[gmx-users] NVT simulation and mdp file
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 4 23:30:41 CET 2010
teklebrh at ualberta.ca wrote:
> Hi Justin,
>
> It does not work. I eliminated the hydrogen atoms and check the entire
> .pdb file but could not solve the problem.
>
> the modified 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
> CH2
>
> HETATM 2 CG PHE 0 -1.158 -1.336
> 0.000 C
>
> HETATM 3 CD1 PHE 0 -0.000 -2.004 0.000
> CR1
>
> HETATM 4 CD2 PHE 0 1.158 -1.336 0.000
> CR1
>
> HETATM 5 CE1 PHE 0 1.158 0.001 0.000
> CR1
>
> HETATM 6 CE2 PHE 0 -0.000 0.670 0.000
> CR1
>
> HETATM 7 CZ PHE 0 -0.000 2.167 0.000
> CR1
>
> END
>
>
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> WARNING: masses will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> 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 Tolene.pbd.gro...
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: futil.c, line: 330
>
> File input/output error:
> Tolene.pbd.gro
> -------------------------------------------------------
>
> "It's So Lonely When You Don't Even
>
>
> Any comment on that.
>
It's a pretty obvious typo; .pbd != .pdb.
-Justin
> Rob
>
>
>
>
>
>
>
>
>
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>>
>> 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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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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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