[gmx-users] NVT simulation and mdp file
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 3 23:10:37 CET 2010
teklebrh at ualberta.ca wrote:
> Dear Justin,
>
> I really appreciate your help and feedback. once again thank you for
> your time.
>
> --------This could be some visualization artifact, or the components of
> your
> system have condensed within the box. Without actually seeing it,
> it's hard to tell. If you post an image online (Photobucket, etc)
> then we might get a better sense of what's going on.
> Here is my .gro file taht looks like condensed.------------
>
> Attached please find the NVT.gro file
>
> or the images in .jpeg file format
>
Please note that this is not what I suggested you do. Posting images online
(not to the list) is a far better method. Users who subscribe to the list in
digest format will not get these attachments, and thus you alienate others who
might be able to help you. Also, for the security-conscious, download
attachments is not always preferable.
It seems pretty clear from what's going on that your system is simply
condensing, so your initial configuration placed all the molecules too far apart
(at too low of a density). Display the box vectors in VMD and you will see
exactly what's going on:
(Tk console)
package require pbctools
pbc box
-Justin
>
> Best,
>
> Rob
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>>
>> teklebrh at ualberta.ca wrote:
>>> Dear Gromacs Users,
>>>
>>> I have encountered the following issues while I was running my MD
>>> simulation. Can anybody comment on what the meaning of these notes
>>> are. Is there anything I could do to avoid them.
>>>
>>> NOTE 2 [file PAP.top, line unknown]:
>>>
>>> The largest charge group contains 12 atoms.
>>>
>>> Since atoms only see each other when the centers of geometry of the
>>> charge
>>>
>>> groups they belong to are within the cut-off distance, too large charge
>>>
>>> groups can lead to serious cut-off artifacts.
>>>
>>> For efficiency and accuracy, charge group should consist of a few
>>> atoms.
>>>
>>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>>>
>>> My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file with
>>> only one group charge only.
>>>
>>
>> That's almost certainly wrong. See, for instance, the PHE side chain
>> in the relevant .rtp entry for a more reasonable charge group setup.
>> If you're using PRODRG defaults, then the charges are probably
>> unsatisfactory, as well.
>>
>> The rationale for the charge group size is summed up here:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2008-November/038153.html
>>
>>> NOTE 1 [file nvt.mdp, line unknown]:
>>>
>>> The Berendsen thermostat does not generate the correct kinetic energy
>>>
>>> distribution. You might want to consider using the V-rescale
>>> thermostat.
>>>
>>>
>>
>> See the literature about this one, as well as the numerous list
>> archive discussions. For initial equilibration, a weak coupling
>> scheme is probably fine, but you can also use V-rescale. Also of
>> interest:
>>
>> http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>>> NOTE 3 [file aminoacids.dat, line 1]:
>>>
>>> The optimal PME mesh load for parallel simulations is below 0.5
>>>
>>> and for highly parallel simulations between 0.25 and 0.33,
>>>
>>> for higher performance, increase the cut-off and the PME grid spacing
>>>
>>
>> This all depends on the size of your system, how much of the work is
>> distributed between the real-space Coulombic interaction and PME.
>>
>>>
>>> In addition to the above notes I have also some questions about the
>>> NVT and NPT simulation.
>>>
>>> 1)I am using toluene as a solvent to simulate my polymer, do I need
>>> to use the compressibility of toluene which is 9.2e-5 or the default
>>> value 4.5e-5 1/bar.
>>
>> Well, 4.5e-5 corresponds to water, which you aren't using...
>>
>> For NVT, this won't matter since the box is fixed, but for NPT, the
>> compressibility will affect the response of your system to pressure.
>> The differences may be minimal, but if you know the right value, why
>> accept a wrong one?
>>
>>> 2)What about the dielectric constant (the dielectric constant for
>>> toluene is 2-2.4), but the default value is 80 ( I assume this is for
>>> water- am I right).
>>
>> Yes, the default again assumes water as the solvent.
>>
>>> 3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have to
>>> increase my box size of the solute at the beginning to a min of 2*1.4
>>> =2.8 ( min image convection). Is this the right way to do!
>>
>> At an absolute minimum. Keep in mind that the box vectors will
>> fluctuate under NPT, so if the box decreases even a little bit below
>> 2.8, you will be violating the minimum image convention.
>>
>>> 4)I run an NVT simulation to equilibrate my system for 100 ps. When
>>> I checked my simulation at the end (successfully completed) I noticed
>>> that the shape of my simulation box looks CIRCULAR! some how the
>>> rectangular shape looks distorted. What does this tell! Do you guys
>>> think something is wrong in my simulation.
>>
>> This could be some visualization artifact, or the components of your
>> system have condensed within the box. Without actually seeing it,
>> it's hard to tell. If you post an image online (Photobucket, etc)
>> then we might get a better sense of what's going on.
>>
>>> 5)I included the polar and aromatic hydrogens in my simulation (
>>> ffG43a1.itp - GROMOS96.1 in PRODRG). Does these hydrogen influence my
>>> result as the force field is a united atom force field. Or How can I
>>> get rid of them if I want. With or without the aromatic hydrogen gave
>>> good results ( besides lower computational cost). Does Gromos96 model
>>> correctly aromatic-Aromatic interaction.
>>>
>>
>> Well, "correct" is a relative term for all force fields, but you need
>> to follow the prescribed setup of the force field itself, otherwise
>> you can throw it all away. If you lump the hydrogens into the ring
>> carbons and have an uncharged ring, the result will be different than
>> if you have the hydrogens there with a small charge on each C and H.
>> Again, refer to the force field .rtp file for examples. You can also
>> create a better toluene topology by renaming the residue in your
>> coordinate file PHE and trick pdb2gmx:
>>
>> pdb2gmx -f toluene.pdb -missing
>>
>> Then change the mass of the CH2 group (which pdb2gmx thinks is a CB
>> for PHE) to reflect a CH3 group. Make an .itp file out of the
>> resulting .top by removing the unnecessary #includes, [system], and
>> [molecule] directives. Then you don't have to worry about messing
>> with PRODRG. I should note, as well, that this is about the only
>> appropriate use of -missing I can think of at the moment (just for
>> clarity in the archives; I usually warn against using -missing).
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
> ------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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