Re: [gmx-users] Questions about CO2.
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 ptypesigma epsilon D 22.0049 0. A 0. 0. CA 0.0.6512 A 0.2757 0.2339 CO 0. -0.3256 A 0.3033 0.6695 [moleculetype] ; name nrexcl CO22 [atoms] ; nr type resnr residue atom cgnr charge mass 1 D 1 CO2 D1 10. 22.0049 2 D 1 CO2 D2 10. 22.0049 3 CA1 CO2CA 10.6512 0. 4 CO1 CO2OC11 -0.3256 0. 5 CO1 CO2OC21 -0.3256 0. [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-pairsfudgeLJ fudgeQQ 1 2 no 1.0 1.0 [atomtypes] ;name mass charge ptype sigma epsilon CA 12.011000.6512 A 0.27570.2339 CO 15.99940 -0.3256 A 0.30330.6695 [ nonbond_params ] ; i j funct sigmaepsilon CA CO10.2892 0.3955 [moleculetype] ; name nrexcl CO22 [atoms] ; nr type resnr residue atom cgnr charge mass 1 CA1 CO2 CA 1 0.6512 12.0110 2 CO1 CO2 OC1 1 -0.3256 15.9994 3 CO1 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. sp...@xray.bmc.uu.se
[gmx-users] Questions about CO2.
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. 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 ptypesigma epsilon D 22.0049 0. A 0. 0. CA 0.0.6512 A 0.2757 0.2339 CO 0. -0.3256 A 0.3033 0.6695 [moleculetype] ; name nrexcl CO22 [atoms] ; nr type resnr residue atom cgnr charge mass 1 D 1 CO2 D1 10. 22.0049 2 D 1 CO2 D2 10. 22.0049 3 CA1 CO2CA 10.6512 0. 4 CO1 CO2OC11 -0.3256 0. 5 CO1 CO2OC21 -0.3256 0. [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-pairsfudgeLJ fudgeQQ 1 2 no 1.0 1.0 [atomtypes] ;name mass charge ptype sigma epsilon CA 12.011000.6512 A 0.27570.2339 CO 15.99940 -0.3256 A 0.30330.6695 [ nonbond_params ] ; i j funct sigmaepsilon CA CO10.2892 0.3955 [moleculetype] ; name nrexcl CO22 [atoms] ; nr type resnr residue atom cgnr charge mass 1 CA1 CO2 CA 1 0.6512 12.0110 2 CO1 CO2 OC1 1 -0.3256 15.9994 3 CO1 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.