Sv: Re: [gmx-users] surface simulation
If vapour pressure is not too high, I think it is physically more relevant to simulate a CCl_4 slab with periodic boundary conditions suck that you get an infinite 2-slab repeated in the third dimension such that you get a vapour slab in between (surface tensions etc are normally measured in equilibrium with the vapour). So, in my opinion, the easiest thing to do is to simulate a slab of CCl_4 together with the vapour (at least you get less artefacts from bad wall models in that way). At least that is a somewhat physical system. Normally I do not think that position restraints are needed (but I have no experience with CCl_4) Cheers, Peter Dr. Peter Ahlström School of Engineering University of Borås SE-501 90 Borås Ph. +46-33-435 46 75 Fax +46-33-435 40 08 [EMAIL PROTECTED] Mark Abraham [EMAIL PROTECTED] 08-11-03 05:08 Hongyan Xiao wrote: Hi, Mark Abraham, I accepted your suggestion on the language. I simulated the CCl_4 surface system. In order to simplify model, using the vacuum replaced the gas phase. Furthermore, I found some paper by other people also deal with the gas/liquid using the vacuum. In vacuum/CCl_4 , can I control the CCl_4 molecule not to run to the vacuum using the gromacs? For example, using the wall, but I do not set up wall parameters well. Please give me some suggestion. Thanks again! Some position restraints will keep your surface intact. See the manual for details. GROMACS will report how much energy is going from the restraints and you should check your parameterization by seeing that this energy is pretty small. 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 ___ 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] surface simulation
Hi, all gmx-users, I was simulating a CCl4 surface system. I encounter some problems. I hope for your help. First I built a 3x3x3 nm3 CCl4 box, then solved it into a 3x3x15 box in order to form gas/CCl4/gas surface system. After simulating in NVT, two CCl4 molecules run away to the gas phase. I want to know how to control CCl4 not to run to gas phase. I used the gromos96 force field. Can you help me? I expect your answer. Thanks a lot! H. Y. Xiao ___ 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] surface simulation
Hongyan Xiao wrote: Hi, all gmx-users, I was simulating a CCl_4 surface system. I encounter some problems. I hope for your help. First I built a 3x3x3 nm^3 CCl_4 box, then solved it into a 3x3x15 box in order to form gas/CCl4/gas surface system. After simulating in NVT, two CCl_4 molecules run away to the gas phase. I want to know how to control CCl_4 not to run to gas phase. I used the gromos96 force field. Can you help me? I don't follow. What's the gas? Anyhow, it seems your CCl_4 surface is sublimating, which might not be surprising. I expect your answer. Thanks a lot! I suspect this is just a language issue, but expect in English carries the implication that someone is obliged to make an answer. All of us here who might answer your email are volunteers. A paragraph like I'll look forward to any answers. Thanks a lot! will avoid annoying people :-) 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
[gmx-users] surface simulation
Hi, Mark Abraham, I accepted your suggestion on the language. I simulated the CCl4 surface system. In order to simplify model, using the vacuum replaced the gas phase. Furthermore, I found some paper by other people also deal with the gas/liquid using the vacuum. In vacuum/CCl4, can I control the CCl4 molecule not to run to the vacuum using the gromacs? For example, using the wall, but I do not set up wall parameters well. Please give me some suggestion. Thanks again! H. Y. Xiao ___ 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] surface simulation
Hongyan Xiao wrote: Hi, Mark Abraham, I accepted your suggestion on the language. I simulated the CCl_4 surface system. In order to simplify model, using the vacuum replaced the gas phase. Furthermore, I found some paper by other people also deal with the gas/liquid using the vacuum. In vacuum/CCl_4 , can I control the CCl_4 molecule not to run to the vacuum using the gromacs? For example, using the wall, but I do not set up wall parameters well. Please give me some suggestion. Thanks again! Some position restraints will keep your surface intact. See the manual for details. GROMACS will report how much energy is going from the restraints and you should check your parameterization by seeing that this energy is pretty small. 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
