[gmx-users] shell molecular dynamics
Hello, I would like to run a simulation using the shell option. I tried to restraint solvent molecules which were found within the range of 5-10 angstroms from the box center. I couldn't find any way to do so. I didn't find any information about this topic anywhere else i.e. GROMACS manual, online tutorials etc. Can anybody help me with this problem or guide me to appropriate tutorial. Thanks in advance. Michael -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] shell molecular dynamics
On 29/12/2011 9:43 PM, michael zhenin wrote: Hello, I would like to run a simulation using the shell option. I tried to restraint solvent molecules which were found within the range of 5-10 angstroms from the box center. I couldn't find any way to do so. I didn't find any information about this topic anywhere else i.e. GROMACS manual, online tutorials etc. There are some threads in the mailing list archives. You need to make two different moleculetypes, one which is position restrained, and one that isn't. Then you need to identify the ones you want to restrain, e.g. with an index group made by g_select. Then you'll need to do some cut-and-paste to get the block of restrained solvent contiguous. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] shell molecular dynamics
Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell atom, what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? 2. What does the 1 in [ polarization ] part mean in sw.itp? 3. Is it reasonable to set initial position of shell arbitrally and let energy minimization to find the optimum position for shell? I also do not understand [ exclusion ] part: ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 For the first line, does that mean that the interaction of 2, 3, 4 and 5 with 1 is excluded? If so, this table will exclude all the interactions. Is it right? Thank you in advance. Shuangxing Dai___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shell molecular dynamics
Shuangxing Dai wrote: Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell atom, what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? Anything you like. Gromacs does not use this information anyway. 2. What does the 1 in [ polarization ] part mean in sw.itp? Function type, see manual ch. 5. 3. Is it reasonable to set initial position of shell arbitrally and let energy minimization to find the optimum position for shell? At first step the shell will be put in the place of the virtual site and will be minimized from there. I also do not understand [ exclusion ] part: ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 For the first line, does that mean that the interaction of 2, 3, 4 and 5 with 1 is excluded? If so, this table will exclude all the interactions. Is it right? Yes. You need at least two molecules to do anything useful. Thank you in advance. Shuangxing Dai ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shell molecular dynamics
Thank you for help. The harmonic potential between core and shell is attractive. The charges they have are opposite, this means that there will only be attractive force between them. My result also show that they nearly overlap. Is this reasonable and shell model correctly used? If not, where is the problem. Shuangxing Dai - Original Message - From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 13 April, 2009 11:15 AM Subject: Re: [gmx-users] shell molecular dynamics Shuangxing Dai wrote: Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell atom, what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? Anything you like. Gromacs does not use this information anyway. 2. What does the 1 in [ polarization ] part mean in sw.itp? Function type, see manual ch. 5. 3. Is it reasonable to set initial position of shell arbitrally and let energy minimization to find the optimum position for shell? At first step the shell will be put in the place of the virtual site and will be minimized from there. I also do not understand [ exclusion ] part: ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 For the first line, does that mean that the interaction of 2, 3, 4 and 5 with 1 is excluded? If so, this table will exclude all the interactions. Is it right? Yes. You need at least two molecules to do anything useful. Thank you in advance. Shuangxing Dai ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shell molecular dynamics
Shuangxing Dai wrote: Thank you for help. The harmonic potential between core and shell is attractive. The charges they have are opposite, this means that there will only be attractive force between them. My result also show that they nearly overlap. Is this reasonable and shell model correctly used? If not, where is the problem. This is fine. The shell interacts with other molecules. In the SW paper we have computed the distribution of dipole moments in the liquid phase, and the average dipole is 2.7 D, compared to 1.85 in the gas phase. Hence the shell particle moves sufficiently far away from the core to get effective polarization. Shuangxing Dai - Original Message - From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 13 April, 2009 11:15 AM Subject: Re: [gmx-users] shell molecular dynamics Shuangxing Dai wrote: Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell atom, what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? Anything you like. Gromacs does not use this information anyway. 2. What does the 1 in [ polarization ] part mean in sw.itp? Function type, see manual ch. 5. 3. Is it reasonable to set initial position of shell arbitrally and let energy minimization to find the optimum position for shell? At first step the shell will be put in the place of the virtual site and will be minimized from there. I also do not understand [ exclusion ] part: ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 For the first line, does that mean that the interaction of 2, 3, 4 and 5 with 1 is excluded? If so, this table will exclude all the interactions. Is it right? Yes. You need at least two molecules to do anything useful. Thank you in advance. Shuangxing Dai ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
