[gmx-users] Re: Using Morse potentials with ENCAD force field
Using the parameters listed earlier I equalized my system after trying to place the oxygen and nitrogen molecules evenly throughout my system. The result showed the nitrogen molecules fairly even throughout the system but all the oxygen molecules on one side. Any ideas on why the system might not be equalizing out to an even distribution of oxygen by nitrogen? What's the density of O2 and N2 in your system? What's all the oxygen molecules on one side? What side? Are you sure no occasional charges are present on some site in your system? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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] Re: Using Morse potentials with ENCAD force field
Using the parameters listed earlier I equalized my system after trying to place the oxygen and nitrogen molecules evenly throughout my system. The result showed the nitrogen molecules fairly even throughout the system but all the oxygen molecules on one side. Any ideas on why the system might not be equalizing out to an even distribution of oxygen by nitrogen? Andy It seems because your box should be a bit longer to succeed. Try to enlarge the side (13.2 nm) length. 2008/8/21 Andy Shelley [EMAIL PROTECTED]: No problem the term flattens is porbably not the best technical description. A better one would be the cnt collapses. Andy On Thu, Aug 21, 2008 at 8:34 AM, Vitaly Chaban [EMAIL PROTECTED] wrote: Actually I think I am using the gromos force field. I have been using Christopher Stiles page as a guide to get started with using CNT http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were made to ffgmx files. So I believe I am using the gromos forcefield. Is the forcefield used defined by the parameters? I have added nonbonded parameters to ffgmxnb.itp as the following: [ nonboned_params ] ON1 0.00691.4016E-05 OO1 0.00619.9676E-06 NN1 0.00761.8778E-05 CO1 0.00304.7908E-06 CN1 0.00336.5271E-06 and the same for pairtypes [ pairtypes ] CN1 0.0033 6.5271E-06 CO1 0.0030 4.7908E-06 NN1 0.0076 1.8778E-05 OO1 0.0061 9.9676E-06 ON1 0.0069 1.4016E-05 I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm box with a 10,10 cnt length 12.3nm. The nitrogen molecules appear to not even interact with the cnt but it still flattens. Any ideas? Andy, Hi. Sorry for my English, what do you mean saying cnt flattens? Again, is everything right with your box side length. I mean if the cnt fits in the box (the rim atoms)? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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] Re: Using Morse potentials with ENCAD force field
Actually I think I am using the gromos force field. I have been using Christopher Stiles page as a guide to get started with using CNT http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were made to ffgmx files. So I believe I am using the gromos forcefield. Is the forcefield used defined by the parameters? I have added nonbonded parameters to ffgmxnb.itp as the following: [ nonboned_params ] ON1 0.00691.4016E-05 OO1 0.00619.9676E-06 NN1 0.00761.8778E-05 CO1 0.00304.7908E-06 CN1 0.00336.5271E-06 and the same for pairtypes [ pairtypes ] CN1 0.0033 6.5271E-06 CO1 0.0030 4.7908E-06 NN1 0.0076 1.8778E-05 OO1 0.0061 9.9676E-06 ON1 0.0069 1.4016E-05 I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm box with a 10,10 cnt length 12.3nm. The nitrogen molecules appear to not even interact with the cnt but it still flattens. Any ideas? Andy, Hi. Sorry for my English, what do you mean saying cnt flattens? Again, is everything right with your box side length. I mean if the cnt fits in the box (the rim atoms)? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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] Re: Using Morse potentials with ENCAD force field
It seems because your box should be a bit longer to succeed. Try to enlarge the side (13.2 nm) length. 2008/8/21 Andy Shelley [EMAIL PROTECTED]: No problem the term flattens is porbably not the best technical description. A better one would be the cnt collapses. Andy On Thu, Aug 21, 2008 at 8:34 AM, Vitaly Chaban [EMAIL PROTECTED] wrote: Actually I think I am using the gromos force field. I have been using Christopher Stiles page as a guide to get started with using CNT http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were made to ffgmx files. So I believe I am using the gromos forcefield. Is the forcefield used defined by the parameters? I have added nonbonded parameters to ffgmxnb.itp as the following: [ nonboned_params ] ON1 0.00691.4016E-05 OO1 0.00619.9676E-06 NN1 0.00761.8778E-05 CO1 0.00304.7908E-06 CN1 0.00336.5271E-06 and the same for pairtypes [ pairtypes ] CN1 0.0033 6.5271E-06 CO1 0.0030 4.7908E-06 NN1 0.0076 1.8778E-05 OO1 0.0061 9.9676E-06 ON1 0.0069 1.4016E-05 I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm box with a 10,10 cnt length 12.3nm. The nitrogen molecules appear to not even interact with the cnt but it still flattens. Any ideas? Andy, Hi. Sorry for my English, what do you mean saying cnt flattens? Again, is everything right with your box side length. I mean if the cnt fits in the box (the rim atoms)? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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
