Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
Payman
On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote:
>
> 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@gromacs.org
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> >>>>>>>>>>>>>> _______________________________________________
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> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>> gmx-users mailing list gmx-users@gromacs.org
> >>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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@gromacs.org
> >>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >>>>>>>>
> >>>>>>>>
> >>>
> >
> >
>
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