Re: [gmx-users] Lateral Diffusion of Lipids

Am 8/12/13 5:26 AM, schrieb Kieu Thu Nguyen: > Dear users, > > I want to use g_msd to measure diffusion coefficients of lipid bilayer. But > i do not know how to choose the reference atom per lipid for an any type of > lipid, such as POPC, DOPC,... > Where i can get these references ? One sugge

Re: [gmx-users] Re: Unkwown Keyword HILLS

This is Sent from my iPhone On Aug 14, 2013, at 1:40, Albert wrote: > Does anybody have any idea what's the problem? > > I use the tutorial example and I don't know why it doesn't work. > > THX > > > On 08/13/2013 07:19 PM, Albert wrote: >> Dear: >> >> I am trying to run plumed with gromac

Re: [gmx-users] Re: Unkwown Keyword HILLS

This is a plumed error, not a gromacs error. Gromacs never handles those keywords. Sent from my iPhone On Aug 14, 2013, at 1:40, Albert wrote: > Does anybody have any idea what's the problem? > > I use the tutorial example and I don't know why it doesn't work. > > THX > > > On 08/13/2013

Re: [gmx-users] Re: Unkwown Keyword HILLS

On 08/14/2013 12:26 PM, Michael Shirts wrote: This is a plumed error, not a gromacs error. Gromacs never handles those keywords. Sent from my iPhone IC THX, it works now. I found some "strange characters" in the plumed.dat file. After delete them, it work now -- gmx-users mailing listg

[gmx-users] how can we control output ?

Hello: I am producing MD production with command: mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x md.xtc -o md.trr -e md.edr I notice that it generate two additional files: HILLS COLVAR the output in this two files are very frequent such as: #! FIELDS time cv1 cv2 vbi

Re: [gmx-users] Yet another question about what force field to use

On 8/13/13 10:26 PM, Pedro Lacerda wrote: Hi all, Many questions about how to choose a force field are addressed to this list, sorry if this one was already answered. Some argue that proteins are better modeled with ff99sb-ildn or charmm22* because occur great agreement between NMR experiment

Re: [gmx-users] how can we control output ?

On 8/14/13 9:43 AM, Albert wrote: Hello: I am producing MD production with command: mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x md.xtc -o md.trr -e md.edr I notice that it generate two additional files: HILLS COLVAR the output in this two files are very frequent

[gmx-users] plans for mdrun features to deprecate in GROMACS 5.0

Hi gmx-users and gmx-developers, There are a number of features of GROMACS that we plan to drop for 5.0 (scheduled for early 2014). We don’t like doing this, but if things are broken or cause developers pain, then they will go unless there is manpower to support them. We’d like to keep you informe

[gmx-users] charmm36 proteins

Hello all, Does anyone know if there is a working version of charmm36 proteins forcefield converted for gromacs? Thank you. -Dina -- 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/Ma

[gmx-users] All molecules being coupled for free energy of self solvation simulation

Dear users, I am attempting to determine the free energy of self solvation of several small molecules. Starting with an equilibrated box of pure fluid (for example, ethanol - which I am calling thr) I am renaming all of the molecules except for the first in the .gro file SOL, then updating the .top

[gmx-users] Re: All molecules being coupled for free energy of self solvation simulation

I found the error, I had B states defined for my solvent molecules in the topology file. On Wed, Aug 14, 2013 at 2:47 PM, Brittany Zimmerman wrote: > Dear users, > I am attempting to determine the free energy of self solvation of several > small molecules. > Starting with an equilibrated box of

Re: [gmx-users] plans for mdrun features to deprecate in GROMACS 5.0

I am interested in Generalized Born. My coding skills are limited, but I would like to help to whatever extent I can. I am also interested in helping towards revamping the tutorials if the need should arise. On Wed, Aug 14, 2013 at 8:36 PM, Mark Abraham wrote: > Hi gmx-users and gmx-developers,

[gmx-users] VDW switched off in CHARMM tip3p model

>From my inspection of the force field files included in gromacs-4.6.1, when you use the charmm ff and the charmm tip3p (tips3p.itp) you get the hydrogen type HT, which does have LJ on the hydrogen atoms, whereas you only get the hydrogen type HWT3 when you use the non-charmm tip3p (tip3p.itp).

[gmx-users] charmm36 proteins

What is the charmm36 protein force field? (can you provide a reference to what you are referring to). As far as I know, there is no such thing as "charmm36" proteins. There are charmm27+cmap proteins (implemented in gromacs already) and charmm36 lipids (implemented in gromacs already). -- orig

Re: [gmx-users] charmm36 proteins

On 8/14/13 6:22 PM, Christopher Neale wrote: What is the charmm36 protein force field? (can you provide a reference to what you are referring to). As far as I know, there is no such thing as "charmm36" proteins. There are charmm27+cmap proteins (implemented in gromacs already) and charmm36 l

[gmx-users] "Sign convention" g_energy total energies

Hi everybody. I wonder how the "sign convention" of GROMACS (or better g_energy ) is: Is U(state_i):= _t correct or do i have to choose the other sign U(state_i)= -1.0* _t ?  (<>_t denotes the time average)   I need the correct sign for further calculations since i need to add something (-T\Delta

Re: [gmx-users] "Sign convention" g_energy total energies

On 8/14/13 6:42 PM, gg jj wrote: Hi everybody. I wonder how the "sign convention" of GROMACS (or better g_energy ) is: Is U(state_i):= _t correct or do i have to choose the other sign U(state_i)= -1.0* _t ? (<>_t denotes the time average) I need the correct sign for further calculations since

[gmx-users] Re: VDW switched off in CHARMM tip3p model

TIP3P and TIPS3P (which I found later is the CHARMM TIP3P) produce slightly different water bulk density: 0.96 vs. 1.01 when using CHARMM ff set, but TIPS3P is almost two times slower than original TIP3P. For the benefit of TIPS3P, I think it heavily depends on applications. Weilong Christopher

Re: [gmx-users] charmm36 proteins

Thanks Justin. I will just modify the existing charmm files for gromacs to make the charmm36 version. I just wanted to see if anyone had already done this, so as not to redo something that's already been done. -D On Wed, Aug 14, 2013 at 6:31 PM, Justin Lemkul wrote: > > > On 8/14/13 6:22 PM,