Re: [gmx-users] Re:the vapor-liquid interface of a solution at low pressure

beibei wrote: > Hi, all > In fact, I want to verify the hygroscopic of lithium bromide solution, > so I want to make some water moleculars in the vapor region. But I found > that at 0.008bar, 303K and very small box(the unit of the length of the > box is nm), there may be zero vapor moleculars.

Re: [gmx-users] unable to run md after installing another gromacs 3.3.3 after 3.3.2

Ross KK Leung wrote: Dear all, I have both old 3.3.2 and new 3.3.3 gromacs installed and I don't know how to uninstall the old one. Is there any good solution to it? Go to the 3.3.2 installation directory and issue "make uninstall". Or if you used an .rpm or such, look up how to uninstall wit

[gmx-users] Re:the vapor-liquid interface of a solution at low pressure

Hi, all In fact, I want to verify the hygroscopic of lithium bromide solution, so I want to make some water moleculars in the vapor region. But I found that at 0.008bar, 303K and very small box(the unit of the length of the box is nm), there may be zero vapor moleculars. Thus I think I cannot

[gmx-users] unable to run md after installing another gromacs 3.3.3 after 3.3.2

Dear all, I have both old 3.3.2 and new 3.3.3 gromacs installed and I don't know how to uninstall the old one. Is there any good solution to it? Because I keep getting "segmentation fault" due to inappropriate configuration, I guess. Thanks a lot ___ g

[gmx-users] pressure coupling for self-assembly of bilayer

Dear GMX-users, I'm trying to do self-assembly of bilayer. I'm using coarse-grained model (MARTINI), and there are 1280 CG lipids and 30110 CG waters. I followed procedures of Marrink and de Vries's atomistic simulations of the bilayer self-assembly. So, I simulated the randomly-positioned sy

Re: [gmx-users] bicelle gromacs MD simulation CG model?

On Friday 13 June 2008 16:43, Justin A. Lemkul wrote: > ANINDITA GAYEN wrote: > > if i refine the chaps.itp with opls charges, will it be active? Wouldn't that do if you just got your all-atom .pdb from PRODRG (as Justin says) - or elsewehre! - and used ffopls* files to set the parameters in to

Re: [gmx-users] bicelle gromacs MD simulation CG model?

ANINDITA GAYEN wrote: if i refine the chaps.itp with opls charges, will it be active? I doubt it; you're still using nonbonded parameters from one force field, and bonded parameters from another. Besides, OPLS is all-atom (although an old UA version exists, too, but I believe it is som

Re: [gmx-users] bicelle gromacs MD simulation CG model?

if i refine the chaps.itp with opls charges, will it be active? If not, what can i do then? should i use cholesterol in place of chaps? if yes, where to do download from ? --- On Fri, 13/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject:

[gmx-users] cholesterol in OPLS-BERGER

Can anyone give me the pdb and topolohy file for cholesterol in OPLS-BERGER field? Meet people who discuss and share your passions. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ ___ gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] trjcat -demux

Dear gromacs users, I tried using trjcat like this: trjcat -f gromacs*.trr -demux replica_index.xvg (see below for replica_index.xvg and logfile) there are 20 trajectories containing each 2001 frames, with timestep of 0.5ps (I checked it with gmxcheck). The error: Reading frame 60 time

[gmx-users] pbc-replica exchange-trjconv

For a given temperature, I will make them continues again then before analysis. Thanks for the help! kind regards, servaas Hoi Servaas, Was that the trajectory for a given temperature, or for a given system? It should be for the latter, as otherwise, there will be weird shifts introduced.

Re: [gmx-users] bicelle gromacs MD simulation CG model?

ANINDITA GAYEN wrote: I have build the itp file from PRODG2 DUNDEE server. and then replaced the stom types from OPLS. Can you comment about the itp file, i can serve that to u. Please make sure you are replying to the gmx-users listserv; that way this thread will be archived for others

Re: [gmx-users] bicelle gromacs MD simulation CG model?

ANINDITA GAYEN wrote: You can find my paper on Langmuir vol 24, Issue 10, pages 5422-5432 2008, I have made two bicelle samples experimentally, and now i want to model those two bicelles theorically to connect the theory with the NMR experimental data. I have euilibrated a dmpc bilayer in OP

Fw: Re: [gmx-users] bicelle gromacs MD simulation CG model?

--- On Fri, 13/6/08, ANINDITA GAYEN <[EMAIL PROTECTED]> wrote: > From: ANINDITA GAYEN <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] bicelle gromacs MD simulation CG model? > To: [EMAIL PROTECTED] > Date: Friday, 13 June, 2008, 4:09 PM > You can find my paper on Langmuir vol 24, Issue 10, pages

Re: [gmx-users] bicelle gromacs MD simulation CG model?

Can you be more specific as to what you need help on? I'm familiar with a couple of these papers, and the methods sections are quite good. Files are freely available on S.J. Marrink's site, as well as a list of pertinent publications detailing their methodology. -Justin ANINDITA GAYEN wrote

[gmx-users] mass changes in free energy calculations

Dear all, I am calculating FE using TI. I have a question about mutating existing atoms with different mass. for example, using ffG53a6 force field, in one case i need to mutate CH2 to CH3, should I use [ atoms ] 17CH3 2ALA CB 6 0 15.035 CH20