[gmx-users] Forming a micelles

[Chih-Ying Lin]

Hi
Would you please say more about your system?
How do you design / decide your simulation size of 100 surfactants +100
co-surfactants + 4000 water molecules??

How many surfactants will form a micelle?
How many atoms does one surfactant have?
How many atoms does one co-surfactant have?

Do you start from the critical micelle concentration?
You mentioned that it took 3 x 600 ps to see the micelles.
Do you mean that you have 3 computers to do the parallel simulation?

How long does it take to simulate 600 ps?
Do you visualize the whole 600 ps-image and SEE the micelle?
Or, other technique to KNOW the surfactants forming the micelles
without visualizing the system?

Thank you
Lin





Hello there...
   I carried out simulations of mixture of cationic
surfactants, fatty alcohols and water with various ratios of
surfactant/alcohol.  Usually for a system of 100 surfactants +100
co-surfactants + 4000 water molecules, it took 3 x 600 ps to see the
micelles and other structures  forming from random configurations.

Arun
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[gmx-users] urey-bradley format

[Piotr Adam Pieniazek]

Hi,
I'm trying to put in a Urey-Bradly type term into my force field, but  
the format is not specified in the manual.


atom_1 atom_2 atom_3  5  angle angle_force  bond bond_force

I'm particularly confused about the last two terms. I've tried both  
combinations and the results look reasonable in both cases.


Thanks,
Piotr


This message was sent using IMP, the Internet Messaging Program.

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Re: [gmx-users] Problem sasa 3.2.1 vs 3.3.2

[Anthony Cruz]

Thank you for your answer. Today I send the email directly to David and Erik. 
I hove they could help me. I will post the answer in the list. Thank you.

Cheers,

Anthony
On Thursday 18 September 2008 03:59:29 pm Tsjerk Wassenaar wrote:
> Hi Anthony,
>
> It's not even that different. The order is swapped (the colors) and
> the most notable difference is that the noise is higher in the newer
> version. The running averages will probably give very similar results.
> Still interesting to know what happened to the noise. The answer is
> probably in the source (and may be in a head belonging to a
> developer).
>
> Cheers,
>
> Tsjerk
>
> On Thu, Sep 18, 2008 at 3:39 PM, Anthony Cruz <[EMAIL PROTECTED]> wrote:
> > Hi users:
> > Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I
> > make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 .  When I do the
> > sasa analysis I observe differences in the sasa values between the two
> > versions. The total sasa seems to be same in the two graphs but the
> > hydrophobic and hydrophilic looks very different (see attached pictures).
> > What could be the problem? Which version will be the best for analysis?
> >
> > Cheers,
> > Anthony
> >
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Re: [gmx-users] Fwd: charges,resonance and electrostatics

[Justin A. Lemkul]

Omer Markovitch wrote:


There is no non-bonded interaction between these two oxygens,
unless you are using an Urey-Bradley potential for the angle,
like in the CHARMM force field. Most (if not all) of the
standard force fields in Gromacs treat the interaction of these
oxygens within an angle definition, which is a bonded term.

-Justin

So no coloumb law between the two oxygens?  10x, Omer.


Right, 1-3 interactions are accounted for within bonded (angle) definitions, 
unless you are applying an Urey-Bradley potential.


-Justin






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--


Justin A. Lemkul
Graduate Research Assistant
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] Fwd: charges,resonance and electrostatics

[Omer Markovitch]

>
>
>> There is no non-bonded interaction between these two oxygens, unless you
>> are using an Urey-Bradley potential for the angle, like in the CHARMM force
>> field. Most (if not all) of the standard force fields in Gromacs treat the
>> interaction of these oxygens within an angle definition, which is a bonded
>> term.
>>
>> -Justin
>
> So no coloumb law between the two oxygens?  10x, Omer.
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Re: [gmx-users] Fwd: charges,resonance and electrostatics

[Justin A. Lemkul]

Omer Markovitch wrote:

Hello,
There is a point, I want to clear out for myself:
Say we focus on the aspartate residue. It has a formal charge of -1.
This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 & 
OD2), according to one of the force fields employed in GROMACS.
 
What is the right way to calculate electrostatics here:

1) "As is", and letting the two oxygens repel one another.
2) Ignore this specific pair when calculating?
 
How does GROMACS operates? I think that (1) is the common practice, but 
I want to be sure.
 


There is no non-bonded interaction between these two oxygens, unless you are 
using an Urey-Bradley potential for the angle, like in the CHARMM force field. 
Most (if not all) of the standard force fields in Gromacs treat the interaction 
of these oxygens within an angle definition, which is a bonded term.


-Justin


Thank you, Omer Markovitch.
(this email was sent to gmx-dev. by mistake)

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/




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--


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


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[gmx-users] Fwd: charges,resonance and electrostatics

[Omer Markovitch]

 Hello,
There is a point, I want to clear out for myself:
Say we focus on the aspartate residue. It has a formal charge of -1.
This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 & OD2),
according to one of the force fields employed in GROMACS.

What is the right way to calculate electrostatics here:
1) "As is", and letting the two oxygens repel one another.
2) Ignore this specific pair when calculating?

How does GROMACS operates? I think that (1) is the common practice, but I
want to be sure.

Thank you, Omer Markovitch.
(this email was sent to gmx-dev. by mistake)

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Error in .gro after energy minimization

[Justin A. Lemkul]

Weird behavior begs lots of questions...

Which version of Gromacs is this?  How was it compiled (i.e., what is your gcc 
version)?  What is your architecture?  Are you running in parallel or serial?


-Justin

vivek sharma wrote:

Hi there,
while running energy minimization using the steep integrator..
I am getting corrupted .gro file ...which is having irregularity in file 
format.. Can anybody help me in figuring out the reason and how can I 
get rid of this problem ?

I am not able to continue for further steps with this .gro file
Following is a part of the generated .gro file after energy minimization


 1545SOL OW 6510   0.909   1.951   5.716
 1545SOLHW1 6511   0.944   1.958   5.622
 1545SOLHW2 6512   0.971   1.896   5.771
 1546S18   5.883
 1542SOLH 2.021   6.086
 1546691   5.944
514   1.796   2.010   6.016
   2.705   5.788
 1543SOL OW 6504   1.794   3.585   6.747
 1543SOLHW1 6505   1.853   3.619   6.673
 1543SOLHW2 6506   1.754   3.497   6.720
 1544SOL OW 6507   1.243   3.597   6.688


With Thanks,
Vivek




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--


Justin A. Lemkul
Graduate Research Assistant
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] dna-protein simulation

[Justin A. Lemkul]

prasun kumar wrote:

Hello Tsjerk,

while running pdb2gmx I was getting error like

h1 is not found while assigning improper dihedral

so I just modified the forcefield(ffG43a1.rtp)file by default it was 
considering ADE also inplace of considering DADE part only,so I removed 
ADE,CYT,GUA part also(is it right to do so?)




You shouldn't have to do this.  You should be able to re-name each residue in 
the .pdb file to agree with with nomenclature in the .rtp file.


Before addressing the problems below, I would suggest you go back and fix these 
initial steps.  If you're getting too creative at the pdb2gmx step, probably 
something is wrong :)



after that I am not getting any error in this step.

Now the topology file that is generated is not having angle type and 
dihedral type


If the topology is incomplete, something has gone wrong.  I would stop right 
here and evaluate the initial pdb2gmx step (see above).


-Justin



for example:

1.18   1920(which is nothing but the angle betwen OA   P   OM)
2.18   1922(OAP OA)

3.17   18   19   20(CH1  OA   P   OM)
4.18   19   22   23(OA  POA   CH2)

then I searched in the ffG43a1bon.itp and get the values llike(I guess 
it is correct,you please give your suggestion)


1. ga_13(its given for OM   P   OA)
2.ga_4  (given for same)
3.gd_9  &  gd_11 (given for -OA-P-)

I added these values to the topology file.It makes the grompp command 
running

I minimized the structure also but the problem I am facing is following:


Fatal error:
Group other not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the 
'-n' option of grompp.

In that case use the '-n' option.

Actually gromacs is not recognizing the DNA molecule.while running 
genbox command I found the following:


system is having
1687 :other residue(4 dna and 1683 water molecule)
0:protein
0:dna

Now what should I do?

I am sure that I am doin something wrong in the beginning itself
can you please help me in identifying that error or can you please send 
me a sample pdb file having dna molecules


with regards

--
PRASUN (ASHOKA)




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--


Justin A. Lemkul
Graduate Research Assistant
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] problem with genion

[Justin A. Lemkul]

sarbani chattopadhyay wrote:
 
Hi everyone,
  I am facing a peculiar problem with "genion". I have a 
system with overall charge

0f +3.
I want genion to add enough ions to make the cocncentration 10 
micromoles/litre.

When I give the command
genion -s em.tpr -o ions.gro -conc 0.1 -pname NA+ -nname CL- -p 
topol.top ,


it gives the message
"No ions to add and no potential to calculate."
If I use the "-neutral" option with the "genion " command, it adds 3 CL- 
ions.


However it works perfectly fine when I specify the concentration to be 
0.15 Moles/litre.
The number of ions added to the system matches with calculations done 
manually.




Probably your box size is such that 0.1 is interpreted as zero.  Gromacs 
calculates concentrations by taking the volume of the unit cell in the .tpr 
file, and it probably rounds 10 uM to zero.


-Justin


However I can't figure out what is the problem with the low 
concentration command.


Any suggestion will be extremely heplful.
Thanks in advance
Sarbani



Rediff Shopping 






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--


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


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[gmx-users] Error in .gro after energy minimization

[vivek sharma]

Hi there,
while running energy minimization using the steep integrator..
I am getting corrupted .gro file ...which is having irregularity in file
format.. Can anybody help me in figuring out the reason and how can I get
rid of this problem ?
I am not able to continue for further steps with this .gro file
Following is a part of the generated .gro file after energy minimization


 1545SOL OW 6510   0.909   1.951   5.716
 1545SOLHW1 6511   0.944   1.958   5.622
 1545SOLHW2 6512   0.971   1.896   5.771
 1546S18   5.883
 1542SOLH 2.021   6.086
 1546691   5.944
514   1.796   2.010   6.016
   2.705   5.788
 1543SOL OW 6504   1.794   3.585   6.747
 1543SOLHW1 6505   1.853   3.619   6.673
 1543SOLHW2 6506   1.754   3.497   6.720
 1544SOL OW 6507   1.243   3.597   6.688


With Thanks,
Vivek
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