[gmx-users] NVT simulation and mdp file
teklebrh at ualberta.ca
teklebrh at ualberta.ca
Fri Mar 5 17:39:54 CET 2010
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.
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
>>>>>>> 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
>>> 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.
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