[gmx-users] NVT simulation and mdp file
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 4 22:38:04 CET 2010
teklebrh at ualberta.ca wrote:
> Dear Justin,
>
> It really help all the feedback you gave me and thank you for that,.
>
> I have one issues as well.
>
> I try to generate the topology file the way you recommend me using the
> pdb2gro but failed to get both the topology and gromacs file.
>
> This is my Toluene file in pdb file
>
> REMARK This PDB file is created by CS Chem3D
>
> REMARK
>
> COMPND Tolene.pdb
>
> HETATM 1 CB PHE 0 -1.158 0.001
> 0.000 C
>
> HETATM 2 CG PHE 0 -1.158 -1.336
> 0.000 C
>
> HETATM 3 CD1 PHE 0 -0.000 -2.004
> 0.000 C
>
> HETATM 4 CD2 PHE 0 1.158 -1.336
> 0.000 C
>
> HETATM 5 CE1 PHE 0 1.158 0.001
> 0.000 C
>
> HETATM 6 CE2 PHE 0 -0.000 0.670
> 0.000 C
>
> HETATM 7 CZ PHE 0 -0.000 2.167
> 0.000 C
>
> HETATM 8 H16 PHE 0 -2.111 0.551
> 0.000 H
>
> HETATM 9 H17 PHE 0 -2.111 -1.886
> 0.000 H
>
> HETATM 10 H18 PHE 0 -0.000 -3.104
> 0.000 H
>
> HETATM 11 H19 PHE 0 2.110 -1.886
> 0.000 H
>
> HETATM 12 H20 PHE 0 2.110 0.551
> 0.000 H
>
> HETATM 13 H21 PHE 0 1.049 2.538
> 0.000 H
>
> HETATM 14 H22 PHE 0 -0.524 2.537
> -0.909 H
>
> HETATM 15 H23 PHE 0 -0.525 2.537
> 0.909 H
>
> END
>
>
> I run
> pdb2gmx -ff G43a1 -f TOL.pdb -o TOL.gro -p TOL.top -missing
>
> but I go the following error.
>
> Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading YY.pdb...
> Read 'Tolene.pdb', 15 atoms
> Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 1 residues with 15 atoms
>
> chain #res #atoms
> 1 ' ' 1 15
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
> Atomtype 1
>
>
> I tried many times but could not get the topology file.
>
> Can you comment on this please.
>
What you've shown isn't an error. It reflects the fact that you don't even have
occupancy values in this .pdb file. You will certainly have a nomenclature
problem, though - your H atoms are not named according to what the .rtp file
expects, so you'll either need to delete the H atoms and let pdb2gmx rebuild
them from the .hdb entries, or use -ignh.
-Justin
> 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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