[gmx-users] pdb2gmx -water-> grompp; grompp error
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 25 23:22:44 CEST 2009
Paymon Pirzadeh wrote:
> I realized sth about the previous error message I posted. In the
> following I have copied the lines (with their line number) which
> grompp gives warning on!
>
>
> in .gro file:
> 65868 10940SOL HW265866 5.038 5.739 6.407
> 65869 10940SOL MW65867 5.103 5.710 6.455
> 65870 10940SOL LP165868 5.061 5.644 6.524
> 65871 10940SOL LP265869 5.144 5.630 6.405
> 65872 10941Na Na65870 1.844 0.957 1.889
> 65873 5.40000 6.23500 10.24600
>
> in .top file:
> 4147 [ molecules ]
> 4148 ; Compound #mols
> 4149 Protein_A 1
> 4150 SOL 10903
> 4151 Na+ 1
>
> I have tested that if I remove the "+" sign, grompp will not work at all
> and says "such molecule does not exists".
> So, I am not sure where the Na-NA mismatch comes from?!
>
Ion names are force field-specific. If you left -pname as the default, it
assigns Na (for ffgmx). Check ions.itp for the correct name.
-Justin
> Payman
>
>
>
>
>
>
>
>
> On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
>> Paymon Pirzadeh wrote:
>>> When I look at the .top file generated by pdb2gmx, the last lines show
>>> how this -0.99 is generated:
>>>
>>> 442 opls_302 37 ARG CZ 138 0.64 12.011 ;
>>> qtot -0.33
>>> 443 opls_300 37 ARG NH1 139 -0.8 14.0067 ;
>>> qtot -1.13
>>> 444 opls_301 37 ARG HH11 139 0.46 1.008 ;
>>> qtot -0.67
>>> 445 opls_301 37 ARG HH12 139 0.46 1.008 ;
>>> qtot -0.21
>>> 446 opls_300 37 ARG NH2 140 -0.8 14.0067 ;
>>> qtot -1.01
>>> 447 opls_301 37 ARG HH21 140 0.46 1.008 ;
>>> qtot -0.55
>>> 448 opls_301 37 ARG HH22 140 0.46 1.008 ;
>>> qtot -0.09
>>> 449 opls_271 37 ARG C 141 0.7 12.011 ;
>>> qtot 0.61
>>> 450 opls_272 37 ARG O1 141 -0.8 15.9994 ;
>>> qtot -0.19
>>> 451 opls_272 37 ARG O2 141 -0.8 15.9994 ;
>>> qtot -0.99
>>>
>>> The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
>>> simulation is supposed to be close to 7.0, I believe one of the
>>> negatively-charged side chains needs to be neutralized. That's why I
>>> think one Na+ might be helpful.
>>>
>> That's probably correct. I just wanted to verify what was in your system. If
>> you just had water, it made no sense. But with a protein involved with lots of
>> partial charges, these rounding issues do occur. You really do have a system
>> with -1 charge.
>>
>> -Justin
>>
>>> Payman
>>>
>>>
>>> On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
>>>> Paymon Pirzadeh wrote:
>>>>> OK! It worked! Thanks a lot again. But I have a final technical
>>>>> question. After running grompp, it shows that my box has a net charge of
>>>>> -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
>>>>> OK?! or even this 0.01 charge will cause me troubles?
>>>> Depending on the size of your system, rounding errors can occur. It is unusual
>>>> that the hundredths place would be showing this error. Usually you'd get
>>>> something like 0.99998 or something. Your water topology has a zero net charge;
>>>> is there something else in your system causing the -1 charge?
>>>>
>>>> Adding a single Na+ to neutralize the charge may be appropriate, but that's up
>>>> to you based on what's in your system (something else may be broken, but I just
>>>> don't know).
>>>>
>>>> -Justin
>>>>
>>>>> Sorry for tons of e-mails.
>>>>> regards,
>>>>>
>>>>> Payman
>>>>>
>>>>>
>>>>> On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
>>>>>> Paymon Pirzadeh wrote:
>>>>>>> OK! That's fine. But what if I do not have permissions to make such
>>>>>>> changes in the itp files? Also, isn't that the case that when you define
>>>>>> That's why I said copy the force field files into your local directory. Once
>>>>>> there, you can modify them.
>>>>>>
>>>>>>> sth for the second time, grompp will take the second one? Sorry for mass
>>>>>>> of e-mail!
>>>>>>>
>>>>>> That is only true in the case of .mdp files.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> Payman
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
>>>>>>>> Paymon Pirzadeh wrote:
>>>>>>>>> I have done that already! I use my local copy to make my files. but how
>>>>>>>>> can I get rid of this error? get into the oplsaanb.itp or include this
>>>>>>>>> water model in the topology file before oplsaa.itp?
>>>>>>>>>
>>>>>>>> I don't understand what you're saying you've already done.
>>>>>>>>
>>>>>>>> The problem is this: when grompp attempts to assemble the .tpr file, it reads
>>>>>>>> all of the information from the ffoplsaa*.itp files. It finds the directives
>>>>>>>> like [defaults], [atomtypes], etc in a pre-defined order. If, later, it finds a
>>>>>>>> duplicate of these directives, it complains. So when you #include your .itp
>>>>>>>> file with new [atomtypes], it generates the error because it is a duplicate
>>>>>>>> directive. You have to include the new atom types in ffoplsaanb.itp in the
>>>>>>>> [atomtypes] directive of this file. The rest of the topology shouldn't cause a
>>>>>>>> problem, just the [atomtypes] directive.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>>> Payman
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
>>>>>>>>>> Paymon Pirzadeh wrote:
>>>>>>>>>>> OK!
>>>>>>>>>>> here is the .itp file which I generated. I might upload it because it
>>>>>>>>>>> has passed the initial tests.
>>>>>>>>>>>
>>>>>>>>>>> ; This is an itp file to describe water's six-site model by H. Nada and
>>>>>>>>>>> J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
>>>>>>>>>>> (2003)
>>>>>>>>>>> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
>>>>>>>>>>> and 3 Coulomb sites
>>>>>>>>>>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
>>>>>>>>>>> 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
>>>>>>>>>>>
>>>>>>>>>>> [ defaults ]
>>>>>>>>>>> ; non-bondedtype combrule genpairs FudgeLJ
>>>>>>>>>>> FudgeQQ N
>>>>>>>>>>> 1 2 NO
>>>>>>>>>>>
>>>>>>>>>>> [ atomtypes ]
>>>>>>>>>>> ;name mass charge ptype c6 c12
>>>>>>>>>>> OW 15.9994 0.0 A 0.3115 0.714845562
>>>>>>>>>>> HW 1.00800 0.477 A 0.0673 0.11541
>>>>>>>>>>> MW 0.000 -0.866 D 0.00 0.00
>>>>>>>>>>> LW 0.00 -0.044 D 0.00 0.00
>>>>>>>>>>>
>>>>>>>>>>> [ moleculetype ]
>>>>>>>>>>> ;molname nrexcl
>>>>>>>>>>> SOL 2
>>>>>>>>>>>
>>>>>>>>>>> [ atoms ]
>>>>>>>>>>> ; nr atomtype resnr residuename atom cgnr charge
>>>>>>>>>>> 1 OW 1 SOL OW 1 0.0
>>>>>>>>>>> 2 HW 1 SOL HW1 1 0.477
>>>>>>>>>>> 3 HW 1 SOL HW2 1 0.477
>>>>>>>>>>> 4 MW 1 SOL MW 1 -0.866
>>>>>>>>>>> 5 LW 1 SOL LP1 1 -0.044
>>>>>>>>>>> 6 LW 1 SOL LP2 1 -0.044
>>>>>>>>>>>
>>>>>>>>>>> [ settles ]
>>>>>>>>>>> ; OW function doh dhh
>>>>>>>>>>> 1 1 0.0980 0.15856
>>>>>>>>>>>
>>>>>>>>>>> [ dummies3 ]
>>>>>>>>>>> ; These set of parameters are for M site which can be easily calculated
>>>>>>>>>>> using TIP4P calculations from tip4p.itp
>>>>>>>>>>> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
>>>>>>>>>>> b*(r(i)-r(k))
>>>>>>>>>>> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
>>>>>>>>>>> Remember that OM is in the same direction of OH bonds.
>>>>>>>>>>> ; Remember this site is in the same plane of OH bonds; so, its function
>>>>>>>>>>> 1
>>>>>>>>>>> ;
>>>>>>>>>>> ; site from function a b
>>>>>>>>>>> 4 1 2 3 1 0.199642536 0.199642536
>>>>>>>>>>>
>>>>>>>>>>> ; Now we define the position of L sites which can be obtained from
>>>>>>>>>>> tip5p.itp
>>>>>>>>>>> ; So, it will be described as dummy site 3out: r(v) = r(i) +
>>>>>>>>>>> a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
>>>>>>>>>>> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
>>>>>>>>>>> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
>>>>>>>>>>> bonds, a minus sign is added. This part is similar to M site.
>>>>>>>>>>> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
>>>>>>>>>>> the magnitude of vector product of OH bonds.
>>>>>>>>>>> ; This sites are tetrahedral sites; so, its function 4
>>>>>>>>>>> ;
>>>>>>>>>>> ; site from function a b
>>>>>>>>>>> c
>>>>>>>>>>> 5 1 2 3 4 -0.437172388 -0.437172388
>>>>>>>>>>> 8.022961206
>>>>>>>>>>> 6 1 2 3 4 -0.437172388 -0.437172388
>>>>>>>>>>> -8.022961206
>>>>>>>>>>>
>>>>>>>>>>> [ exclusions ]
>>>>>>>>>>> 1 2 3 4 5 6
>>>>>>>>>>> 2 1 3 4 5 6
>>>>>>>>>>> 3 1 2 4 5 6
>>>>>>>>>>> 4 1 2 3 5 6
>>>>>>>>>>> 5 1 2 3 4 6
>>>>>>>>>>> 6 1 2 3 4 5
>>>>>>>>>>>
>>>>>>>>>>> and here is the message I get from grompp:
>>>>>>>>>>>
>>>>>>>>>>> Program grompp_d_mpi, VERSION 4.0.5
>>>>>>>>>>> Source code file: topio.c, line: 415
>>>>>>>>>>>
>>>>>>>>>>> Fatal error:
>>>>>>>>>>> Syntax error - File sixsitewater.itp, line 12
>>>>>>>>>>> Last line read:
>>>>>>>>>>> '[ atomtypes ]'
>>>>>>>>>>> Invalid order for directive atomtypes
>>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>>>
>>>>>>>>>>> I believe the original files of GROMACS need admin permissions which I
>>>>>>>>>>> do not have on the cluster that I am currently using and I am not sure
>>>>>>>>>>> if that might not cause troubles for other users. So, I thought how I
>>>>>>>>>>> can keep the changes local.
>>>>>>>>>>>
>>>>>>>>>> Make a copy in your local directory; grompp will use these before looking for
>>>>>>>>>> system-wide files. As a general rule, whenever developing new parameters or
>>>>>>>>>> adjusting files, do so locally before potentially messing yourself (or others) up :)
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>>>> Payman
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
>>>>>>>>>>>> Paymon Pirzadeh wrote:
>>>>>>>>>>>>> Hello,
>>>>>>>>>>>>> Just a reminder that I had troubled with combination rules between my
>>>>>>>>>>>>> water model and GROMACS forcefields. I fixed the problem by adjusting my
>>>>>>>>>>>>> water model's parameters. BUT, now, I specified the new parameters in
>>>>>>>>>>>>> my .itp file under [ atomtype ] category and grompp makes errors out of
>>>>>>>>>>>>> the orders. Now I am using OPLSaa. I suspect again the problem comes
>>>>>>>>>>>>> from the presence of the second [atomtype ]. How can I keep my new
>>>>>>>>>>>>> parameters and use them in my water model's itp file? Or should I change
>>>>>>>>>>>>> these parameters in the OPLSaa.itp file?
>>>>>>>>>>>> You can't have a second [atomtypes] directive. You can add new parameters to
>>>>>>>>>>>> ffoplsaanb.itp to account for the atom types you are implementing, though.
>>>>>>>>>>>>
>>>>>>>>>>>> If you want anything more specific, you'll probably have to provide the topology
>>>>>>>>>>>> file you're working with, as well as any actual error messages you're seeing.
>>>>>>>>>>>>
>>>>>>>>>>>> -Justin
>>>>>>>>>>>>
>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Payman
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
>>>>>>>>>>>>>> Paymon Pirzadeh wrote:
>>>>>>>>>>>>>>> I checked all the force-fields available in the GROAMCS. None of them
>>>>>>>>>>>>>>> have the #2 combination rule which matches my water model! Any
>>>>>>>>>>>>>>> alternatives (rather than changing my water model)?
>>>>>>>>>>>>>> A water model that isn't compatible with the model of the solutes isn't
>>>>>>>>>>>>>> of any value, so it looks like you have put the cart before the horse.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
>>>>>>>>>>>>>>>> Paymon Pirzadeh wrote:
>>>>>>>>>>>>>>>>> That was very helpful! But I realized a problem. The OPLSaa uses the
>>>>>>>>>>>>>>>>> combination rule #3 in [ defaults ] while my water model uses #2. Now if
>>>>>>>>>>>>>>>>> I comment out my water model's combination, I am not sure what I am
>>>>>>>>>>>>>>>>> going to face! Any comments?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Then I would say that your water model's combination rule is inconsistent with
>>>>>>>>>>>>>>>> the method of nonbonded calculations in OPLS. It appears that the only
>>>>>>>>>>>>>>>> difference between combination rules 2 and 3 comes when a specific interaction
>>>>>>>>>>>>>>>> is not defined in the [nonbond_params] section. The specifics of these
>>>>>>>>>>>>>>>> combination rules are given in manual section 5.3.3.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> -Justin
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Payman
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:
>>>>>>>>>>>>>>>>>> Paymon Pirzadeh wrote:
>>>>>>>>>>>>>>>>>>> Well,
>>>>>>>>>>>>>>>>>>> I changed the topology file of the system and manually typed the .itp of
>>>>>>>>>>>>>>>>>>> my own water model. Just a reminder that I have used my own water
>>>>>>>>>>>>>>>>>>> model's .itp file successfully in pure water systems. This .itp file
>>>>>>>>>>>>>>>>>>> starts from [ defaults ] and contains all information needed. But when
>>>>>>>>>>>>>>>>>>> it comes to grompp, the following error appears:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Program grompp_d_mpi, VERSION 4.0.5
>>>>>>>>>>>>>>>>>>> Source code file: topio.c, line: 415
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Fatal error:
>>>>>>>>>>>>>>>>>>> Syntax error - File sixsitewater.itp, line 6
>>>>>>>>>>>>>>>>>>> Last line read:
>>>>>>>>>>>>>>>>>>> '[ defaults ]'
>>>>>>>>>>>>>>>>>>> Invalid order for directive defaults
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The only time that [defaults] should appear is in the force field that you are
>>>>>>>>>>>>>>>>>> calling (i.e., ffoplsaa.itp):
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> -Justin
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> I am trying to use this water model with OPLSaa. what kind of directive
>>>>>>>>>>>>>>>>>>> am I missing?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Payman
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
>>>>>>>>>>>>>>>>>>>> Paymon Pirzadeh wrote:
>>>>>>>>>>>>>>>>>>>>> Hello,
>>>>>>>>>>>>>>>>>>>>> I am trying to use a different water model for my proteins (using oplsaa
>>>>>>>>>>>>>>>>>>>>> force field). I use the .itp file which I developed, but pdb2gmx does
>>>>>>>>>>>>>>>>>>>>> not accept it. I am a bit confused on how I can make my water model work
>>>>>>>>>>>>>>>>>>>>> with OPLSaa. Based on what I saw from spc.itp or other samples, do I
>>>>>>>>>>>>>>>>>>>>> need to change the names of my particles in my water .itp file by
>>>>>>>>>>>>>>>>>>>>> including _FF_OPLS?
>>>>>>>>>>>>>>>>>>>> I don't know how pdb2gmx decides how to recognize water models; it may be
>>>>>>>>>>>>>>>>>>>> hard-coded. In any case, your atom types have to be consistent with OPLS
>>>>>>>>>>>>>>>>>>>> standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file,
>>>>>>>>>>>>>>>>>>>> you may not need it if OPLS is the only force field with which it will be used.
>>>>>>>>>>>>>>>>>>>> The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> -Justin
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Payman
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>>>>>>>>
>>>>>>>> --
>>>>>>>> ========================================
>>>>>>>>
>>>>>>>> Justin A. Lemkul
>>>>>>>> Ph.D. Candidate
>>>>>>>> ICTAS Doctoral Scholar
>>>>>>>> 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
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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