[gmx-users] NVT simulation and mdp file

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 5 18:44:08 CET 2010



teklebrh at ualberta.ca wrote:
> Hi Justin,
> 
> That is really confusing. I tried to run this PDB file many times. But 
> still I could not get it the topology file. I waited for so long (10 
> hrs)but still the code looks in a deadlock.
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
> 
> 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 JUsti.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
> 
> [1]+  Stopped
> 
> REMARK   This PDB file is created by CS Chem3D
> 
> REMARK
> 
> COMPND   Tolene.pdb
> 
> ATOM    1  CB  PHE     1      -1.158   0.001   
> 0.000                       C
> 
> ATOM    2  CG  PHE     1      -1.158  -1.336   
> 0.000                       C
> 
> ATOM    3  CD1 PHE     1      -0.000  -2.004   
> 0.000                       C
> 
> ATOM    4  CD2 PHE     1       1.158  -1.336   
> 0.000                       C
> 
> ATOM    5  CE1 PHE     1       1.158   0.001   
> 0.000                       C
> 
> ATOM    6  CE2 PHE     1      -0.000   0.670   
> 0.000                       C
> 
> ATOM    7  CZ  PHE     1      -0.000   2.167   
> 0.000                       C
> 
> END
> 
> 
> 
> can you please tell me what modifications you have done so that your 
> pdb2gmx works fine.
> 

I assumed the blank lines between each ATOM entry were a consequence of my email 
client; is your .pdb file actually double-spaced?  If so, that's the wrong 
format.  Other than that, I have no idea, it worked fine for me.  Does pdb2gmx 
correctly work on other .pdb files?

-Justin

> thank you for your time
> 
> Rob
> 
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>>
>>
>> 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!
>>>>>>>> Please don't post (un)subscribe requests to the list. Use the 
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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 
>>>>>> 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!
>>>> 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
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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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