[gmx-users] NVT simulation and mdp file
Justin A. Lemkul
jalemkul at vt.edu
Fri Mar 5 00:45:22 CET 2010
teklebrh at ualberta.ca wrote:
> Hi Justin,
>
> Thank you pointing out that!
>
> I made all the changes and still cannot go past this line.
>
> 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
>
> END
>
>
> As you can see I used this PDB file but still no topology out put.
>
> Select the Force Field:
> 0: GROMOS96 43a1 force field
> 1: GROMOS96 43a2 force field (improved alkane dihedrals)
> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 6: [DEPRECATED] Gromacs force field (see manual)
> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
> 8: Encad all-atom force field, using scaled-down vacuum charges
> 9: Encad all-atom force field, using full solvent charges
>
> 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.pdb...
> Read 'Tolene.pdb', 7 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 7 atoms
>
> chain #res #atoms
> 1 ' ' 1 7
>
> 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
>
Is this actually where pdb2gmx stops? There's no fatal error here, the program
should continue to run, at least until it prints out a real error message. Your
.pdb file works fine, I just ran it through pdb2gmx myself.
-Justin
> best
>
> Rob
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>>
>> 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
>>>>>>
>>>>>> ========================================
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>>> posting!
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>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
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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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
>
--
========================================
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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