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
Sv: Re: [gmx-users] PEO polymer (Away from my mail/Borta från min post)
Unfortunately I am away from my mail till the 8th of August. For VERY urgent matters phone +46 (0)733 72 26 93 Tyvärr är jag borta från min post till den 8 augusti För MYCKET brådskande ärenden ring 0733 72 26 93 >>> gmx-users 2006-7-7 13:51 >>> Hello Peter, I found few of your papers earlier on poly (ethylene oxide). Good to see your email in my inbox now. If you can send the required topology files to simulate PEO, that would be great. Thanks in advance, -Vishy! On 7/7/06, Peter Ahlström <[EMAIL PROTECTED]> wrote: > > Hello, > I have got some experience with simulating pure Poly Propylene Oxide (no > water) using the force field of Borodin and Smith. IIRC they also made a > force field for PEO. I could try to dig out the topology files I used albeit > they are for an older version of Gromacs. Just mail me if you wish them - > but I will be on holiday for the coming weeks. > Good luck > > Peter > (references - in TeX-format: > P.~Ahlstr\"om, O.~Borodin, G.~Wahnstr\"om, E.~Wensink, > P.~Carlsson \& G.D.~Smith\\ > Molecular Dynamics studies of poly(propylene oxide) using a > new quantum chemical force field.\\ > J.Chem.Phys., 112 (2000) 10669-10679. > > C.~Tengroth, P.~Carlsson, D.~Engberg, P.~Ahlstr\"om$^*$, > G.~Wahnstr\"om, W.S.~Howells, L.~B\"orjesson > The segmental and rotational dynamics of PPO, above the glass > transition, investigated by > Neutron Scattering and Molecular Dynamics simulation. > Soft Materials, 3 (2005), 1-20. > > > Dr. Peter Ahlström > School of Engineering > University College of Borås > SE-501 90 Borås > Ph. +46-33-435 46 75 Fax +46-33-435 40 08 > [EMAIL PROTECTED] > >>> [EMAIL PROTECTED] 06-07-07 06:53 >>> > Hi Gmx Users, > Has anyone used Gromacs to simulate Poly Ethylene Oxide polymer in water? > If so, are there any relevant websites and tutorials? > I was involved in MD simulations of bilayers till now, and I know few > sites > of Dr.Tieleman's etc. Similarly are there any for Polymers too? > Thanks in advance! > -Vishy. > -- > Viswanadham Sridhara, > Graduate Research Assistant, > Old Dominion University, > Norfolk, VA-23529. > > -- Viswanadham Sridhara, Graduate Research Assistant, Old Dominion University, Norfolk, VA-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Sv: [gmx-users] PEO polymer
Hello, I have got some experience with simulating pure Poly Propylene Oxide (no water) using the force field of Borodin and Smith. IIRC they also made a force field for PEO. I could try to dig out the topology files I used albeit they are for an older version of Gromacs. Just mail me if you wish them - but I will be on holiday for the coming weeks. Good luck Peter (references - in TeX-format: P.~Ahlstr\"om, O.~Borodin, G.~Wahnstr\"om, E.~Wensink, P.~Carlsson \& G.D.~Smith\\ Molecular Dynamics studies of poly(propylene oxide) using a new quantum chemical force field.\\ J.Chem.Phys., 112 (2000) 10669-10679. C.~Tengroth, P.~Carlsson, D.~Engberg, P.~Ahlstr\"om$^*$, G.~Wahnstr\"om, W.S.~Howells, L.~B\"orjesson The segmental and rotational dynamics of PPO, above the glass transition, investigated by Neutron Scattering and Molecular Dynamics simulation. Soft Materials, 3 (2005), 1-20. Dr. Peter Ahlström School of Engineering University College of Borås SE-501 90 Borås Ph. +46-33-435 46 75 Fax +46-33-435 40 08 [EMAIL PROTECTED] >>> [EMAIL PROTECTED] 06-07-07 06:53 >>> Hi Gmx Users, Has anyone used Gromacs to simulate Poly Ethylene Oxide polymer in water? If so, are there any relevant websites and tutorials? I was involved in MD simulations of bilayers till now, and I know few sites of Dr.Tieleman's etc. Similarly are there any for Polymers too? Thanks in advance! -Vishy. -- Viswanadham Sridhara, Graduate Research Assistant, Old Dominion University, Norfolk, VA-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
