Re: [gmx-users] acetone parameter
Mark Abraham wrote: JMandumpal wrote: Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE -- [ atoms ] ; nrtyperesnr resid atom cgnr chargemass 1opls_0691 ACETCAA10.000 15.0350 2opls_2801 ACETC_210.470 12.0110 3opls_0691 ACETCAD10.000 15.0350 4opls_2811 ACETO_21 -0.470 15.9994 --- But on the other hand, when I checked the literature, JPC 94, 1990, p.1683, I found out, the parameters are given in the following manner, TABLE TWO : TABLE TWO atom types charge sigma epsilon CH3 0.062 3.910 0.160 C0.300 3.750 0.105 O -0.424 2.960 0.210 ** For keeping total charge in the system to zero, I used the opls_069 for methyl group (zero charge), in my input file, compared to what has been published. I would like to know whether the parameters (charge) I chose is right, else which atom type I must use for methyl group. Different models will have different charges. What is correct to use depends on how those models were parameterized to interact with which other force fields, and for what purpose they were intended. Finding this out and making these decisions is your job, not ours. Apart from that: just test it. Simulate bulk acetone and compare the properties to experimental data (densite DHvap etc.) -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] acetone parameter
Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE -- [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_0691 ACETCAA 10.000 15.0350 2 opls_2801 ACETC_2 10.470 12.0110 3 opls_0691 ACETCAD 10.000 15.0350 4 opls_2811 ACETO_2 1 -0.470 15.9994 --- But on the other hand, when I checked the literature, JPC 94, 1990, p.1683, I found out, the parameters are given in the following manner, TABLE TWO : TABLE TWO atom types charge sigma epsilon CH3 0.062 3.910 0.160 C0.300 3.750 0.105 O -0.424 2.960 0.210 ** For keeping total charge in the system to zero, I used the opls_069 for methyl group (zero charge), in my input file, compared to what has been published. I would like to know whether the parameters (charge) I chose is right, else which atom type I must use for methyl group. thanking in advance, Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] acetone parameter
JMandumpal wrote: Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE -- [ atoms ] ; nrtyperesnr resid atom cgnr chargemass 1opls_0691 ACETCAA10.000 15.0350 2opls_2801 ACETC_210.470 12.0110 3opls_0691 ACETCAD10.000 15.0350 4opls_2811 ACETO_21 -0.470 15.9994 --- But on the other hand, when I checked the literature, JPC 94, 1990, p.1683, I found out, the parameters are given in the following manner, TABLE TWO : TABLE TWO atom types charge sigma epsilon CH3 0.062 3.910 0.160 C0.300 3.750 0.105 O -0.424 2.960 0.210 ** For keeping total charge in the system to zero, I used the opls_069 for methyl group (zero charge), in my input file, compared to what has been published. I would like to know whether the parameters (charge) I chose is right, else which atom type I must use for methyl group. Different models will have different charges. What is correct to use depends on how those models were parameterized to interact with which other force fields, and for what purpose they were intended. Finding this out and making these decisions is your job, not ours. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
