[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly
Hi, Justin, Thank you for your reply. It is a little weird and inconvienient that genbox does not update the No. of solute molecules. Is it designed in this way? Does it have any reason for that? For my case, the inear, 3-atom model of CO2 works pretty well. I got the model from a paper from Zhenhao Duan. I guess I will use this model for the project before I get something wrong. Best Regards, Kai -- Message: 5 Date: Thu, 04 Oct 2012 17:34:22 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] The No. of the CO2 melecules in top file can not be updated correctly. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 506e00de.9050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 10/4/12 5:29 PM, Bao Kai wrote: Hi, all, I am still working on the molecular simulation of CO2 and H2O mixture. The information of the molecules types and the force field model are all defined in the a.top file. 1 [ defaults ] 2 ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 3 1 3 yes 0.50.5 4 [ atomtypes ] 5 ; type at.nummasschargeptypesigma epsilon 6 CO 6 12.01100.5888A 0.27918 0.2398 7 OC 8 15.9994 -0.2944A 0.3 0.6872 8 OW 6 15.99940 -0.8476A 0.316557 0.650194 9 HW 1 1.008000.4238A 0.0 0.0 10 [ moleculetype ] 11 ;name nrexcl 12 CO2 3 13 [atoms] 14 ; nr type resnr residue atom cgnr charge mass 32 [moleculetype] 33 ; molname nrexcl 34 SOL 2 35 [atoms] 36 ; nr type resnr residue atom cgnr charge mass ... 47 [system] 48 sparkling water 49 [molecules] 50 CO2 100 51 SOL 3000 I create on co2.gro file to put one CO2 molecule inside. Then I used genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top to put 190 CO2 molecules inside the box. Then I used genbox -cp a.gro -o b.gro -box 7 -cs -maxsol 9810 -p a.top to put 9810 H2O molecules inside the box. In the file a.top, the No. of the H2O was updated correctly, while the No. of the CO2 molecules was not updated. The No. of the atoms in .gro files are correct. Can you please tell me the reason or how to solve it? genbox only updates water molecules in the topology. Anything else is up to you. Beware that a linear, 3-atom model of CO2 is probably not going to work due to issues with linear angles, as has been discussed frequently on the list. A more robust approach involves virtual sites. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] The No. of the CO2 melecules in top file can not be updated correctly
On 10/5/12 5:18 AM, Bao Kai wrote: Hi, Justin, Thank you for your reply. It is a little weird and inconvienient that genbox does not update the No. of solute molecules. Is it designed in this way? Does it have any reason for that? The principal function of genbox is to solvate systems, usually with water. The other things it can do are added on, but the code is designed around the most commmon usage. Insertion of molecules is not guaranteed to work, so if a user specifies a number of molecules to add and then genbox cannot, then either it will update with topology with the actual number inserted (which may disagree with the command line, and users may ignore any failures and proceed) or the number requested (which may then fail for the opposite reason). You can see how it becomes a slippery slope to try to make software out-think the user. For my case, the inear, 3-atom model of CO2 works pretty well. I got the model from a paper from Zhenhao Duan. I guess I will use this model for the project before I get something wrong. Good luck. Linear angles are generally not stable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] The No. of the CO2 melecules in top file can not be updated correctly.
Hi, all, I am still working on the molecular simulation of CO2 and H2O mixture. The information of the molecules types and the force field model are all defined in the a.top file. 1 [ defaults ] 2 ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 3 1 3 yes 0.50.5 4 [ atomtypes ] 5 ; type at.nummasschargeptypesigmaepsilon 6 CO 6 12.01100.5888A 0.27918 0.2398 7 OC 8 15.9994 -0.2944A 0.3 0.6872 8 OW 6 15.99940 -0.8476A 0.316557 0.650194 9 HW 1 1.008000.4238A 0.0 0.0 10 [ moleculetype ] 11 ;name nrexcl 12 CO2 3 13 [atoms] 14 ; nr type resnr residue atom cgnr charge mass 32 [moleculetype] 33 ; molname nrexcl 34 SOL 2 35 [atoms] 36 ; nr type resnr residue atom cgnr charge mass ... 47 [system] 48 sparkling water 49 [molecules] 50 CO2 100 51 SOL 3000 I create on co2.gro file to put one CO2 molecule inside. Then I used genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top to put 190 CO2 molecules inside the box. Then I used genbox -cp a.gro -o b.gro -box 7 -cs -maxsol 9810 -p a.top to put 9810 H2O molecules inside the box. In the file a.top, the No. of the H2O was updated correctly, while the No. of the CO2 molecules was not updated. The No. of the atoms in .gro files are correct. Can you please tell me the reason or how to solve it? Thank you very much. Best Retards, Kai -- 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] The No. of the CO2 melecules in top file can not be updated correctly.
On 10/4/12 5:29 PM, Bao Kai wrote: Hi, all, I am still working on the molecular simulation of CO2 and H2O mixture. The information of the molecules types and the force field model are all defined in the a.top file. 1 [ defaults ] 2 ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 3 1 3 yes 0.50.5 4 [ atomtypes ] 5 ; type at.nummasschargeptypesigmaepsilon 6 CO 6 12.01100.5888A 0.27918 0.2398 7 OC 8 15.9994 -0.2944A 0.3 0.6872 8 OW 6 15.99940 -0.8476A 0.316557 0.650194 9 HW 1 1.008000.4238A 0.0 0.0 10 [ moleculetype ] 11 ;name nrexcl 12 CO2 3 13 [atoms] 14 ; nr type resnr residue atom cgnr charge mass 32 [moleculetype] 33 ; molname nrexcl 34 SOL 2 35 [atoms] 36 ; nr type resnr residue atom cgnr charge mass ... 47 [system] 48 sparkling water 49 [molecules] 50 CO2 100 51 SOL 3000 I create on co2.gro file to put one CO2 molecule inside. Then I used genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top to put 190 CO2 molecules inside the box. Then I used genbox -cp a.gro -o b.gro -box 7 -cs -maxsol 9810 -p a.top to put 9810 H2O molecules inside the box. In the file a.top, the No. of the H2O was updated correctly, while the No. of the CO2 molecules was not updated. The No. of the atoms in .gro files are correct. Can you please tell me the reason or how to solve it? genbox only updates water molecules in the topology. Anything else is up to you. Beware that a linear, 3-atom model of CO2 is probably not going to work due to issues with linear angles, as has been discussed frequently on the list. A more robust approach involves virtual sites. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
