[gmx-users] Questions about CO2.
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 25 14:58:36 CET 2014
On 2014-12-25 08:13, sujithkakkat . wrote:
> Dear all,
>
> I went through the mails about the use of virtual sites for
> representing linear molecules like CO2. I also read that GROMACS cannot
> handle angle bending potentials at 180 degrees in an appropriate manner.
There is an (undocumented) linear angle potential in gromacs. Check
source code and manual.
>
> My system consists of EPM2-CO2 dissollved in TIP4- H2O.
>
> I made topology files for CO2 with virtual sites and also made
> another topology without the use of virtual sites providing the equilibrium
> angle (180) and the bending force constant. Both these are given at the end.
>
> I am trying to use the EPM2 model for CO2 reported in* J. Phys.
> Chem. 1995,99, 12021-12024* by *Jonathan G. Harris and Kwong H. Yung* under
> the title "Carbon Dioxide's Liquid-Vapor Coexistence Curve and Critical
> Properties As Predicted by a Simple Molecular Model".
>
> I have the following questions;
>
> (i) I am using gromacs 4.6.5. Is the problem related to treating angle
> bending potentials for linear molecules solved in later versions of gromacs?
>
> (ii) The authors Harris and Yung stress that their model is flexible in
> terms of bending in the abstract of their article. So if I build this model
> using virtual sites then I believe I am neglecting the flexibility. Also
> while using virtual sites the model looks more like a dimer with two point
> masses, instead of a a three point EPM2 model. So can I call this an EPM2
> model any more.? Do you think introducing virtual sites affects the results
> which are expected from a simple looking EPM2 model, with three
> charged-Lennard-Jones point masses with a flexible angle.
>
> I appreciate (and often surprised by) the fact that a simple model like
> EPM2 which can be specified by a total of just nine parameters can
> accurately predict the properties of CO2 at supercritical conditions which
> otherwise may a be a very intricate condensed system to study. This prompts
> me to think that any small change in the model can impart an error that can
> get magnified for a system of thousands of molecules.
>
> (iii) I found that I am getting highly positive energy values when using
> the topology built using virtual sites. To add to this I am forced to use
> very short time steps (0.2 fs) for simulations, since with 2fs, system was
> unstable which I believe has to do with the positive energy and high force
> values. Whereas, using the topology built in the usual way without virtual
> sites, I get negative energy values and simulations could easily be
> performed using a 2fs time step (system may be more stable) . I checked the
> angles in this case at the final state of the system, and found them lying
> between 175 to 180 degrees, which I am not sure if it is all right.
> Is this slight deviation from 180 degree caused by the failure of
> GROMACS to maintain linearity? Or, is it perfectly normal since the model
> itself is flexible.?
>
>
> Please share your views.
>
> Regards,
>
> Sujith.
>
>
>
> *TOPOLOGY USING VIRTUAL SITES:*
>
>
> [atomtypes]
>
> ; name mass charge ptype sigma epsilon
>
> D 22.0049 0.0000 A 0.0000 0.0000
> CA 0.0000 0.6512 A 0.2757 0.2339
> CO 0.0000 -0.3256 A 0.3033 0.6695
>
> [moleculetype]
>
> ; name nrexcl
> CO2 2
>
> [atoms]
>
> ; nr type resnr residue atom cgnr charge mass
> 1 D 1 CO2 D1 1 0.0000 22.0049
> 2 D 1 CO2 D2 1 0.0000 22.0049
> 3 CA 1 CO2 CA 1 0.6512 0.0000
> 4 CO 1 CO2 OC1 1 -0.3256 0.0000
> 5 CO 1 CO2 OC2 1 -0.3256 0.0000
>
> [constraints]
> ; i j funct doc
> 1 2 1 0.195948
>
> [virtual_sites2]
> ; i j k funct a
> 3 1 2 1 0.5
> 4 1 2 1 1.08638006
> 5 2 1 1 1.08638006
>
>
> *TOPOLOGY WITHOUT VIRTUAL SITES:*
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 no 1.0 1.0
>
> [atomtypes]
>
> ;name mass charge ptype sigma epsilon
> CA 12.01100 0.6512 A 0.2757 0.2339
> CO 15.99940 -0.3256 A
> 0.3033 0.6695
>
> [ nonbond_params ]
>
> ; i j funct sigma epsilon
>
> CA CO 1 0.2892 0.3955
>
> [moleculetype]
>
> ; name nrexcl
>
> CO2 2
>
> [atoms]
>
> ; nr type resnr residue atom cgnr charge mass
> 1 CA 1 CO2 CA 1 0.6512 12.0110
> 2 CO 1 CO2 OC1 1 -0.3256 15.9994
> 3 CO 1 CO2 OC2 1 -0.3256 15.9994
>
> [angles]
>
> ; i j k funct ao
> ak
> 3 1 2 1 180 1236
>
>
> [constraints]
>
> ; i j funct doc
>
> 1 2 1 0.1149
> 1 3 1 0.1149
>
> [exclusions]
>
> 1 2 3
> 2 1 3
> 3 1 2
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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