[gmx-users] NVT simulation and mdp file
teklebrh at ualberta.ca
teklebrh at ualberta.ca
Fri Mar 5 00:41:05 CET 2010
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
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!
>>>>> 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
>>>
>>> ========================================
>>> --
>>> 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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>>>
>>>
>>
>>
>
> --
> ========================================
>
> 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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