Re: [gmx-users] how to simulate at a specific dielectric constant

nur avneet wrote: Dear all How can i set the dielectric constant of my choice in the simulations What do you mean? You can change the solvent, or change the ionic strength. There is not a simulation parameter that you can change that will influence the dielectric constant of your system. -

Re: [gmx-users] how to simulate at a specific dielectric constant

yes. In the .mdp, epsilon_r gives the relative permittivity of the medium2006/11/15, Mark Abraham <[EMAIL PROTECTED]>: > Dear all>  How can i set the dielectric constant of my choice in the simulationsPlease read the manual.Mark ___ gmx-users mailing list

Re: [gmx-users] how to simulate at a specific dielectric constant

> Dear all > How can i set the dielectric constant of my choice in the simulations Please read the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reque

Re: [gmx-users] water in protein itp file

Dear Mark, Thaks for your replies and I end this discussion with this. B.Nataraj On Wed, 15 Nov 2006 11:51:37 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear Mark, > > Well and thanks again, QM-MM is a good option, as you said for analyzing > > the energetic of water liga

[gmx-users] how to simulate at a specific dielectric constant

Dear all How can i set the dielectric constant of my choice in the simulations regards nur Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW___

Re: [gmx-users] water in protein itp file

raja wrote: Dear Mark, Well and thanks again, QM-MM is a good option, as you said for analyzing the energetic of water ligating process. But my case not concerning to that process, rather study a system consists of a macromolecule as a whole, where this water bound zinc is a part of it. If this i

[gmx-users] Installation Problem

I have installed gromacs 3.3 on intel core2duo.I did everything.now when i try 2 run any program of its.. i get an error like this:"./pdb2gmx: error while loading shared libraries: libXm.so.2: cannot open shared object file: No such file or directory" I have this libXm.so.2 is /usr/X11R6/ lib/But i

[gmx-users] Re: Gromacs/CPMD QM/MM example

Hi Steven,Thanks for your message. The 'CAPPING' flag for additional hydrogen atoms is a feature of Gromos/CPMD interface and is not persuaded in Gromacs/CPMD. Sorry about that.regards,Pradip.-Steven Kirk <[EMAIL PROTECTED]> wrote: -To: [EMAIL PROTECTED]From: Steven Kirk <[EMAIL PROTECTED]>

Re: [gmx-users] nucleic acis simulation

Hi Erik, Yep, the problem was indeed with the ifdefs... I'm sorry, I thought I had posted a solution. My bad. Miguel En/na Erik Marklund ha escrit: > Hi everyone. > > I found this old thread and noticed that Miguel Ortis Lombardia had the > same problems I had just half an hour ago. It seems

[gmx-users] nucleic acis simulation

Hi everyone. I found this old thread and noticed that Miguel Ortis Lombardia had the same problems I had just half an hour ago. It seems that it is indeed the included spc.itp that causes the problem, but NOT the position where it is included as David van der Spoel suggests. A closer look at spc.i

[gmx-users] The ensembles!

hi,   I am not very clear about the ensembles in MD. For example, if i want to calculate the diffusion coefficient in a flexible zeolite. which ensemble should i choose? NVT or NPT?   ___ gmx-users mailing listgmx-users@gromacs.org http

[Fwd: Re: [gmx-users] calculating dielectric constant]

Hi David, Yes, I run the mdrun at T=425K. I simulated the simplest ionic liquid (mmimCl). I don't find the reported dielectric constant of this one, but I have some reported data of some other ionic liquid at hand, epsilon~ 10 - 20. Therefore, the data from gromacs is quite big. (Should I prov

Re: [gmx-users] error says "segnentation fault"

Hi, It is more likely that due to some very large forces mdrun tries to 'move a particle' to some region of the memory it doesn't have access to. I'd say the system is wrong. You may have overlapping particles or something alike. Check your system: the topology, the structure, the box. You did pe