


When we applied position restrain, the position of backbone atom is restrained..
I make my assumption as like follow..
No = no scalling in position of atoms.(system maintain rigidity).
all  = the system bcome flexible

com= ? ( scalling com means changing com co-ordinates or something else)




I get confused


Please accept my apology for stupid question
Please help to come out through the confusion.

With best wishes and regards

Rama david
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Re: [gmx-users] checkpoint file

2012-08-14 Thread rama david

Hi  Juliette ,

If your data is more and because of that may be  -append not support you.

Then these may be help you ..

mdrun -v -deffnm use different name than previous -s your tpr file
-cpi cpt

See carefully the output and check the time  at which the run
start..Is the  starting time point matches your crash point.

lastly when run complete, use trajcat ( catenate two trajectory),
catenate two trajectory...(previous and latest)

you can also catenate edr file..

So 1st make clear that why run crash??? If no abnormality then proceed
further...

These is the way I tackle my crash run on Gromacs 4.5.4


With best wishes and regards,
Rama David
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Re: [gmx-users] grommp warning

2012-08-14 Thread rama david

Dear shima and Justin,

These error is come on Gromacs 4.5.5 at the time of NPT if
refcoord_scaling option not used..

But it is not come on Gromacs 4.5.4 when you not use  refcoord_scaling
option at npt

Is any one else has same experience?
I really surprised by my observation  

With best wishes and regards
Rama David..
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Re: [gmx-users] grommp warning

2012-08-14 Thread rama david

Justin,
Thank you for your reply,

I check the manual but it is giving only small information..

I would be greatly thankfull to you if you shed some light on
these option ...

With best wishes and regards
Rama David
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Re: [gmx-users] grommp warning

2012-08-14 Thread rama david

Hi Justin ,

Thank you for immediate reply and providing the link.

But I am wonder for following things...

For protein simulation in your lysozyme tutorial we use
refcoord_scaling = com
In lipid tutorial also same one..

So Is there are any case when to use
refcoord_scaling no or all .??

Is there any way to find out which option to use when

How all the things going to affect the result

I goes trough archive but not find satisfactory answer...
I am looking for clear and simple explanation...


Thank you in advance..

With Best wishes and regards
Rama david
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Re: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

2012-08-08 Thread rama david

 directory `/opt/gromacs-4.5.4/src/kernel'
(cd ./src/kernel  make install-mdrun ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/kernel'
/bin/sh ../../config/mkinstalldirs /opt/gmx_4.5.4/bin
if test -f mdrun; then \
  f=`echo mdrun|sed 's/$//;s$_mpi;s/$//'`; \
  echo   /bin/sh ../../libtool  --mode=install /usr/bin/install -c
mdrun /opt/gmx_4.5.4/bin/$f; \
   /bin/sh ../../libtool  --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/$f; \
else :; fi
  /bin/sh ../../libtool  --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/mdrun_mpi
/usr/bin/install -c mdrun /opt/gmx_4.5.4/bin/mdrun_mpi
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/kernel'
[root@prashant gromacs-4.5.4]# make links
cd /opt/gmx_4.5.4/bin  programs=`ls`  cd /usr/local/bin  \
for i in $programs; do \
   (test ! -f $i  ln -s /opt/gmx_4.5.4/bin/$i . ; exit 0); \
done


When I am giving the command
pdb2gmx_mpi
pdb2gmx_mpi: error while loading shared libraries: libmpi.so.1: cannot
open shared object file: No such file or directory


I have a small experience in linux only, That why I may be missing or
done something wrong???
So please tell me where is the problem 

Thank you in advane..

With Best wishes and regards,
Rama david.
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[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

2012-08-07 Thread rama david

Hi Gromacs Friends,

I am trying to install gromacs 4.5.4  in parallel operating system fedora 17
I am using dell T 3500 precision , 6C.

I downloaded openmppi-1.6
Command line to install
   ./configure --prefix=/usr/local
 make all install

For fftw 3.3.2 installation command line was .

./configure --enable-float
make
make install

To Gromacs I wrote..
./configure --enable-mpi --with-fft=fftw3 --program-suffix=_mpi


System reply with
  configure error : cannot compute sizeof ( off_t)...

config .log show following error...It very big..I am pesting only a
small part...

Please tell me the reason for such error ...?? And how to overcome these???
.
.
.
.
.
.
configure:5529: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.4
| #define PACKAGE_STRING gromacs 4.5.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE_URL 
| #define PACKAGE gromacs
| #define VERSION 4.5.4
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Aug  7 10:46:37 IST 2012
| #define BUILD_MACHINE Linux 3.5.0-2.fc17.x86_64 x86_64
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| /* end confdefs.h.  */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:5551: result: no
configure:6229: checking how to run the C preprocessor
configure:6260: mpicc -E -I/usr/local/lib conftest.c
configure:6260: $? = 0
configure:6274: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6274: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.4
| #define PACKAGE_STRING gromacs 4.5.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE_URL 
| #define PACKAGE gromacs
| #define VERSION 4.5.4
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Aug  7 10:46:37 IST 2012
| #define BUILD_USER prashant@prashant
| #define BUILD_MACHINE Linux 3.5.0-2.fc17.x86_64 x86_64
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h.  */
| #include ac_nonexistent.h
configure:6299: result: mpicc -E
configure:6319: mpicc -E -I/usr/local/lib conftest.c
configure:6319: $? = 0
configure:6333: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6333: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.4
| #define PACKAGE_STRING gromacs 4.5.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE_URL 
| #define PACKAGE gromacs
| #define VERSION 4.5.4
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Aug  7 10:46:37 IST 2012
| #define BUILD_USER prashant@prashant
| #define BUILD_MACHINE Linux 3.5.0-2.fc17.x86_64 x86_64
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h.  */
| #include ac_nonexistent.h
configure:6362: checking for grep that handles long lines and -e
configure:6420: result: /usr/bin/grep
configure:6425: checking for egrep
configure:6487: result: /usr/bin/grep -E
configure:6492: checking whether ln -s works
configure:6496: result: yes
configure:6895: checking whether mpicc accepts -O3
configure:6913: result: yes
configure:7193: checking whether mpicc accepts -msse2
configure:7211: result: yes
configure:7225: checking whether mpicc accepts -funroll-all-loops
configure:7243: result: yes
configure:7255: checking whether mpicc accepts -std=gnu99
configure:7273: result: yes
configure:7288: checking whether mpicc accepts -fexcess-precision=fast
configure:7306: result: yes
configure:7347: checking whether mpicc accepts  -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
configure:7365: result: yes
configure:8089: checking whether byte ordering is bigendian
configure:8104: mpicc -c  -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast -I/usr/local/lib conftest.c 5
conftest.c:23:9: error: unknown type name 'not'
conftest.c:23:15: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'universal'
conftest.c:23:15: error: unknown type name 'universal'
configure:8104: $? = 1
configure: failed program was:
| /* confdefs.h */
|

[gmx-users] About system requirement to gromacs

2012-08-01 Thread rama david

Hi Gromacs friends,

If anyone has a free time please reply to my Query..

Please accept my  SINCERE APOLOGY for my stupid query...
I have a limited knowledge about the computer hardware...

Is it possible to install Gromacs in parrallel mode in following system
in order to perform Replica Exchange Molecular Dynamics ( REMD )???...

1. Intel I5 processor, Dell Desktop.


and

2. Dell precision T 3500 Intel (R)Xeon (R)W3670 3.2 GHZ, 12M cache
  4.8 GT/s QPI, Tutbo, HT, 6C.

Is it possible to install gromacs-openmpi in both system to perform REMD
  or on only one ( Dell Precision T 3500 )...






With best Wishes and Regards...
Rama David
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Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread rama david

Thank you Mark for your Reply..

I install open-mpi through Ubuntu  software package ..
I know that these are not officially supported by the GROMACS team...


I made two different tpr file with the grompp command that has two
different temp..
( 300 K and 310 K) ..topol0.tpr topol1.tpr as your previous suggestion to me..

my command line was ..


mpirun mdrun_mpi -np 4  -multi 2 -replex 10


Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

My Heart is Just a Muscle In a Cavity (F. Black)

Halting program mdrun_mpi

gcq#101: My Heart is Just a Muscle In a Cavity (F. Black)

--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--






So what is wrong???

With best wishes and regards
Rama david
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Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread rama david

Thank you Mark for reply..

I run mdrun and mpirun with following command. I pasted output also..
Please help me to parse it..


1.   mdrun -v -deffnm topol1
2.   mpirun -np 4 mdrun -v -deffnm topol1


1.mdrun -v -deffnm topol1


step 30, will finish Wed Aug  1 16:49:28 2012
 Average load imbalance: 12.3 %
 Part of the total run time spent waiting due to load imbalance: 5.1 %

NOTE: 5.1 % performance was lost due to load imbalance
  in the domain decomposition.
  You might want to use dynamic load balancing (option -dlb.)


Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  2.035  2.035100.0
   (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:109.127  5.744  2.632  9.117

gcq#98: You're About to Hurt Somebody (Jazzy Jeff)



2. mpirun -np 4 mdrun -v -deffnm topol1

Getting Loaded...
Reading file topol1.tpr, VERSION 4.5.5 (single precision)
Starting 4 threads
Starting 4 threads
Starting 4 threads
Starting 4 threads
Loaded with Money

Loaded with Money

Loaded with Money

Loaded with Money

Making 1D domain decomposition 4 x 1 x 1
Making 1D domain decomposition 4 x 1 x 1


Making 1D domain decomposition 4 x 1 x 1
Making 1D domain decomposition 4 x 1 x 1

starting mdrun 'Protein in water'
5 steps,100.0 ps.
starting mdrun 'Protein in water'
5 steps,100.0 ps.

starting mdrun 'Protein in water'
5 steps,100.0 ps.
starting mdrun 'Protein in water'
5 steps,100.0 ps.

NOTE: Turning on dynamic load balancing


NOTE: Turning on dynamic load balancing

step 0
NOTE: Turning on dynamic load balancing

step 100, will finish Wed Aug  1 19:36:10 2012vol 0.83  imb F  2% vol
0.84  imb step 200, will finish Wed Aug  1 19:32:37 2012vol 0.87  imb
F 16% vol 0.86  imb step 300, will finish Wed Aug  1 19:34:59 2012vol
0.88  imb F  4% vol 0.85  imb step 400, will finish Wed Aug  1
19:36:27 2012^Cmpirun: killing job...

--
mpirun noticed that process rank 0 with PID 4257 on node  VPCEB34EN
exited on signal 0 (Unknown signal 0).
--
4 total processes killed (some possibly by mpirun during cleanup)
mpirun: clean termination accomplished




As you can also see the mdun command estimate to complete Aug  1 16:49:28 2012
while mpirun taking the time Wed Aug  1 19:36:10 2012vol

Mpirun command taking more time...

so from above output I can  guess In mpirun 4 processor are used


Sorry if I take any wrong meaning from output..

Thank you for giving your valuable time..


With best wishes and regards

Rama David
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Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread rama david

Thank you for reply and your suggestion..

As I mentioned earlier I installed Gromacs-openmpi 4.5.5  from Ubuntu
software package manager

So I want to just check is it performing REMD or  not???

So as per previous suggestion of Mark ...
I made two tpr file that has two different temp 300 k and 310
k..topol0.tpr and topol1.tpr  respectively


I used command line

 mpirun -c 4   mdrun_mpi  -v -multi 2 -replex 10

output as follow.


node 0 par_fn 'topol0.tpr'
node 0 par_fn 'topol1.tpr'
node 0 par_fn 'traj1.trr'
node 0 par_fn 'traj1.xtc'
node 0 par_fn 'state1.cpt'
node 0 par_fn 'state1.cpt'
node 0 par_fn 'confout1.gro'
node 0 par_fn 'ener1.edr'
node 0 par_fn 'traj0.trr'
node 0 par_fn 'md1.log'
log
node 0 par_fn 'traj0.xtc'
node 0 par_fn 'dhdl1.xvg'
node 0 par_fn 'field1.xvg'
node 0 par_fn 'state0.cpt'
node 0 par_fn 'rerun1.xtc'
node 0 par_fn 'tpi1.xvg'
node 0 par_fn 'tpidist1.xvg'
node 0 par_fn 'state0.cpt'
node 0 par_fn 'sam1.edo'
node 0 par_fn 'confout0.gro'
node 0 par_fn 'bam1.gct'
node 0 par_fn 'gct1.xvg'
node 0 par_fn 'ener0.edr'
node 0 par_fn 'deviatie1.xvg'
node 0 par_fn 'runaver1.xvg'
node 0 par_fn 'md0.log'
node 0 par_fn 'pullx1.xvg'
node 0 par_fn 'pullf1.xvg'
node 0 par_fn 'nm1.mtx'
log
node 0 par_fn 'dipole1.ndx'
node 0 par_fn 'dhdl0.xvg'

Back Off! I just backed up md1.log to ./#md1.log.4#
Getting Loaded...
Reading file topol1.tpr, VERSION 4.5.5 (single precision)
node 0 par_fn 'field0.xvg'
node 0 par_fn 'rerun0.xtc'
node 0 par_fn 'tpi0.xvg'
node 0 par_fn 'tpidist0.xvg'
node 0 par_fn 'sam0.edo'
node 0 par_fn 'bam0.gct'
node 0 par_fn 'gct0.xvg'
node 0 par_fn 'deviatie0.xvg'
node 0 par_fn 'runaver0.xvg'
node 0 par_fn 'pullx0.xvg'
node 0 par_fn 'pullf0.xvg'
node 0 par_fn 'nm0.mtx'
node 0 par_fn 'dipole0.ndx'

Back Off! I just backed up md0.log to ./#md0.log.4#
Getting Loaded...
Reading file topol0.tpr, VERSION 4.5.5 (single precision)
Loaded with Money

Loaded with Money

Making 1D domain decomposition 2 x 1 x 1

Back Off! I just backed up traj0.trr to ./#traj0.trr.4#

Back Off! I just backed up ener0.edr to ./#ener0.edr.4#
Making 1D domain decomposition 2 x 1 x 1

Back Off! I just backed up traj1.trr to ./#traj1.trr.4#

Back Off! I just backed up ener1.edr to ./#ener1.edr.4#

---
Program mdrun_mpi, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/repl_ex.c, line: 177

Fatal error:
The properties of the 2 systems are all the same, there is nothing to exchange
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I Do It All the Time (Magnapop)


---
Program mdrun_mpi, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/repl_ex.c, line: 177

Fatal error:
The properties of the 2 systems are all the same, there is nothing to exchange
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I Do It All the Time (Magnapop)

Error on node 2, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 2 out of 4
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 4

gcq#197: I Do It All the Time (Magnapop)


gcq#197: I Do It All the Time (Magnapop)

--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
--
mpirun has exited due to process rank 0 with PID 9919 on
node VPCEB34EN exiting without calling finalize. This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--
[VPCEB34EN:09918] 1 more process has sent help message
help-mpi-api.txt / mpi-abort
[VPCEB34EN:09918] Set MCA parameter orte_base_help_aggregate to 0 to
see all help / error messag



Thanks a lot for hearing my problem

So from above output is it able to perform REMD or not ?
Is the gromacs installation  on my system is right for open-mpi


With Best Wishes and regards

Rama david
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[gmx-users] Gromacs installation

2012-07-30 Thread rama david

Hi GROMACS FRIENDS,
  I have dell T3500 precision, 64 bits, 6C workstation with fedora
operating system.
I want to install gromacs in parallel mode with mpi...
I am planning to performed Replica Exchange Molecular Dynamics ( REMD ).
As per REMD instruction
http://www.gromacs.org/Documentation/How-tos/REMD?highlight=remd,
GROMACS should not compile in threading.
I install open mpi with  command line yum -y install openmpi.
I found that fedora add/remove software package has gromacs 4.5.5
version that can be
easily installed by  command yum  ..
It  enlisted with  total 15 different packages : eg.. two packages..

1. GROMACS Open MPI binaries and libraries
2 . GROMACS OPEN MPI shared libraries

and a more..

Please can you tell me which packages I have to install so that I can
run GROMACS 4.5.5 in parallel to do REMD.


Thank you in advance
Have a nice day..


With Best Wishes and regards.
Rama David
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Re: [gmx-users] Gromacs installation

2012-07-30 Thread rama david

thank you for immediate reply...
Suppose, If I installed from Fedora software packages
How to check that  Gromacs installed in Parallel version and can
performed REMD



Thank you in Advance..
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Re: [gmx-users] Gromacs installation

2012-07-30 Thread rama david

Thank you M.ark..
I got following reply..

Fatal error :
mdrun -multi is not supported with thread library .Please compile
gromacs with MPI support.

I have to try to compile gromacs as per the webpage instructions...


With best wishes and regards..
Rama David..
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[gmx-users] Re: About lipid simulation...

2012-07-18 Thread rama david

 Hi Gromacs friends



 I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
 Surface tension coupling work with only Berendsen Press coupling.

 Please , would you tell me how to calculate lateral surface tension from
 P|| ( lateral press ) and  Pz( Perpendicular press )  ???
 ( Why to say  P||  =   -30  Pz = 1 , will give the teral tension of
 20 mNm/m  ???)




 I found out the way to calculate the lateral pressure..

  As per the article ..Biophysics Journal, October 1995, vol 65, page no
  1230.

  The formula as per article is

  Boundary lateral press =  1 -   ( Surface Tension / Thickness in Z
 dimension.)...


 ; Temperature coupling is on
 tcoupl= Berendsen; More accurate thermostat
 tc-grps= Protein DPPCSOL_CL; three coupling groups -
 more accurate
 tau_t= 0.10.10.1; time constant, in ps
 ref_t= 323 323323; reference temperature,
 one for each group, in K
 ; Pressure coupling is on
 pcoupl=  Berendsen; Pressure coupling on in NPT
 vectors, independent z
 tau_p= 0.5; time constant, in ps
 ref_p=  -30.01.0; reference pressure, x-y,z (in
 bar)

 compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1
 pcoupltype= 

 What pcoupltype  shouild be used ???
 semiisotropic or Surface-tension 



 Please give me the valuable suggestion in these regard

 Thank you in advance.

 Have a nice Day.
 With best wishes and regards,


 Rama David


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[gmx-users] About Surface tension in lipid simulation.....

2012-07-18 Thread rama david

Hi Gromacs Friends,

I completed the Justin Protein KALP  - lipid tutorial ...

 I  want to simulate the DPPC lipid bilayer membrane under
 Stress condition ( Lateral  tension = 20 mNm/m)..

 For stress condition I made the following npt.mdp

; Temperature coupling is on
tcoupl   = Berendsen; More accurate thermostat
tc-grps  = Protein DPPCSOL_CL; three coupling groups
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t = 323 323323; reference
temperature,one for each group,
; Pressure coupling is on
pcoupl   =  Berendsen; Pressure coupling on in NPT
pcoupltype  =  ??; uniform scaling of x-y box
vectors, independent z
tau_p   = 0.5; time constant, in ps
ref_p   =  -30.01.0; reference pressure, x-y,
z (in bar)
compressibility  = 5.0e-55.0e-5; isothermal compressibility, bar^-1


What pcoupl type Should be used Semisotropic or Surface tension.. and why???

Thank you in advance...

With Best Wishes and regards ,
Rama.
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Re: [gmx-users] genconf command

2012-07-17 Thread rama david

Dear cuong nguyen..
I think use following commands.

 Try editconf -rotate  for rotaion angle along axis
along these use -center  co-ordinate  if you want to place canter of
box at particular position

Try editconf -translate For translation along axis 



On Tue, Jul 17, 2012 at 2:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 17/07/2012 4:32 PM, cuong nguyen wrote:

 Dear Gmx-users,

 I created a box size 4 4 2 and named layer.gro. Then genconf was
 used to doulble this box:
 genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8
 However, the copied box has the same direction as the original box.
 Could you please help me to rotate 180 degrees the copied one?


 Start with genconf -h.

 Mark

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[gmx-users] About lipid simulation npt.mdp

2012-07-09 Thread rama david

Hi Gromacs friends,

I am trying to  reproduced the result of article  ¨Antimicrobial
peptide in Action¨
Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q

As per article they used two conditions,

1. Stress free ( Lateral  Tension = 0)
2. Stress condition ( Lateral  tension = 20 mNm/m)

parameter for simulation as follow,

Weakly coupled temp 323 k ( Coupling time = 0.1)
Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1)

Keep the P|| ( lateral press ) and  Pz( Perpendicular press ) same
P||  = Pz = 1 ,
Result will be stress free bilayer ( Lateral  Tension = 0).

For other condition of P||  =   -30  Pz = 1 , result in a lateral tension of
20 mNm/m

for stress free condition I made following npt.mdp
; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p= 1.01.0; reference pressure, x-y, z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


And for stress condition I made the following npt.mdp

; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p=  -30.01.0; reference pressure, x-y,
z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


Please help to make right npt.mdp from above  mention parameter.


I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
Surface tension coupling work with only Berendsen Press coupling.

Please , would you tell me how to calculate lateral surface tension from
P|| ( lateral press ) and  Pz( Perpendicular press )  ???
( Why to say  P||  =   -30  Pz = 1 , will give the teral tension of
20 mNm/m  ???)


Please give me the valuable suggestion in these regard

Thank you in advance.

Have a nice Day.
With best wishes and regards,


Rama David
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[gmx-users] About lipid simulation...

2012-07-09 Thread rama david

Hi Gromacs friends,

I am very novice to the lipid simulation study..
My problem may be very simple, But very imp to me to know it.

I am trying to  reproduced the result of article  ¨Antimicrobial
peptide in Action¨
Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q



As per article they used two conditions,

1. Stress free ( Lateral  Tension = 0)
2. Stress condition ( Lateral  tension = 20 mNm/m)

parameter for simulation as follow,

Weakly coupled temp 323 k ( Coupling time = 0.1)
Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1)

Keep the P|| ( lateral press ) and  Pz( Perpendicular press ) same
P||  = Pz = 1 ,
Result will be stress free bilayer ( Lateral  Tension = 0).

For other condition of P||  =   -30  Pz = 1 , result in a lateral tension of
20 mNm/m

for stress free condition I made following npt.mdp
; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p= 1.01.0; reference pressure, x-y, z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


And for stress condition I made the following npt.mdp

; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p=  -30.01.0; reference pressure, x-y,
z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


Please help to make right npt.mdp from above  mention parameter.


I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
Surface tension coupling work with only Berendsen Press coupling.

Please , would you tell me how to calculate lateral surface tension from
P|| ( lateral press ) and  Pz( Perpendicular press )  ???
( Why to say  P||  =   -30  Pz = 1 , will give the teral tension of
20 mNm/m  ???)


Please give me the valuable suggestion in these regard

Thank you in advance.

Have a nice Day.
With best wishes and regards,


Rama David
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[gmx-users] Fwd: Determine sec structure by MD

2012-06-28 Thread rama david

Hi Gromacs Friends,

        I have the experimental result of change in Secondary
structure of peptide from random coil to Beta sheet, as  the conc
increases
( but  not know the Parallel or anti-parallel )

                       I run Simulation of ( 30ns ) two peptide in random coil
structure put sufficiently apart  (2.4 nm) so they are not interacting to each
other initially, I found they are coming close to each other in anti-parallel
fashion, But they remain in random coil.To extend these study I run simulation
of four peptide they also come close to each other in anti-parallel way
(Show the change in secondary structure from random coil to
anti-parallel beta sheet)
After these I put the peptide in anti-parallel way  to form the fiber structure,
they show the some parallel and anti-parallel  arrangement in fiber.

Note- If I put the two peptide in random state, close enough in parallel to each
other they also form parallel beta sheet structure ..
As the MD study is affected by initial arrangement.

I am interested How to Determine by Molecular Dynamics, Is  structure
favor Parallel
or Anti-parallel state ?  also the energy difference in two,
parallel  and anti-parallel 

Please give me some some valuable suggestion and method to solve my query.

Thank you in advance


Have a nice day
With Best Wishes and Regards
Ramadavid
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Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

2012-06-27 Thread rama david

 Thank you Justin for your Explaination

 Please Would you me the Reason Why these parameter is present in
 Equilibration mdp and
 not in production run mdp file ( for both lysozyme and lipid simulation )

 With Best Wishes and regardsRama
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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

2012-06-27 Thread rama david

Thank you Justin,

But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter  in Umbrella sampling??

I run the simulation of peptide withought any
refcoord_scaling = com in mdp  file
and now  is it will affect result  significantly??
Is it wrong simulation???

How to check these parameter affect my result sensitivity???

Please give me valuable guidance to solve my query..

With Best Wishes and regards,
Rama David
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[gmx-users] Lipid-protein simulation....

2012-06-26 Thread rama david

Hi Gromacs Friends,

 I completed Justin-Lipid Tutorial.
I plan to simulate protein-lipid system  to study protein-lipid interaction.
My Query is like

1. I plan to use DPPC (128) lipid from Tieleman Website.
  I removed its periodicity as per tutorial instruction..
  I found that I need the z box Dimension more than 6.59650.
  ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer).
So with help of editconf command I changed the Z box Dimension to 8.00
while  x and y are same .

Is these process is right or any good suggestion in my work-flow ???

2. I wish to put lipid membrane away from protein ( Protein is not
embedded in lipid ).
Should I use InflateGro?? Should I use Strong position restrain
during Energy minimisation???


please give me valuable Guidance

With Best Wishes and regards
Rama
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[gmx-users] Re: Lipid-protein simulation....

2012-06-26 Thread rama david

On Tue, Jun 26, 2012 at 9:32 PM, rama david ramadavidgr...@gmail.com wrote:
 Hi Gromacs Friends,

  I completed Justin-Lipid Tutorial.
 I plan to simulate protein-lipid system  to study protein-lipid interaction.
 My Query is like

 1. I plan to use DPPC (128) lipid from Tieleman Website.
  I removed its periodicity as per tutorial instruction..
  I found that I need the z box Dimension more than 6.59650.
  ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer
 I deleted SOL molecule from DPPC layer, I plan to solvate  system
after catenation
of lipid and protein gro file).
 So with help of editconf command I changed the Z box Dimension to 8.00
 while  x and y are same .

 Is these process is right or any good suggestion in my work-flow ???

 2. I wish to put lipid membrane away from protein ( Protein is not
 embedded in lipid ).
    Should I use InflateGro?? Should I use Strong position restrain
 during Energy minimisation???


 please give me valuable Guidance

 With Best Wishes and regards
 Rama
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[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

2012-06-26 Thread rama david

Hi Gromacs Friends,
    I am doing Justin-lipid tutorialer
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

In these the npt.mdp has a parameter
refcoord_scaling = com
Why these parameter is introduced in NPT of lipid-protein simulation
 and not use in Lysozyme in water simulation ???

Please give the detail on why to use these parameter??


Thank you in advance

With best Wishes and Regards,
Rama
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[gmx-users] simulated annealing mdp

2012-06-12 Thread rama david

Hi Gromacs Friends,

I planed to do simulated annealing...
My protocol is as follow
( forcefield G96 53a6   spc water model)

1. nvt at 310 k for 100 ps
2. Sa (mdp is posted below )
3. NPT at 310 k for 100 ps

Is it right ??

Please suggest me improvements...

Sa mdp file

title= gromacs
define= -DPOSRES; position restrain the protein

nstcomm= 1
comm-mode= Linear; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 1000; save coordinates every 0.2 ps
nstvout= 1000; save velocities every 0.2 ps
nstenergy= 1000; save energies every 0.2 ps
nstlog= 1000; update log file every 0.2 ps
; Bond parameters
continuation= yes; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 0.9; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9; short-range electrostatic cutoff (in nm)
vdw-type= Cut-off
rvdw= 1.4; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 310 310; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off
; Simulated annealing
annealing   = single single
annealing_npoints=  4  4
annealing_time  =  0  200  400 600 0 200 400 600
annealing_temp  = 310 323 300 310  310 323 300 310




Thank you in advance

With Best Wishes,
Rama David
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[gmx-users] Press Equilibration

2012-06-12 Thread rama david

Hi Gromacs Friends,

I did NPT for 100 ps with folowing parameter

; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 310 310; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar


I got foolowing result by using g_energy

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -3.99675   0.66518.604   -2.89716  (bar)


Is it is right??
Is the system is equilibrated or I need to give more time ?
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Re: [gmx-users] simulated annealing mdp

2012-06-12 Thread rama david

THANK YOU Justin,
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[gmx-users] Re: Press Equilibration

2012-06-12 Thread rama david

On Tue, Jun 12, 2012 at 4:40 PM, rama david ramadavidgr...@gmail.comwrote:


 Hi Gromacs Friends,

 I did NPT for 100 ps with folowing parameter

 ; Temperature coupling is on
 tcoupl= V-rescale; modified Berendsen thermostat
 tc-grps= Protein Non-Protein; two coupling groups - more
 accurate
 tau_t= 0.10.1; time constant, in ps
 ref_t= 310 310; reference temperature, one for each group,
 in K
 ; Pressure coupling is on
 pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
 pcoupltype= isotropic; uniform scaling of box vectors
 tau_p= 2.0; time constant, in ps
 ref_p= 1.0; reference pressure, in bar


 I got foolowing result by using g_energy

 Energy  Average   Err.Est.   RMSD  Tot-Drift

 ---
 Pressure   -3.99675   0.66518.604   -2.89716  (bar)


 Is it is right??
 Is the system is equilibrated or I need to give more time ?

 I am worried because of avg is -ve ...
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Re: [gmx-users] Press Equilibration

2012-06-12 Thread rama david

thank you for Quick reply
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Re: [gmx-users] simulated annealing mdp

2012-06-12 Thread rama david

Hello Justin and Ravi,

Lets explain me Why I  did simulated anealing?? ..


I synthesise peptide and I have experimental data for its self assembly,
I just want to reproduced these data.


I arranged the 32 protein in axis to petide fibre, in antiparrallel Beta
sheet structure.
I dont have crystal structure ,

Thats why I did SA in the hope that after these the side chain may be get
properly oriented with respect to each other.That will give me good
structure for production run.
 I also run system withought SA , but I get good result by following SA
protocol.

In posrestrain only backbone is restrained and the sidechain is free to
move, So I
think it may be help to achieve my goal.

After these I also plan  to use SA as production run, then compare the
result with previous protocols.

Please give valuable suggestion to improve my study protocol..


With Best Wishes,
Rama David.
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Re: [gmx-users] simulated annealing mdp

2012-06-12 Thread rama david

Thank you for reply
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[gmx-users] LINCS warnings

2012-06-11 Thread rama david

Hi Gromacs Friends ..

I am trying to simulate octa-peptide in water model spc using G96 53a6
force field.
my aim is to study the self assembly nature of these octapetide.
I did following type of arrangment.

I make antiparrallel arrangment of four peptide with distance of 0.5 nm in
y direction,
Then I translate these layer  in z direction, Such that separation in each
layer is 0.5 ,

I arranged six layer in Z direction(total 24 peptide 6 * 4=24 ),

I did Steepest Descent

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  100

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 108 steps,
but did not reach the requested Fmax  100.
Potential Energy  = -9.2318734e+04
Maximum force =  6.8985820e+04 on atom 1359
Norm of force =  9.8921991e+02


For nvt run I got Lincs Error


Step 772, time 1.544 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001014, max 0.009497 (between atoms 1360 and 1358)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1359   1358   61.40.1000   0.1004  0.1000

Step 773, time 1.546 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003091, max 0.027499 (between atoms 1359 and 1358)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1360   1358   32.10.0991   0.0985  0.1000
   1359   1358   90.00.1004   0.1027  0.1000

---
Program mdrun, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/mdlib/constr.c, line: 176

Fatal error:
Too many LINCS warnings (1001)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Carry Me Away (Motors)


When I check the website at http://www.gromacs.org/Documentation/Errors

I come to know that system is unstable or not properly energy minimised
(e+04) is the source for such type of errors.

But Truly I dont Want to change the arrangment (distance 0.5 nm),

Please Help me to solve the above problem,

All suggestion are welcome



With Best Wishes,
Rama David
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Re: [gmx-users] LINCS warnings

2012-06-11 Thread rama david

Hi MARK,
 Thank you to your  Quick reply,
Please accept my apology for incomplete information...

 I did simulationm of single, Double and four peptide..

I also tried following
I make antiparrallel arrangment of four peptide with distance of 0.4 nm in
y direction,
Then I translate these layer  in z direction, Such that separation in each
layer is 0.4 ,

I arranged eight layer in Z direction(total 24 peptide 8 * 4=32 ),
All things was right.



Thank you in Advance

With Best Wishes,
Rama David
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Re: [gmx-users] LINCS warnings

2012-06-11 Thread rama david

Hi Mark,

I did simulation of the same system in vacuum, and system behave the
normally,
So the instability  in the system is due to the spc Water model???
As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up

I think the source is (Please tell me is it right..?? or any else reason  )
last option :
you have a single water molecule somewhere within the system that is
isolated from the other water molecules.


How to find such water molecule and solve the problem??


Thank you in Advance .

With Best Wishes,
Rama David
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Re: [gmx-users] LINCS warnings

2012-06-11 Thread rama david

Hi  Justin, thank you for quick reply.
You are right I have practicle result, And I want to replicate them..

Thank you for your suggestion..

With Best Wishes,
Rama David

On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 On 6/11/12 6:23 AM, rama david wrote:


 Hi Mark,

 I did simulation of the same system in vacuum, and system behave the
 normally,
 So the instability  in the system is due to the spc Water model???
 As per the link http://www.gromacs.org/**Documentation/Terminology/**
 Blowing_Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up


 The water model is not the problem.  Your solvated system has clashes that
 cause instability.  In vacuo, your solute has greater freedom to shift
 around.


  I think the source is (Please tell me is it right..?? or any else reason
  )
 last option :
 you have a single water molecule somewhere within the system that is
 isolated
 from the other water molecules.


 How to find such water molecule and solve the problem??


 I think this is unlikely.  If you have any isolated waters, they might be
 sandwiched somewhere in your protein layers and should be easy to spot.
  The best strategy is to use the output of EM to your advantage.  Look at
 the atom that had the highest force on it.  What is it near?  What might it
 be clashing with?  What if you run EM in vacuo, followed by solvation, and
 another round of EM?

 From your earlier description, it seems to me that the system has been
 constructed to replicate some known experimental spacing, but doing so does
 not guarantee that whatever peptide structure you are replicating will
 necessarily produce a sensible result, or one that is free from clashes.
  Hence, you need to refine the model before continuing.

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[gmx-users] About extend the run,,

2012-06-02 Thread rama david

Hi Gromacs Friends,

I run a Production run with saving the  co-ordinates and velocity
after every 500 steps for 20ns..
Now I want to extend the run but with saving the  co-ordinates and velocity
after every 1000 steps for next 30ns (total 50ns)

To perform these task I am using following command
1. grompp -f New mdp file just change in  saving output  -t .cpt  -c
.gro file(gro file from position restrained run )  -o new.tpr


2. tpbconv -s new.tpr -0 extend.tpr  -extend 3

3. mdrun -v -deffnm extend  -cpi .cpt -append

Is these approach is correct??

Second query;

To rerun the crash run, users give .cpt file as input to -mdrun,
My query is, There are two cpt file a) pre.cpt  b) .cpt ,
So which one has to given as input???

All suggestion are welcome...

With Best Wishes,
Rama david
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Re: [gmx-users] About extend the run,,

2012-06-02 Thread rama david

Thank you Justin for quick reply 

On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 To perform these task I am using following command
 1. grompp -f New mdp file just change in  saving output  -t .cpt  -c
 .gro
 file(gro file from position restrained run )  -o new.tpr


 2. tpbconv -s new.tpr -0 extend.tpr  -extend 3

 3. mdrun -v -deffnm extend  -cpi .cpt -append

 Is these approach is correct??


 No.  The new.tpr file contains instructions to run from 20 - 30 ns.
  There is no need to then invoke tpbconv.  You would also need a new
 invocation of mdrun, since the output frequencies won't match.  You don't
 want to append those files with mdrun (nor will the checkpoint file likely
 let you)


Extremely Sorry for my carelessness , New mdp files means the same as
previous, with same number of steps, but just change in output frequency

So as per your recommendation and experience  Is any alternative to do
these from 20 ns???



 Second query;

 To rerun the crash run, users give .cpt file as input to -mdrun,
 My query is, There are two cpt file a) pre.cpt  b) .cpt ,
 So which one has to given as input???


 Use gmxcheck to understand the contents of each.  The timestamp will also
 tell you a difference, as will reading mdrun -h for an explanation of what
 the -cpt option is doing


As per the link..
http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
I interpreted following things..

1. I have to use the state.cpt , but in the case  problem to these I have
to use prev.cpt,  I can check there
content by gmxcheck..

 But my Query is What are may be the potential problems ?? and how to
find them ??

Crash the run is very often with my system, that why I am worried..
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Re: [gmx-users] About extend the run,,

2012-06-02 Thread rama david

 Thank You  for Quick reply Justin...

On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:


 You'll get a mismatch in your files (checkpoint, trajectory, energy) in
 terms of frame interval.  You should not try to append to these files or
 extend the run.  Just run a new simulation from 20 - 30 ns.  The grompp
 command was correct, assuming you set tinit = 2 in the .mdp file and
 setting nsteps appropriately to give another 10 ns.  Then run it as a new
 simulation.  It will still be an extension of the first simulation (since
 the .cpt preserves the previous state), but without the mdrun -cpi -append
 mechanism, which in this case you don't want (or possibly can't use)


I will follow your advice..





 Second query;

To rerun the crash run, users give .cpt file as input to -mdrun,
My query is, There are two cpt file a) pre.cpt  b) .cpt ,
So which one has to given as input???


Use gmxcheck to understand the contents of each.  The timestamp will
 also
tell you a difference, as will reading mdrun -h for an explanation of
 what
the -cpt option is doing


 As per the link..http://www.gromacs.org/**Documentation/File_Formats/**
 Checkpoint_Filehttp://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
 I interpreted following things..

 1. I have to use the state.cpt , but in the case  problem to these I have
 to use
 prev.cpt,  I can check there
 content by gmxcheck..

  But my Query is What are may be the potential problems ?? and how to
 find
 them ??

 Crash the run is very often with my system, that why I am worried..


 If you're getting frequent crashes, you should investigate why this is
 happening rather than just plowing ahead.  Are there error messages in the
 .log or stdout/stderr output?  Are your energetic terms sensible?  If the
 system is crashing due to physical instability, you're wasting your time
 producing junk. If the crashes are occurring due to hardware or filesystem
 instability, that's something to take up with your sysadmin.


 -Justin

Thank you For Advice...
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[gmx-users] umbrella windows...

2012-06-01 Thread rama david

Hi Gromacs Friends,

I am doing Justin-Umbrella sampling tutorial...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html

After pulling I found the Chain A is moving away from protofibril but
reaches up to the other end of the cell..
So Is these situation Satisfy the Minimum image condition??? or Am I doing
some wrong ..???

as tutorial Says..
GROMACS calculates distances while simultaneously taking periodicity into
account. This, if you have a 10-nm box, and you pull over a distance
greater than 5.0 nm, the periodic distance becomes the reference distance
for the pulling, and this distance is actually less than 5.0 nm! This fact
will significantly affect results, since the distance you *think* you are
pulling is not what is *actually* calculated.

My Query is on very basic concept...
tutorial says

In this example, we will be sampling COM distances from 0.5 - 5.0 nm along
the z-axis using roughly 0.2-nm spacing. The following example commands may
or may not be literally correct (the frame numbers may differ), but will
serve as an example as to how to run grompp on separate coordinate files to
generate all 23 inputs (note as well that 23 is the amount of windows
required to obtain 0.2-nm spacing over roughly 4.5 nm;
my summary_distances.dat has following lines..

00.5011713
10.5068762
20.4948514
..
.
.
1600.6993698
so my 1st configuration will be at 0 (0.5011713) and 160 (0.69936) .Is it
right???

I choose total 28 windows instead of 23 ...So is it good or bad ???

Thank you in Advance...
With Best Wishes,
Rama David
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