From: Ronald Salesky (rsalesky_at_unm.edu)
Date: Mon Mar 08 2010 - 11:46:24 CST
>>My question also is whether the volume can still remain the same even with the shape of the water box changing to cylindrical? Does an NVT simulation place a restriction on the shape or just the total volume of the water box. If its just the volume, cant the water molecules just arrange and rearrange themselves without the volume changing but just the shape?<<
My understanding is the PBC (periodic boundary condition)
you have placed on your system sets a periodic cell with
the x,y,z boundaries you have specified, which means the
system is modeled as if it is really a periodic array of
the same protein/solvent system like in a crystal. Since
the solvent/protein system wants to converge to its
minimum energy, the solvent shape within the cell will
change. If you were to just model a single cube of water
with no solute molecule it would seek its minimum energy
state which would be spherical. I am learning NAMD/VMD as
you are, so those more experienced may disagree with some
of these points.
Research Assistant/PhD candidate
Nanoscience and Microsystems (NSMS)
University of New Mexico
On Sat, 6 Mar 2010 18:50:45 +0100
Pablo Campomanes <pablo.campomanes_at_epfl.ch> wrote:
> On Mar 6, 2010, at 7:15 AM, Aditya Ranganathan wrote:
>> Hi Pablo,
> Hi Aditya,
>> Since I`m not in the lab today and posted this from
>>home, I could not attach the config files or screenshots
>>with this. However , I`ll just tell you the basic setup
>>that I used in the configuration. I have used PME,
>>Periodic Boundary Conditions and Langevin Dynamics for
>>Temperature control. The rest of the setup is pretty much
>>the ones usually used in any protein in water simulation,
>>including cutoff, scaling, exclude 1-4. I have used the
>>wrapwater option but not rigidbonds. I hope this helps.
>>The Periodic Boundary conditions and CellBasis Vector
>>Values was set using the minmax all and measure center of
>>the box in tkcontrol. The margin value used was 0.0.
> If you use Periodic Boundary Conditions in the NVT
>ensemble, the dimensions of your box must be constant
>during the simulation. Have a look to the .xst file to
>check if everything is going fine.
>> I would also like to add that although the shape of the
>>solvent arranged around the peptides has changed (from
>>cubic/parallelogram to cylindrical), there is no bubble
>>or vacuum inside the solvent system nor is the peptide
>>peeping out of the solvent box. I had used the "use
>>molecular dimensions during solvation" in the VMD
>>auto-solvate plugin while solvating.
>> My question also is whether the volume can still remain
>>the same even with the shape of the water box changing to
>>cylindrical? Does an NVT simulation place a restriction
>>on the shape or just the total volume of the water box.
>>If its just the volume, cant the water molecules just
>>arrange and rearrange themselves without the volume
>>changing but just the shape? I`m sorry if all this sounds
>>naive to you since I`m new to he field of MD simulation.
>>Since the system is`nt crashing, does this have an effect
>>on the accuracy of the simulation itself like the
>>interpeptide interaction as the peptides are still well
>>solvated inside the water. Could there be a chance that
>>this is just a graphical thing and won`t have much effect
>>on the actual simulaton. Also, can you please tell me the
>>basic setup for an NVT and an NPT, just in case I`ve
>>missed a few parameters in the configuration.
> If you control the temperature (section 6.4 of NAMD
>manual) and you do not set any pressure coupling scheme
>you will run in the NVT ensemble.
> Concerning NPT, there are several ways to control the
>pressure during a simulation in NAMD. The keywords in the
>input file will depend on the option chosen. Have a look
>to the manual (section 6.5) for more details.
>> Hoping for a reply. Will post the actual files and
>>screenshots on Monday.
>> Srivastav Ranganathan (Aditya)
>> Junior Research Assistant
>> Department of Biosciences and Bioengineering,
>> IIT Bombay,
> Best regards,
>> On Sat, Mar 6, 2010 at 10:20 AM, Pablo Campomanes
>> If you are running a simulation in the NVT ensemble, you
>>are not allowing your simulation box to change by
>> I am afraid that you will not get so much help if you do
>>not provide the appropriate files to investigate what is
>> Pablo Campomanes
>> Laboratory of Computational Chemistry and Biochemistry
>> BCH 4118 EPF Lausanne
>> On Mar 6, 2010, at 4:59 AM, Aditya Ranganathan wrote:
>>> Hi Everyone,
>>> I`m trying to simulate a system of 2 ACTH and 2 Beta
>>>Endorphin peptides and intend to study the interaction
>>>between them. I first minimized the peptides before
>>>solvating it (and added Na and Cl ions to neutralize the
>>>box) and then minimized the solvated system again. I then
>>>heated the system slowly for 300ps with an increment of
>>>0.001K per step and then equilibrated the system at 300K
>>>for another 300ps.
>>> I then started the final production run and intend to
>>>run it for a minimum of 10 ns to study any interaction or
>>>aggregation tendency between the peptides. However, what
>>>started as a Cubical waterbox initially has now become an
>>>almost cylindrical shaped water `box`. The configuration
>>>I`ve used is of an NVT simulation. However, even in the
>>>cylindrical system, the peptides are fully surrounded by
>>>water and not exposed out of the solvent. The simulation
>>>has now run for almost 4ns and still continues to run
>>>without any crashes or errors.
>>> However my question is whether the change in shape of
>>>the water box is a sign of an inappropriate simulation or
>>>an undesirable change.
>>> Srivastav Ranganathan (Aditya)
>>> Junior Research Assistant
>>> Department of Biosciences and Bioengineering,
>>> IIT Bombay,
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